biorxiv

Name: biorxiv
Author: ai4protein

244stars35forks

How to install biorxiv?

ai4protein/venusfactory2/biorxiv

$npx -y skills add ai4protein/VenusFactory2 --skill biorxiv

Installs into the current project.

Summary

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, o

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SKILL.md

1	# bioRxiv & medRxiv
2
3	## Overview
4
5	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).
6
7	## Project Tools (VenusFactory2)
8
9	\| Tool \| Args \| Returns \| Description \|
10	\|------\|------\|---------\|--------------\|
11	\| 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. \|
12	\| 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. \|
13
14	## When to Use Each
15
16	\| Goal \| Tool \|
17	\|---\|---\|
18	\| "Latest bioinformatics preprints" \| `query_biorxiv(query="bioinformatics", days=7)` \|
19	\| "Get me preprint X by DOI" \| `download_biorxiv_by_doi` \|
20	\| Resolve a published paper back to its preprint version \| `download_biorxiv_by_doi(doi=<published-DOI>)` (if a preprint exists with that DOI) \|
21	\| Get JATS XML for ML training data \| `download_biorxiv_by_doi`, then GET the `jatsxml` URL from the metadata \|
22
23	## Server Choice
24
25	- biorxiv (default) — biology preprints (>200K papers, since 2013)
26	- medrxiv — medicine / health-sciences preprints (>40K papers, since 2019)
27
28	If a DOI isn't found on biorxiv, try medrxiv (they share `10.1101/` DOI prefix).
29
30	## Version Handling
31
32	`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.
33
34	## Common Mistakes
35
36	- Wrong server: if you get `NotFound`, try `server="medrxiv"` (or vice versa).
37	- DOI URL not normalized: the tool strips `https://doi.org/`, `http://doi.org/`, `doi:` prefixes — fine to paste a URL.
38	- 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`.
39	- Old DOI on a withdrawn preprint: the API may still return metadata with `type="withdrawn"`. Check `category` / `type` fields if integrity matters.
40
41	## References
42
43	- [bioRxiv API docs](https://api.biorxiv.org/)
44	- [bioRxiv home](https://www.biorxiv.org/) / [medRxiv home](https://www.medrxiv.org/)

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biorxiv

244stars35forks

View on GitHub

How to install biorxiv?

ai4protein/venusfactory2/biorxiv

$npx -y skills add ai4protein/VenusFactory2 --skill biorxiv

Installs into the current project.

Summary

Files · 1

View on GitHub

SKILL.md

1	# bioRxiv & medRxiv
2
3	## Overview
4
5	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).
6
7	## Project Tools (VenusFactory2)
8
9	\| Tool \| Args \| Returns \| Description \|
10	\|------\|------\|---------\|--------------\|
11	\| 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. \|
12	\| 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. \|
13
14	## When to Use Each
15
16	\| Goal \| Tool \|
17	\|---\|---\|
18	\| "Latest bioinformatics preprints" \| `query_biorxiv(query="bioinformatics", days=7)` \|
19	\| "Get me preprint X by DOI" \| `download_biorxiv_by_doi` \|
20	\| Resolve a published paper back to its preprint version \| `download_biorxiv_by_doi(doi=<published-DOI>)` (if a preprint exists with that DOI) \|
21	\| Get JATS XML for ML training data \| `download_biorxiv_by_doi`, then GET the `jatsxml` URL from the metadata \|
22
23	## Server Choice
24
25	- biorxiv (default) — biology preprints (>200K papers, since 2013)
26	- medrxiv — medicine / health-sciences preprints (>40K papers, since 2019)
27
28	If a DOI isn't found on biorxiv, try medrxiv (they share `10.1101/` DOI prefix).
29
30	## Version Handling
31
32	`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.
33
34	## Common Mistakes
35
36	- Wrong server: if you get `NotFound`, try `server="medrxiv"` (or vice versa).
37	- DOI URL not normalized: the tool strips `https://doi.org/`, `http://doi.org/`, `doi:` prefixes — fine to paste a URL.
38	- 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`.
39	- Old DOI on a withdrawn preprint: the API may still return metadata with `type="withdrawn"`. Check `category` / `type` fields if integrity matters.
40
41	## References
42
43	- [bioRxiv API docs](https://api.biorxiv.org/)
44	- [bioRxiv home](https://www.biorxiv.org/) / [medRxiv home](https://www.medrxiv.org/)

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