How do I install the Biorxiv skill?

Run npx skillmds@latest add ai4protein/biorxiv in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

Is Biorxiv safe to use?

This skill has not completed SkillMD's automated safety review yet. SkillMD never runs a skill's scripts for you; review the SKILL.md before installing.

Which AI agents work with Biorxiv?

This skill is tagged as working with Claude Code, Claude.ai, OpenAI Codex. SKILL.md is an open format, so most agents that read a skills directory can load it too.

Is Biorxiv free to use?

Yes. Installing skills from SkillMD is free. This skill is licensed under Unknown (bioRxiv content l….

Who published Biorxiv?

ai4protein (@ai4protein) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Biorxiv by ai4protein — Agent Skill

Name: Biorxiv
Author: ai4protein

Biorxiv

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.

ai4protein Updated Sep 17, 2026

File contents

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

---name: biorxivdescription: 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)---# bioRxiv & medRxiv## OverviewTwo 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- [bioRxiv API docs](https://api.biorxiv.org/)- [bioRxiv home](https://www.biorxiv.org/) / [medRxiv home](https://www.medrxiv.org/)

Frequently asked questions