io.github.cyanheads/biorxiv-mcp-server

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Les 7 outils

• biorxiv_get_fulltext≈ 2230 tokens

  Retrieve a preprint's full text as best-effort Markdown, extracted from its rendered HTML article page. Reads the latest version unless one is requested (the version input, or a vN suffix on the DOI), confirms it via the details API, then fetches and extracts the body — abstract, sections, inline citation labels, and the reference list. Table cells are not on the article page: each table appears as its caption, and omittedTables names it with the URL that serves its cells. 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.

  Paramètres, retour & exemple (5)

  Paramètres

  • doi · string · requis
    Preprint DOI (e.g. 10.1101/2024.05.28.596311 or 10.64898/2026.05.07.723463). A doi.org or biorxiv.org/medrxiv.org article URL, a doi: prefix, or a .full suffix is accepted and stripped; a trailing vN (…596311v2) requests that version. Without one, the latest version is resolved automatically.
  • limit · integer · optionnel
    Maximum number of characters to return in this chunk. Default 20,000; a value past the remaining text returns the rest of the article. Check the length field for the actual count returned.
  • offset · integer · optionnel
    Character offset into the full extracted text at which to start reading. 0 returns the beginning. To read the next chunk, use offset = prior_offset + prior_length (the length field from the previous response).
  • server · string · optionnel · biorxiv | medrxiv | both
    Server the preprint was posted on. "both" (default) checks bioRxiv and medRxiv in parallel to resolve the DOI — the full-text fetch itself only ever targets whichever server resolved, and the output server field names it.
  • version · integer · optionnel
    Preprint version to read (1, 2, …) — the revision numbers biorxiv_get_preprint lists. Omit for the latest version. Must match a vN suffix on the DOI when both are given.

  Exemple d'appel

  {"name": "biorxiv_get_fulltext", "arguments": {"doi": "texte"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"cap": 1, "doi": "texte", "error": {}, "shown": 1, "title": "texte", "length": 1, "notice": "texte", "offset": 1, "server": "biorxiv", "content": "texte", "hasMore": true, "version": "texte"}}

• biorxiv_get_preprint≈ 2053 tokens

  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. Each call looks up the first 10 distinct DOIs and returns the rest, never looked up, in unprocessed[] — pass that list as dois in another call to continue; a repeated DOI is looked up once and an unparseable entry is reported in failed[], so neither counts toward the 10. 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. preprints[], failed[], and unprocessed[] follow input order. DOIs must match the pattern 10.NNNN/…; a doi.org or article URL, a doi: label, and a trailing vN / .full suffix are stripped first, and results report the bare DOI.

  Paramètres, retour & exemple (2)

  Paramètres

  • dois · array · requis
    Preprint DOIs to look up, up to 200 entries. The first 10 distinct DOIs are looked up; the rest are returned in unprocessed.
  • server · string · optionnel · biorxiv | medrxiv | both
    Server to query. "both" checks bioRxiv and medRxiv in parallel for each DOI.

  Exemple d'appel

  {"name": "biorxiv_get_preprint", "arguments": {"dois": []}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"cap": 1, "error": {}, "shown": 1, "failed": [], "notice": "texte", "preprints": [], "truncated": true, "unprocessed": []}}

• biorxiv_get_published_version≈ 1288 tokens

  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 their DOI prefixes, so server="both" (the default) checks both in parallel and the response reports which server answered. Works for 10.1101/ and 10.64898/ DOIs alike; when the crosswalk holds no record for a published preprint, the journal DOI still comes back from the preprint's own record, without journal name or date, and a notice says so. Returns a not-found error only when no server holds the preprint or it lists no journal version at all.

