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bioRxiv API

skills/paper-lookup/references/biorxiv.md

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bioRxiv API

bioRxiv is a preprint server for biology. The API provides metadata for preprints, including title, authors, abstract, DOI, and publication status.

Important: The bioRxiv API has no keyword search. It supports date-range browsing and DOI lookup only. For keyword search of bioRxiv preprints, use Semantic Scholar, OpenAlex, or CORE instead.

Base URL

https://api.biorxiv.org

Authentication

None required. Fully public API.

Key Endpoints

1. Content Detail -- Browse by date range

GET /details/biorxiv/{interval}/{cursor}/{format}
ParameterValuesDescription
intervalYYYY-MM-DD/YYYY-MM-DDDate range (inclusive). Keep ranges narrow (1-3 days) to avoid timeouts.
N (integer)N most recent preprints
Nd (integer + "d")Last N days
cursorInteger (default 0)Absolute record offset. /details/ returns 30 per page, so step by 30 -- see Pagination.
formatjson (default), xmlResponse format

Optional query parameter: ?category=neuroscience (filter by category, use underscores for spaces)

Examples:

https://api.biorxiv.org/details/biorxiv/2024-01-01/2024-01-31/0
https://api.biorxiv.org/details/biorxiv/5
https://api.biorxiv.org/details/biorxiv/10d
https://api.biorxiv.org/details/biorxiv/2024-01-01/2024-01-31?category=neuroscience

2. Content Detail -- DOI lookup

GET /details/biorxiv/{doi}/na/{format}

Example:

https://api.biorxiv.org/details/biorxiv/10.1101/2024.01.16.575895/na/json

3. Published Article Links

GET /pubs/biorxiv/{interval}/{cursor}
GET /pubs/biorxiv/{doi}/na

Links preprints to their published journal versions. Accepts both preprint DOI and published DOI.

4. Publisher Filter

GET /publisher/{prefix}/{interval}/{cursor}

Find bioRxiv papers published by a specific publisher (by DOI prefix).

https://api.biorxiv.org/publisher/10.15252/2024-01-01/2024-06-01/0

Hazard: this endpoint returns {"messages":[{"status":"no articles found"}],"collection":[]} for many valid publisher prefixes, including the one above (EMBO, verified 2026-07-27) -- with HTTP 200, so an empty collection is indistinguishable from a genuine no-match. Treat an empty result here as inconclusive, not as evidence that a publisher issued no bioRxiv preprints. To answer "which bioRxiv preprints did publisher X publish", prefer /pubs/ (below) and group by published_journal, or query Crossref with filter=prefix:10.15252.

Response Format

json
{
  "messages": [{
    "status": "ok",
    "category": "all",
    "interval": "2024-01-01:2024-01-03",
    "funder": "all",
    "cursor": 0,
    "count": 30,
    "count_new_papers": "232",
    "total": "360"
  }],
  "collection": [{
    "title": "Paper title...",
    "authors": "Surname, A.; Surname, B.",
    "author_corresponding": "Full Name",
    "author_corresponding_institution": "Institution",
    "doi": "10.1101/2024.01.16.575895",
    "date": "2024-01-20",
    "version": "1",
    "type": "new results",
    "license": "cc_no",
    "category": "cancer biology",
    "jatsxml": "https://www.biorxiv.org/content/early/.../source.xml",
    "abstract": "Full abstract text...",
    "published": "10.1158/2159-8290.CD-24-0187",
    "server": "bioRxiv"
  }]
}
  • published is "NA" if not yet published in a journal, or the published DOI if it has been.
  • type values: new results, confirmatory results, contradictory results

The messages block is not uniform -- check before reconciling

The counting fields exist only on interval queries. Verified 2026-07-27:

Requestmessages[0] contains
/details/biorxiv/2024-01-01/2024-01-03/0status, category, interval, funder, cursor, count, count_new_papers, total
/details/biorxiv/{doi}/na/jsonstatus, category only -- no counts
/details/biorxiv/5 (N most recent)status, category only -- no counts
/pubs/biorxiv/{interval}/{cursor}status, interval, cursor, count, total

So the skill's "count first, then reconcile" step has nothing to reconcile against on DOI and N-most-recent lookups. Use len(collection) there and say in the provenance that the endpoint exposes no total.

total and count_new_papers count different things. For 2024-01-01:2024-01-03, total was 360 and count_new_papers was 232: total counts every version record in the interval, while count_new_papers counts distinct first-posting preprints. Paginating to total and then deduplicating by DOI lands near count_new_papers, not total -- reconcile against the right one and report which you used.

Pagination

Page size differs by endpoint -- verified 2026-07-27, and the difference is silent:

EndpointRecords per pageStep cursor by
/details/{server}/{interval}/{cursor}3030
/pubs/{server}/{interval}/{cursor}100100

cursor is an absolute record offset, not a page number, and out-of-step values are accepted without complaint: cursor=100 on a /details/ query returns records 100-129 and HTTP 200. Stepping a /details/ walk by 100 therefore skips records 30-99 of every hundred and looks successful. Step by the count the response actually reported, and stop when cursor + count >= total or collection comes back empty.

scripts/paginate.py --api biorxiv implements this walk with the right step and reconciles the retrieved total against total and count_new_papers.

Rate Limits

No documented rate limits. No authentication required. Be reasonable with request frequency.

Categories

animal-behavior-and-cognition, biochemistry, bioengineering, bioinformatics, biophysics, cancer-biology, cell-biology, clinical-trials, developmental-biology, ecology, epidemiology, evolutionary-biology, genetics, genomics, immunology, microbiology, molecular-biology, neuroscience, paleontology, pathology, pharmacology-and-toxicology, physiology, plant-biology, scientific-communication-and-education, synthetic-biology, systems-biology, zoology