| name | biorxiv |
| description | bioRxiv & medRxiv — biology / medicine preprint servers. Search by keyword + date window, fetch a specific preprint's full metadata (with all version history + abstract + JATS XML link) by DOI. Use for cutting-edge biology/medicine work that hasn't gone through peer review yet, or to find the original preprint version of a paper you only have the DOI for. |
| license | Unknown (bioRxiv content licensed by individual authors) |
| metadata | {"version":"1.0","skill-author":"VenusFactory2 (download_biorxiv_by_doi adapted from Google DeepMind)."} |
bioRxiv & medRxiv
Overview
Two tools: existing query_biorxiv_tool (keyword/category date-window search) + new download_biorxiv_by_doi (fetch one preprint by DOI with all metadata, including version history).
Project Tools (VenusFactory2)
| Tool | Args | Returns | Description |
|---|
| query_biorxiv | query (category or keyword), max_results (default 5, max 50), days (default 30; date window) | JSON list of paper records inline | Browse recent preprints in a category. |
| download_biorxiv_by_doi | doi (bare 10.1101/... or DOI URL), out_dir, server (biorxiv | medrxiv; default biorxiv), include_abstract (default True), timeout (default 30s) | rich JSON envelope; full metadata + version list at file_info.file_path; biological_metadata extracts title/authors/date/category/license/jatsxml URL | Fetch one preprint by DOI. |
When to Use Each
| Goal | Tool |
|---|
| "Latest bioinformatics preprints" | query_biorxiv(query="bioinformatics", days=7) |
| "Get me preprint X by DOI" | download_biorxiv_by_doi |
| Resolve a published paper back to its preprint version | download_biorxiv_by_doi(doi=<published-DOI>) (if a preprint exists with that DOI) |
| Get JATS XML for ML training data | download_biorxiv_by_doi, then GET the jatsxml URL from the metadata |
Server Choice
- biorxiv (default) — biology preprints (>200K papers, since 2013)
- medrxiv — medicine / health-sciences preprints (>40K papers, since 2019)
If a DOI isn't found on biorxiv, try medrxiv (they share 10.1101/ DOI prefix).
Version Handling
download_biorxiv_by_doi returns all versions in latest_versions[*]. The top-level latest field is the most recent version (newest version number). Use latest.jatsxml for full-text XML, latest.date for publication date.
Common Mistakes
- Wrong server: if you get
NotFound, try server="medrxiv" (or vice versa).
- DOI URL not normalized: the tool strips
https://doi.org/, http://doi.org/, doi: prefixes — fine to paste a URL.
- Trying to download the PDF directly: this tool returns the metadata JSON (which includes a PDF URL). To download the PDF, follow the URL via
WebFetch or requests.
- Old DOI on a withdrawn preprint: the API may still return metadata with
type="withdrawn". Check category / type fields if integrity matters.
References
