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\n

@cyanheads/biorxiv-mcp-server

\n

Search and retrieve bioRxiv and medRxiv preprints — by DOI, date interval, or keyword — via MCP. STDIO or Streamable HTTP.\n

6 Tools
\n

\n
\n\n
\n\n[![Version](https://img.shields.io/badge/Version-0.3.0-blue.svg?style=flat-square)](./CHANGELOG.md) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![Docker](https://img.shields.io/badge/Docker-ghcr.io-2496ED?style=flat-square&logo=docker&logoColor=white)](https://github.com/users/cyanheads/packages/container/package/biorxiv-mcp-server) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^2.0.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![npm](https://img.shields.io/npm/v/@cyanheads/biorxiv-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/biorxiv-mcp-server) [![TypeScript](https://img.shields.io/badge/TypeScript-^7.0.2-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-v1.4.0-blueviolet.svg?style=flat-square)](https://bun.sh/)\n\n
\n\n
\n\n[![Install in Claude Desktop](https://img.shields.io/badge/Install_in-Claude_Desktop-D97757?style=for-the-badge&logo=anthropic&logoColor=white)](https://github.com/cyanheads/biorxiv-mcp-server/releases/latest/download/biorxiv-mcp-server.mcpb) [![Install in Cursor](https://cursor.com/deeplink/mcp-install-dark.svg)](https://cursor.com/en/install-mcp?name=biorxiv-mcp-server&config=eyJjb21tYW5kIjoibnB4IiwiYXJncyI6WyIteSIsIkBjeWFuaGVhZHMvYmlvcnhpdi1tY3Atc2VydmVyIl19) [![Install in VS Code](https://img.shields.io/badge/VS_Code-Install_Server-0098FF?style=for-the-badge&logo=visualstudiocode&logoColor=white)](https://vscode.dev/redirect?url=vscode:mcp/install?%7B%22name%22%3A%22biorxiv-mcp-server%22%2C%22command%22%3A%22npx%22%2C%22args%22%3A%5B%22-y%22%2C%22%40cyanheads/biorxiv-mcp-server%22%5D%7D)\n\n[![Framework](https://img.shields.io/badge/Built%20on-@cyanheads/mcp--ts--core-67E8F9?style=flat-square)](https://www.npmjs.com/package/@cyanheads/mcp-ts-core)\n\n
\n\n
\n\n**Public Hosted Server:** [https://biorxiv.caseyjhand.com/mcp](https://biorxiv.caseyjhand.com/mcp)\n\n
\n\n---\n\n## Overview\n\nbioRxiv and medRxiv preprint metadata and full text, searchable via EuropePMC. Fetch preprints by DOI, browse by date interval or subject category, search by keyword and author, resolve journal-publication crosswalks, and extract full text from the rendered article page, from any MCP client. Runs as a stdio process, a local Streamable HTTP server, or the public hosted endpoint above.\n\n### Tools\n\n| Tool | Description |\n|:---|:---|\n| `biorxiv_get_preprint` | Fetch full metadata, abstract, revision history, and journal crosswalk for one or more preprints by DOI |\n| `biorxiv_list_recent` | List preprints posted or updated within a date interval, with optional server, category, and funder filters |\n| `biorxiv_search_preprints` | Search preprints by keyword and/or author via EuropePMC for relevance ranking, enriched with bioRxiv/medRxiv metadata |\n| `biorxiv_get_published_version` | Resolve a preprint DOI to its journal publication record (journal DOI, name, published date) |\n| `biorxiv_get_fulltext` | Retrieve a preprint's full text as best-effort Markdown extracted from its rendered HTML article page |\n| `biorxiv_list_categories` | List valid subject category strings for bioRxiv and medRxiv |\n\n## Capability reference\n\n### `biorxiv_get_preprint` tool\n\n- Batch fetch up to 10 DOIs in a single request\n- Accepts a bare DOI or a pasted form of one — `https://doi.org/…`, `doi:…`, a `biorxiv.org`/`medrxiv.org` article URL, a `vN` or article-page suffix (`.full`, `.full.pdf`, `.article-metrics`, …) — and reports the bare DOI\n- Each DOI returns its full revision history in `revisions[]` — one API call per DOI, no enumeration loop\n- Includes title, authors, abstract, category, license, grant award numbers (`awards`), JATS XML full-text link (`jatsxmlUrl`), and published journal DOI (`publishedJournalDoi`) once accepted\n- `awards` holds