Curator Desk

BioAnalyzer × BugSigDB

Curator Desk

Review BioAnalyzer’s extracted fields for candidate microbiome studies, confirm ontology mappings, record curator ground truth per PMID, and send validated rows straight into the BugSigDB curation pipeline.

Browse candidate papers View source on GitHub

99Candidate papers

67Fully ontology-mapped

99Already in BugSigDB

0Awaiting curation

How this works

1

Find papers quickly

Search, sort, and filter the table below by any field, year, or BugSigDB status.

2

Record ground truth

Open a PMID in the curator feedback form and enter the curator TRUE label, plus an optional “was the prediction correct?” flag, for each field.

3

Share feedback

Submit straight to a GitHub issue with the feedback CSV pre-filled — no install, no login beyond GitHub.

NoteData Source & Setup

The table is built from data stored in the data/ folder. To analyze your own papers:

1. Place your CSV (or Parquet) file in data/ (e.g., data/sample.csv).
2. Run quarto render.

The system reads data/sample.csv by default. To use a different source, set the CURATOR_DATA_PATH environment variable to your specific path (e.g., data/analyzed_papers.csv) or use CURATOR_DATA_URL for remote files.

Expected columns

• Required: PMID
• Recommended: Title, Journal, Year
• Value fields: Host Species, Body Site, Condition, Sample Size, Sequencing Type
• Ontology IDs (optional): Host Species Ontology ID, Body Site Ontology ID, Condition Ontology ID

Candidate Curatable Articles

99 rows

Tip:  Use the search box and column filters to narrow your focus. An empty Ontology ID cell means that field needs a curator-confirmed mapping - see the feedback form below.

Show only papers reporting differential abundance (91 of 99)

Curator feedback

5 fields per paper

Use the table above to find papers (click a PMID’s PubMed Link to open it). Then select or enter a PMID below; the page will scroll to the field-by-field validation form where you can enter your review. Feedback uses the same schema as the Streamlit app; because this site is static, saving is done by downloading a CSV per row—submit via your usual process (e.g. email or GitHub issue).

1. Quick select a PMID from the dropdown, or type a PMID and click Load row (the form will scroll into view).
2. For each field, review BioAnalyzer predicted and correct the Curator value if needed; for Host Species/Body Site/Condition, confirm or pick the ontology mapping from the suggested candidates (or enter one manually).
3. Click Submit review (or Download CSV only) to save one row.

Curator ID / initials

BioAnalyzer version (fixed for all submissions)

Quick select for feedback — Select a PMID from the table, or type below.