  Paramètres, retour & exemple (2)

  Paramètres

  • doi · string · requis
    Preprint DOI to resolve (e.g. 10.1101/2024.01.15.575123 or 10.64898/2026.05.07.723463). A doi.org or biorxiv.org/medrxiv.org article URL, a doi: prefix, or a vN / .full suffix is accepted and stripped to the bare DOI.
  • server · string · optionnel · biorxiv | medrxiv | both
    Server the preprint was posted on. "both" (default) checks bioRxiv and medRxiv in parallel — use it when the DOI alone does not tell you which server holds the preprint.

  Exemple d'appel

  {"name": "biorxiv_get_published_version", "arguments": {"doi": "texte"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"error": {}, "notice": "texte", "server": "biorxiv", "preprintDoi": "texte", "preprintDate": "texte", "publishedDoi": "texte", "preprintTitle": "texte", "publishedDate": "texte", "preprintAuthors": "texte", "preprintAbstract": "texte", "preprintCategory": "texte", "publishedJournal": "texte"}}

• biorxiv_list_categories≈ 510 tokens

  List valid subject category strings for bioRxiv and medRxiv — the categories the listing API actually filters on. Use these strings as the `category` filter in biorxiv_list_recent to narrow results to a specific field; case, and "_" or "-" in place of a space, do not matter there. Run this tool before filtering to get the current valid values.

  Paramètres, retour & exemple (0)

  Exemple d'appel

  {"name": "biorxiv_list_categories", "arguments": {}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"error": {}, "biorxiv": [], "medrxiv": []}}

• biorxiv_list_published_versions≈ 2538 tokens

  List preprints that appeared as journal articles within a journal publication-date interval, each with its journal DOI, journal name, publication date, and preprint metadata — the same record biorxiv_get_published_version returns for one DOI. The dates filter on journal publication, not preprint posting, so most rows were posted months or years earlier; use biorxiv_list_recent for preprints posted in an interval. Returns `limit` publications per server (default 25, up to 100 — the page api.biorxiv.org serves; a larger limit returns 100 and says so). Continue at the `nextCursor` a page returns rather than stepping `cursor` by a fixed amount; `limit: 100` walks an interval in the fewest calls. When server="both" (default), per-server pagination state is returned separately, since one cursor can be past the end of one server and inside the other — to continue a single server, pass its `nextCursor` with `server` set to that server. 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[]`. Every attempted server failing raises a retryable upstream_unavailable (or rate_limited) error rather than an empty page. Abstracts are omitted by default to keep the page small — pass include_abstract: true for the whole page. Every preprintDoi, 10.1101/ and 10.64898/ alike, is accepted by biorxiv_get_preprint and the other DOI tools.

  Paramètres, retour & exemple (6)

  Paramètres

  • limit · integer · optionnel
    Rows to return per queried server, starting at cursor. Defaults to 25. Up to 100, the page api.biorxiv.org serves: a larger value returns 100 rows per server and says so in the notice. limit: 100 walks an interval in the fewest calls.
  • cursor · integer · optionnel
    Integer row offset, applied to each queried server. Defaults to 0 (first page). To continue, pass the nextCursor the previous page returned for that server — it advances by the rows actually served.
  • server · string · optionnel · biorxiv | medrxiv | both
    Preprint server to list. "both" lists bioRxiv and medRxiv in parallel; their rows do not overlap.
  • end_date · string · requis
    End of the journal publication-date interval (YYYY-MM-DD), inclusive.
  • start_date · string · requis
    Start of the journal publication-date interval (YYYY-MM-DD), inclusive.
  • include_abstract · boolean · optionnel
    Include each preprint's abstract. Defaults to false: abstracts make up about three quarters of a page, and every other field is returned either way.

  Exemple d'appel

  {"name": "biorxiv_list_published_versions", "arguments": {"end_date": "texte", "start_date": "texte"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"cap": 1, "error": {}, "shown": 1, "failed": [], "notice": "texte", "truncated": true, "pagination": {}, "publications": []}}

• biorxiv_list_recent≈ 2550 tokens

  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. Abstracts are omitted by default to keep the page small — pass include_abstract: true for the whole page, or call biorxiv_get_preprint (up to 10 DOIs per call) for a few. 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; a server that answers a category filter with its unfiltered listing is left out with a notice, and invalid_category is raised when no server applied it. `funder` limits the listing to bioRxiv preprints funded by that organization, given its ROR ID; an ID api.biorxiv.org has no funder record for raises invalid_funder rather than returning an empty page.