each award value as upstream records it (one value can run several grants together), deduplicated; funder names are left out because `api.biorxiv.org` attributes them to unrelated organizations\n- Scope to `biorxiv`, `medrxiv`, or `both` (default `both`); when `both`, each DOI fans out in parallel and partial failures report per-DOI in `failed[]`\n- Each `failed[]` entry carries a `reason` (`not_found`, `invalid_doi_format`, `upstream_unavailable`, `rate_limited`) and a `retryable` flag — a DOI is only reported `not_found` when every attempted server answered\n- A rate-limited lookup (HTTP 429) reports `reason: \"rate_limited\"` rather than folding into `upstream_unavailable`, carrying `retryAfter` — the wait in seconds `api.biorxiv.org` asked for\n\n---\n\n### `biorxiv_list_recent` tool\n\n- Optional server-side category filter — pass a value from `biorxiv_list_categories`, in any case, with `_`, `-`, or a space (`Cell Biology`, `cell_biology`, `cell-biology`)\n- A server that answers the filter with its unfiltered listing is left out with a notice, never returned as filtered; `invalid_category` when no server applied it\n- Optional `funder` filter by ROR ID, bare (`021nxhr62`) or as `https://ror.org/021nxhr62`, checked against the ROR pattern and checksum before any request; combines with `category`\n- The funder filter is bioRxiv-only — medRxiv records carry no funder data — so `server=\"both\"` queries bioRxiv alone with a notice, and `server=\"medrxiv\"` raises `invalid_funder`\n- A ROR ID `api.biorxiv.org` has no funder record for raises `invalid_funder`, never an empty page\n- Fixed page size of 30 (API constraint); advance with integer `cursor` (0, 30, 60, …)\n- Abstracts are omitted by default — they are about three quarters of a page — and every other record field is returned; `include_abstract: true` adds them for the whole page, and `biorxiv_get_preprint` returns them for up to 10 DOIs per call\n- Response includes a `total` count per server; a cursor past the last page is marked `exhausted: true` rather than reading as zero results in the interval\n- When `server=\"both\"` (default), per-server pagination state is independent (`{ biorxiv: { cursor, total }, medrxiv: { cursor, total } }`); one server not answering is named in `failed[]` while the other's page still returns\n- Every attempted server failing raises a retryable `upstream_unavailable` (or `rate_limited`) error instead of an empty page\n\n---\n\n### `biorxiv_search_preprints` tool\n\n- Query and/or author required (author maps to an EuropePMC `AUTH:\"…\"` field query, ANDed with the keyword query); optional `date_from`/`date_to` range and `server` scope (default `both`)\n- Up to 100 results per page (default 25); `cursor_mark` pages through the same ranked list; a page past the last match comes back empty with a notice saying so, and a token EuropePMC does not recognize raises `invalid_cursor_mark`\n- An EuropePMC response missing its result list is retried, never reported as zero matches; one that persists on a first page raises `search_unavailable`\n- EuropePMC powers relevance ranking (indexes new preprints within 1–2 days of posting); the bioRxiv/medRxiv API enriches matches with canonical metadata\n- Enriched results carry the same latest-revision fields as `biorxiv_get_preprint`, including `type`, `license`, `awards`, and `authorCorrespondingInstitution`\n- Enrichment failures degrade to EuropePMC-only metadata, surfaced via `partial_results` and a per-record `enrichment_error` (`service_error`, `rate_limited`, or `not_found`); those records' abstracts come from one EuropePMC lookup keyed by their DOIs, and a failed lookup leaves them without one, with a notice\n- Abstracts are included by default; `include_abstract: false` drops them from every result, enriched and fallback alike, for a response about a third the size, keeping every other field\n- A EuropePMC rate limit (HTTP 429) raises a retryable `rate_limited` error