Curator Desk

BioAnalyzer curator desk

Use this page to review BioAnalyzer’s predicted statuses for candidate papers and record curator ground truth for each PMID.

What you can do here:

• Find papers quickly: Search, sort, and filter the table (Priority score helps surface high‑value candidates).
• Record ground truth: Enter curator TRUE labels and optional “was the prediction correct?” flags per field.
• Share feedback: Submit feedback via a GitHub issue (CSV is pre-filled in the issue body).

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, Summary
• Status values: ABSENT | PARTIALLY_PRESENT | PRESENT

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Candidate Curatable Articles

Interactive Table

Tip: Sort by Priority (descending) to review the most promising candidates first. Use the search box and column filters to narrow your focus.

Curator feedback

Use the table above to find papers (the Open button in the Published column opens the paper on PubMed). 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 set Curator TRUE label and Was BioAnalyzer correct?
3. Click Download feedback CSV to save one row; submit as needed.

Curator feedback form

Curator ID / initials

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

— Select a PMID —31215600 — Relationship between acetaldehyde concentration in…31160598 — Sex-specific association between gut microbiome an…31126003 — Air pollution during the winter period and respira…31123265 — Altered respiratory virome and serum cytokine prof…31053143 — The combination of sport and sport-specific diet i…30919073 — The oral microbiome of patients undergoing treatme…30888539 — Glutamate interactions with obesity, insulin resis…30875283 — Oral microbial dysbiosis in patients with Kostmann…30867067 — Prebiotic supplementation in frail older people af…30866773 — Differential effects of depot medroxyprogesterone …30854760 — Prospective observational study of vaginal microbi…30813950 — Environmental toxicants in breast milk of Norwegia…30803537 — Microbiome of Deep Dentinal Caries from Reversible…30791484 — Daidzein Intake Is Associated with Equol Producing…30791436 — Effect of Selected Stilbenoids on Human Fecal Micr…30770768 — Genome-resolved metagenomics of eukaryotic populat…30764497 — Autism Spectrum Disorder (ASD) with and without Me…30719912 — Modulation of Gut Microbiota by Soybean 7S Globuli…30707176 — Gut microbiota analysis and its significance in va…30696735 — Dynamics of Human Gut Microbiota and Short-Chain F…30682843 — The Effects of Dietary Pattern during Intensified …30678168 — Impact of Grain Sorghum Polyphenols on Microbiota …30665461 — Population structure of human gut bacteria in a di…30664020 — The effect of surgical fecal stream diversion of t…30661321 — Comparison of the Gut Microbiota of Centenarians i…30642268 — Viral species richness and composition in young ch…30633889 — Establishment of vaginal microbiota composition in…30604790 — Modification of wheat bran particle size and tissu…30599284 — Pathogen reservoir hypothesis investigated by anal…

PMID

Title (from table)

Overall paper verdict
Curatable Not curatable Uncertain Not reviewed

Comment (optional)

BioAnalyzer version (fixed for all submissions)

Field-by-field validation (ground truth)

For each field, provide the curator TRUE label (ground truth). Optionally mark whether BioAnalyzer’s predicted status was correct.

Host Species

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

Curator TRUE label for Host Species: Not reviewed ABSENT PARTIALLY_PRESENT PRESENT Was BioAnalyzer correct for Host Species? Not reviewed Correct Incorrect Unclear

Body Site

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

Curator TRUE label for Body Site: Not reviewed ABSENT PARTIALLY_PRESENT PRESENT Was BioAnalyzer correct for Body Site? Not reviewed Correct Incorrect Unclear

Condition

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

Curator TRUE label for Condition: Not reviewed ABSENT PARTIALLY_PRESENT PRESENT Was BioAnalyzer correct for Condition? Not reviewed Correct Incorrect Unclear

Sequencing Type

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

Curator TRUE label for Sequencing Type: Not reviewed ABSENT PARTIALLY_PRESENT PRESENT Was BioAnalyzer correct for Sequencing Type? Not reviewed Correct Incorrect Unclear

Sample Size

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

Curator TRUE label for Sample Size: Not reviewed ABSENT PARTIALLY_PRESENT PRESENT Was BioAnalyzer correct for Sample Size? Not reviewed Correct Incorrect Unclear

Submit review — Opens GitHub to create an issue with your feedback (no file download). A bot will then open a Pull Request with the feedback CSV so the maintainer can view and download it (including your initials and comments).

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

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?