  Paramètres, retour & exemple (7)

  Paramètres

  • cursor · integer · optionnel
    Integer page offset (0, 30, 60, …). Defaults to 0 (first page).
  • funder · string · optionnel
    Funder filter: the funder's ROR ID, bare ("021nxhr62" for the US National Science Foundation) or as a URL ("https://ror.org/021nxhr62"). bioRxiv only — medRxiv records carry no funder data, so server="both" queries bioRxiv alone and server="medrxiv" is rejected. Combines with category. Look the ID up by name at ror.org.
  • server · string · optionnel · biorxiv | medrxiv | both
    Server to query. "both" fans out to bioRxiv and medRxiv in parallel.
  • category · string · optionnel
    Subject category filter, matched case-insensitively with "_" and "-" read as a space — "Cell Biology", "cell biology", "cell_biology", and "cell-biology" are the same filter. Use biorxiv_list_categories for valid values.
  • end_date · string · requis
    End of the date interval (YYYY-MM-DD).
  • start_date · string · requis
    Start of the date interval (YYYY-MM-DD).
  • include_abstract · boolean · optionnel
    Include each preprint's abstract. Defaults to false: abstracts make up about three quarters of a page, and every other field is returned either way.

  Exemple d'appel

  {"name": "biorxiv_list_recent", "arguments": {"end_date": "texte", "start_date": "texte"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"error": {}, "failed": [], "notice": "texte", "preprints": [], "pagination": {}, "categoryNote": "texte"}}

• biorxiv_search_preprints≈ 2393 tokens

  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. Abstracts are included by default; include_abstract: false omits them from every result for a response about a third the size, and biorxiv_get_preprint returns the abstract for up to 10 DOIs per call. 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".

  Paramètres, retour & exemple (8)

  Paramètres

  • limit · integer · optionnel
    Maximum results to return. Defaults to 25. Up to 100 per call: a larger value returns the first 100 and says so, and nextCursorMark continues the ranked list.
  • query · string · optionnel
    Keyword search query. Optional when author is provided — supply at least one of query or author.
  • author · string · optionnel
    Author name to filter by, mapped to an EuropePMC AUTH:"…" field query and ANDed with the keyword query. Optional when query is provided (e.g. "Jennifer Doudna").
  • server · string · optionnel · biorxiv | medrxiv | both
    Server scope for enrichment. "both" checks all matching DOIs on both servers.
  • date_to · string · optionnel
    Latest first-publication date filter (YYYY-MM-DD).
  • date_from · string · optionnel
    Earliest first-publication date filter (YYYY-MM-DD).
  • cursor_mark · string · optionnel
    Opaque page token for ranked EuropePMC results. Omit for the first page; pass the nextCursorMark returned by a prior call to fetch the next page. Pages through the same ranked list rather than raising limit. A token EuropePMC does not recognize fails with invalid_cursor_mark.
  • include_abstract · boolean · optionnel
    Include each result's abstract. Defaults to true. false omits the abstract from every result, enriched and EuropePMC-fallback alike, and keeps every other field.

  Exemple d'appel

  {"name": "biorxiv_search_preprints", "arguments": {"limit": 1, "query": "texte", "author": "texte", "server": "biorxiv", "date_to": "texte", "date_from": "texte"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"cap": 1, "error": {}, "shown": 1, "notice": "texte", "preprints": [], "queryEcho": {}, "truncated": true, "totalCount": 1, "nextCursorMark": "texte", "partial_results": true}}

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Source

https://biorxiv.caseyjhand.com/mcp