# io.github.cyanheads/biorxiv-mcp-server

> Search and retrieve bioRxiv and medRxiv preprints — by DOI, date interval, or keyword — via MCP.

- name: io.github.cyanheads/biorxiv-mcp-server
- version: 0.4.1
- connection class: R0 (autonomous)
- trust: 94/100
- quality: 84/100 (good)
- owner: not claimed
- descriptor: https://api.protogrid.dev/v1/servers/io.github.cyanheads%2Fbiorxiv-mcp-server
- tools: https://api.protogrid.dev/v1/servers/io.github.cyanheads%2Fbiorxiv-mcp-server/tools

**An agent can connect right now, no human step.** Remote endpoint, no authentication, reachable on the last probe.

## Connection (mcpServers)

```json
{
  "mcpServers": {
    "biorxiv-mcp-server": {
      "type": "http",
      "url": "https://biorxiv.caseyjhand.com/mcp"
    }
  }
}
```


## Trust

- hygiene: 100
- liveness: 100
- freshness: 100
- provenance: 80
- drivers: +repository +namespace-matches-repo +reachable +uptime-100% +updated-3d-ago
- Derived from observable signals (official registry feed and our own credential-free probes); no code audit performed.

## Quality 84/100 (good)

### protocol: 88 (weight 25)

- pass `protocol.modern`: supports 2026-07-28 (server/discover)
- pass `protocol.stateless`: answers without a session
- pass `protocol.transport`: streamable HTTP
- warn `protocol.list_ttl`: tools/list declares ttlMs 0, so clients re-fetch it on every use

### authorization: n/a (weight 15)

- n/a `auth.prm`, `auth.as_metadata`, `auth.cimd`: no remote uses OAuth
- n/a `auth.secret_in_url`: no templated URL

### tool hygiene: 79 (weight 30)

- pass `tools.descriptions`: every tool has a description
- warn `tools.description_length`: 4 tools have descriptions over 1,024 characters, which crowds the context
- pass `tools.schemas`: every tool has an object input schema
- pass `tools.annotations`: 7 of 7 tools declare readOnlyHint or destructiveHint
- fail `tools.directory_hints`: no tool declares all four of readOnlyHint, destructiveHint, idempotentHint and openWorldHint; missing: biorxiv_list_categories (destructiveHint); biorxiv_list_recent (destructiveHint, idempotentHint); biorxiv_get_published_version (destructiveHint); …
- pass `tools.token_cost`: about 3,939 tokens to load every tool
- pass `tools.api_dump`: tools are not a one-to-one API dump

### stability: 75 (weight 15)

- warn `stability.changes`: 8 tool changes in 30 days
- pass `stability.rug_pull`: no tool changed its meaning under the same name

### dependencies: 100 (weight 15)

- pass `deps.known_vulns`: no known advisory in 128 resolved packages
- pass `deps.mcp_sdk_version`: @modelcontextprotocol/core 2.3.1, no known advisory
- pass `deps.resolvable`: @cyanheads/biorxiv-mcp-server@0.4.1, @cyanheads/biorxiv-mcp-server@0.4.1 resolved: 128 packages

- tools: 7, about 3,939 tokens to load them all
- tool set hash: d26421120efde320987cb9c0622ce70b
- tools last changed: 2026-10-18T05:12:36.085Z
- badge: [![protogrid quality](https://protogrid.dev/badge/io.github.cyanheads/biorxiv-mcp-server.svg)](https://protogrid.dev/servers/io.github.cyanheads/biorxiv-mcp-server)
- Checks run on what our credential-free, read-only probes observe; tools are never called and no code audit is performed.

### Tool changes

- 2026-10-18 `biorxiv_get_fulltext` changed (outputSchema)
- 2026-10-18 `biorxiv_search_preprints` changed (inputSchema, outputSchema)
- 2026-10-18 `biorxiv_list_published_versions` changed (description, inputSchema, outputSchema)
  - before: 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 up to 100 publications per server per page (fixed by the API); pass `cursor` as an integer offset (0, 100, 200, …) to step through additional pages. 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.
  - after: 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.
- 2026-10-18 `biorxiv_get_published_version` changed (outputSchema)
- 2026-10-18 `biorxiv_get_preprint` changed (description, inputSchema, outputSchema)
  - before: 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/…; a doi.org or article URL, a doi: label, and a trailing vN / .full suffix are stripped first, and results report the bare DOI.
  - after: 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.
- 2026-10-15 `biorxiv_get_fulltext` changed (description, inputSchema, outputSchema)
  - before: 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, 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.
  - after: 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.
- 2026-10-15 `biorxiv_search_preprints` changed (inputSchema, outputSchema)
- 2026-10-15 `biorxiv_list_published_versions` added
  - 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 up to 100 publications per server per page (fixed by the API); pass `cursor` as an integer offset (0, 100, 200, …) to step through additional pages. 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.

Full history: https://api.protogrid.dev/v1/servers/io.github.cyanheads%2Fbiorxiv-mcp-server/changes

## Dependencies

- npm @cyanheads/biorxiv-mcp-server@0.4.1: resolved, 63 dependencies, MCP SDK @modelcontextprotocol/core 2.3.1
- npm @cyanheads/biorxiv-mcp-server@0.4.1: resolved, 63 dependencies, MCP SDK @modelcontextprotocol/core 2.3.1

Dependency graphs from deps.dev; advisories from OSV.dev, including the GitHub Advisory Database and the PyPI Advisory Database; all CC BY 4.0.

## Remotes

- https://biorxiv.caseyjhand.com/mcp (streamable-http, auth none, reachable true, uptime30d 1)

## Packages

- npm @cyanheads/biorxiv-mcp-server@0.4.1
- npm @cyanheads/biorxiv-mcp-server@0.4.1

## Tools (7)

- `biorxiv_get_fulltext`: 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.
- `biorxiv_get_preprint`: 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.
- `biorxiv_get_published_version`: 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.
- `biorxiv_list_categories`: 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.
- `biorxiv_list_published_versions`: 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.
- `biorxiv_list_recent`: 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.
- `biorxiv_search_preprints`: 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".