biorxiv

Research

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.

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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.