bioRxiv Database

Overview

Python tooling over the keyless bioRxiv API for searching and retrieving life-sciences preprints. Searches by keyword, author, date range, and category, returning structured JSON (titles, abstracts, DOIs, authors, versions), and downloads full-text PDFs.

For published, peer-reviewed literature use alterlab-pubmed; for computer-science / physics / math preprints use alterlab-arxiv. bioRxiv covers biology subjects only. The same API also serves medRxiv (swap biorxiv for medrxiv in the endpoint path, e.g. /details/medrxiv/2025-03-21/2025-03-28?category=cardiovascular%20medicine); the bundled script targets bioRxiv, so query medRxiv with curl/requests directly.

How it works (and its limits)

The bioRxiv /details endpoint returns preprints by date range, 30 records per page. It accepts a server-side subject-category filter (?category=cell_biology), but has no keyword or author filter. So this tool:

1. Paginates the date range (following the cursor until all records are retrieved), passing --category to the server so only that subject is fetched, then
2. Filters client-side by keyword (substring over title/abstract) and author (substring over the author list).

Implication: a wide date range means many API calls and a large download. Keep ranges as tight as the question allows, and use --category (cuts API calls) and --limit to bound the work.

When to Use This Skill