— Select a PMID —22339879 — Alterations in composition and diversity of the in…25444008 — Intestinal microbiota development in preterm neona…25599982 — Infant gut microbiota and food sensitization: asso…25944283 — Gut microbiome and innate immune response patterns…26179554 — Colonic bacterial composition in Parkinson’s disea…26181352 — Fusobacterium nucleatum and T Cells in Colorectal …27015276 — Fecal Microbiota, Fecal Metabolome, and Colorectal…27228093 — Intestinal Microbiota Is Influenced by Gender and …27288567 — Possible association of Bifidobacterium and Lactob…27884202 — Extending colonic mucosal microbiome analysis-asse…28457228 — Differences in gut microbial composition correlate…28624933 — Influence of food consumption patterns and Galicia…28765474 — Mucosal microbiome dysbiosis in gastric carcinogen…28852182 — Unveiling the gut microbiota composition and funct…29133803 — Microbial Diversity of Genital Ulcers of HSV-2 Ser…29172724 — Distribution and Diversity of Ocular Microbial Com…29462324 — Endometriosis induces gut microbiota alterations i…29563617 — Cervical microbiome is altered in cervical intraep…29624747 — Fecal microbiome signatures are different in food-…29665823 — Exposure to concentrated ambient PM29791775 — Vaginal microbiome in early pregnancy and subseque…29955075 — HPV infection and bacterial microbiota in the plac…30007242 — Altered gut microbiome composition in children wit…30029052 — Altered gut microbiota profile in patients with ge…30267022 — A study of the correlation between obesity and int…30301893 — Meta-analysis of effects of exclusive breastfeedin…30674011 — Alterations in the intestinal microbiota of patien…31067473 — Comparison of Co-housing and Littermate Methods fo…31100891 — Gut Microbial Composition and Function Are Altered…31200089 — Alteration of the fecal microbiota in North-Easter…31502207 — Characterization and Analysis of the Skin Microbio…31583533 — Intestinal microbiome analysis demonstrates azithr…31699813 — Metagenome-wide association study of gut microbiom…31719139 — Association of Flavonifractor plautii, a Flavonoid…31794002 — The Association Between Smoking and Gut Microbiome…31815177 — Effect of Parkinson’s disease and related medicati…32024079 — Characteristics and Dysbiosis of the Gut Microbiom…32708743 — Effect of a Nutritional Intervention on the Intest…32844256 — Microbiota composition in bilateral healthy breast…33220709 — Microbial function and genital inflammation in you…33273497 — Glioma and temozolomide induced alterations in gut…33429936 — Altered Gut Microbiota in Irritable Bowel Syndrome…33517890 — Gut microbiota-derived propionate mediates the neu…33536555 — Structural changes in the oral microbiome of the a…33552996 — Gut Microbiota Composition Changes in Constipated …33565055 — Inferences in microbial structural signatures of a…33619320 — Gut microbiome diversity is an independent predict…33708251 — Gut Dysbiosis and Abnormal Bile Acid Metabolism in…33732104 — 33828220 — Alteration of the gut fecal microbiome in children…33828910 — Characteristics of the gut microbiome in patients …34168484 — Gut Microbiota Dysbiosis Correlates with Abnormal …34173452 — Analysis of the intestinal microbiota in COVID-19 …34233092 — Differences in the eyelid and buccal microbiome be…34336726 — An Exploratory Study for the Association of Gut Mi…34722781 — Sex Variations in the Oral Microbiomes of Youths w…34799562 — Dysbiosis of human gut microbiome in young-onset c…34809575 — Comparison of fecal and oral collection methods fo…34923209 — Exploring the relationship between the gut microbi…34931394 — Profiling the oral microbiomes in patients with Al…35003794 — Gut microbiota changes and its potential relations…35188868 — The potential of fecal microbiota and amino acids …35291914 — The role of gut microbiota in patients with benign…35298505 — Changes in the gut microbiota of Nigerian infants …35701595 — Alterations in co-abundant bacteriome in colorecta…35849580 — Lichen Planopilaris: The first biopsy layer microb…36539569 — Altered gut microbiome composition by appendectomy…36564826 — Metagenomic analysis of the interaction between th…36803868 — Sputum bacterial load and bacterial composition co…37208728 — Dysbiosis of gut microbiota inhibits NMNAT2 to pro…37329328 — Ischaemic stroke patients present sex differences …37443082 — Effects of gut microbiota on omega-3-mediated ovar…37750731 — Yearly variation coupled with social interactions …37832478 — The potential mechanism of the progression from la…37919319 — Smoking and salivary microbiota: a cross-sectional…37924005 — Alterations in gut microbiota and host transcripto…37978347 — Correlation of gut microbiota with leukopenia afte…38113233 — Differences in the gut microbiota between Gurkhas …38369542 — Multi-omic profiling reveals associations between …38381714 — Microbiome features associated with performance me…38383483 — Distinct intestinal microbial signatures linked to…38424099 — Effect of gut microbiome modulation on muscle func…38481313 — Large-scale causal analysis of gut microbiota and …38798019 — The role of 38942886 — Metagenomic analysis revealed the association betw…38980075 — Microbiological and functional traits of peri-impl…39599727 — Characterization of the Gut and Skin Microbiome ov…39656003 — Gut dysbiosis narrative in psoriasis: matched-pair…39682194 — New Insights into Mucosa-Associated Microbiota in …39694919 — The regulatory effect of chitooligosaccharides on …39818212 — Cervicovaginal microbiome and natural history of C…40259408 — Initial gut microbiota composition is a determinin…40413726 — Bacteroides uniformis-generated hexadecanedioic ac…40597612 — Sputum microbiota profiles of patients with rifamp…40618036 — Fasting builds a favorable environment for effecti…40732984 — Gut Microbiota Shifts After a Weight Loss Program …40849619 — Characteristics of gut and lung microbiota in pati…41803199 — Corn silk ameliorates fatty liver disease by modul…41962594 — Exposure to a high-fat diet compromises gut health…

PMID

Title (from table)

Select a PMID above and click Load row.

Overall paper verdict Curatable Not curatable Uncertain Not reviewed

Comment (optional)

Field-by-field validation (ground truth)

For each field, review BioAnalyzer’s predicted value and correct it if needed. For Host Species, Body Site, and Condition, also confirm or pick the ontology mapping — a dropdown of BioAnalyzer’s suggested candidates appears when a field’s mapping wasn’t auto-applied (see the Ontology ID column in the table above); otherwise enter one manually.

Host Species

Select a PMID above and click Load row to see BioAnalyzer’s prediction.

Curator value for Host Species: Was BioAnalyzer correct for Host Species? Not reviewed Correct Incorrect Unclear

Ontology ID: (load a row to see it)

Ontology mapping for Host Species: Not reviewed

Body Site

Select a PMID above and click Load row to see BioAnalyzer’s prediction.

Curator value for Body Site: Was BioAnalyzer correct for Body Site? Not reviewed Correct Incorrect Unclear

Ontology ID: (load a row to see it)

Ontology mapping for Body Site: Not reviewed

Condition

Select a PMID above and click Load row to see BioAnalyzer’s prediction.

Curator value for Condition: Was BioAnalyzer correct for Condition? Not reviewed Correct Incorrect Unclear

Ontology ID: (load a row to see it)

Ontology mapping for Condition: Not reviewed

Sample Size

Select a PMID above and click Load row to see BioAnalyzer’s prediction.

Curator value for Sample Size: Was BioAnalyzer correct for Sample Size? Not reviewed Correct Incorrect Unclear

Sequencing Type

Select a PMID above and click Load row to see BioAnalyzer’s prediction.

Curator value for Sequencing Type: Was BioAnalyzer correct for Sequencing Type? Not reviewed Correct Incorrect Unclear

Submit review opens GitHub to create an issue with your feedback CSV in the body. A bot acknowledges the issue automatically; maintainers review the CSV directly in the issue.

Notes: Submissions are processed as issues and a tab will be opened for you to just click the create button. Reviewers will look into your submitted issue to evaluate the results.

Curator Desk · BioAnalyzer v1.0.0 · PubMed → BioAnalyzer → Curator Desk → BugSigDB

GitHub repositoryOpen an issueBugSigDBPubMed

Thank you for your time and input in helping to complete this review. Your feedback has been submitted; an issue and pull request are being created in the background.

Would you like to continue reviewing other papers?