biorxiv-mcp-server

List valid subject category strings for bioRxiv and medRxiv. Use these strings as the `category` filter in biorxiv_list_recent to narrow results to a specific field. Run this tool before filtering to get the current valid values.

List preprints posted or revised within a date interval, optionally scoped to one server or a subject category. Returns 30 preprints per page (fixed by the API); pass `cursor` as an integer offset (0, 30, 60, …) to step through additional pages. When server="both" (default), per-server pagination state is returned separately — use each server's `cursor` field for independent advancement. One server failing under server="both" does not abort the call: the other server's page is still returned and the failed one is named in `failed[]`, marking the result set as partial rather than complete. Every attempted server failing is a different case and does abort the call, with a retryable upstream_unavailable (or rate_limited) error — an empty page would otherwise be indistinguishable from an interval that genuinely holds nothing. Call biorxiv_list_categories for valid category strings.

Fetch full metadata, abstract, all revision history, JATS XML full-text links, and published-journal DOI for one or more preprints by DOI. Each DOI returns all revisions in one response. When server="both" (default), each DOI is checked against both bioRxiv and medRxiv; the response includes which server the preprint was found on. Failed lookups are reported per-DOI in failed[] rather than aborting the batch, each carrying a reason (not_found, invalid_doi_format, upstream_unavailable, rate_limited) and a retryable flag; a rate_limited entry also carries the wait in seconds the origin asked for. DOIs must match the pattern 10.NNNN/…

Resolve a preprint DOI to its full journal publication record — journal DOI, journal name, published date, and corresponding author details. Use when the preprint's `publishedJournalDoi` field from biorxiv_get_preprint is present and you need the full crosswalk metadata. bioRxiv and medRxiv share the 10.1101/ DOI prefix, so server="both" (the default) checks both in parallel and the response reports which server answered. Returns a not-found error when no attempted server holds a published record — check biorxiv_get_preprint if you need to confirm the preprint is published at all.

Search preprints by keyword and/or author using EuropePMC for relevance ranking, then enrich matching DOIs with full bioRxiv/medRxiv metadata. Provide a keyword query, an author name, or both — author maps to an EuropePMC AUTH: field query and is ANDed with the keyword query. Covers both servers by default. EuropePMC indexes new preprints within 1–2 days of posting; for preprints posted within the last day, prefer biorxiv_list_recent. A EuropePMC rate limit (HTTP 429) fails the call with a retryable rate_limited error carrying the wait in seconds — a rate-limited metadata enrichment does not, and instead marks the affected record enrichment_error: "rate_limited".

Retrieve a preprint's full text as best-effort Markdown, extracted from its rendered HTML article page. Resolves the latest version via the details API, then fetches and extracts the body — abstract, sections, and references. bioRxiv and medRxiv share the 10.1101/ DOI prefix, so server="both" (the default) resolves the DOI against both in parallel and the response reports which server answered. This is HTML-to-Markdown extraction, not structured JATS: section structure is approximate and not guaranteed. Long articles exceed a single response, so use offset and limit to page through them (the response reports totalChars, remainingChars, and hasMore); paging is cheap because the extracted article is cached per version for an hour after the first read, so only the first chunk pays for a fetch. Not every preprint has an extractable HTML page — some are PDF-only and some origins block programmatic access — in which case a fulltext_unavailable error routes you to biorxiv_get_preprint for the title, abstract, and metadata. For a preprint that has been published in a journal, the journal's version may have richer full text elsewhere.