carrying the origin's `Retry-After` wait — the search itself has no metadata to fall back on, unlike enrichment\n\n---\n\n### `biorxiv_get_published_version` tool\n\n- Uses the `/pubs/{server}/{doi}` endpoint for richer metadata than the `publishedJournalDoi` field on `biorxiv_get_preprint`\n- Returns journal DOI, journal name, published date, and corresponding-author institution; the output `server` field names which server answered (never `\"both\"`)\n- Scope to `biorxiv`, `medrxiv`, or `both` (default `both`) — the two servers share their DOI prefixes, so a DOI alone doesn't identify one\n- `10.64898/` DOIs, which `/pubs` cannot look up by preprint DOI, resolve through the preprint's own journal DOI; when the crosswalk has no record either way, that journal DOI returns alone, without journal name or date, with a notice saying so\n- No server answering raises a retryable `upstream_unavailable`, or `rate_limited` with the origin's wait on an HTTP 429 — never `doi_not_found`, which would assert an absence nothing established\n\n---\n\n### `biorxiv_get_fulltext` tool\n\n- Fetches the rendered HTML article page (`www.{server}.org/content/{doi}v{N}.full`) and extracts Markdown — there is no keyless JATS source\n- Reads the latest version, or the one requested by `version` or a `vN` suffix on the DOI (the two must agree; a version the preprint lacks raises `version_not_found`), confirmed via the details API first; only DOI resolution fans out across `biorxiv`/`medrxiv`/`both` (default `both`) — the full-text fetch itself targets whichever server answered, named in the output `server` field\n- Long articles page via `offset`/`limit` character chunking (default `limit` 20,000, max 50,000); response reports `totalChars`, `remainingChars`, `hasMore`, and a full-article `wordCount` counted from the same Markdown, and the extracted article is cached per version so paging costs one origin fetch\n- PDF-only preprints and blocked/challenge pages return a typed `fulltext_unavailable` error routing to `biorxiv_get_preprint`\n- An origin rate limit (HTTP 429) — on either the article-page host or `api.biorxiv.org` during resolution — returns a retryable `rate_limited` error carrying the origin's `Retry-After` wait, with the recovery hint naming which origin is limiting\n\n---\n\n### `biorxiv_list_categories` tool\n\n- No API call — hardcoded static list (25 bioRxiv + 51 medRxiv categories), limited to the ones the listing API actually filters on\n- Use to validate category strings before passing to `biorxiv_list_recent`\n\n## Features\n\nBuilt on [`@cyanheads/mcp-ts-core`](https://github.com/cyanheads/mcp-ts-core): stdio and Streamable HTTP transports, pluggable auth (`none` / `jwt` / `oauth`), swappable storage (`in-memory`, `filesystem`, `Supabase`, `Cloudflare KV/R2/D1`), structured logging with optional OpenTelemetry tracing.\n\nbioRxiv-specific:\n\n- `BiorxivApiService` wraps `api.biorxiv.org` — details, publications, and crosswalk endpoints with retry and exponential backoff; a 429 is classified as a retryable `rate_limited` error carrying the parsed `Retry-After` wait, with the upstream response body kept out of the payload\n- `EuropePmcService` wraps the EuropePMC search endpoint for relevance-ranked keyword and/or author results, classified the same way on a 429\n- `BiorxivFullTextService` fetches and extracts Markdown from the rendered HTML article pages on `www.biorxiv.org` / `www.medrxiv.org` — a distinct origin from the JSON API\n- Two-server fan-out via `Promise.allSettled` — both `biorxiv` and `medrxiv` queried in parallel when `server=\"both\"`, results merged and deduplicated by DOI\n- Polite `User-Agent` header including a mailto address (`BIORXIV_MAILTO` env var) per Cold Spring Harbor Lab API guidelines\n- Pairs with **pubmed-mcp-server** (post-publication), **openalex-mcp-server** (citation analytics), and **crossref-mcp-server** (DOI metadata)\n\nAgent-friendly output:\n\n- Graceful partial failure — per-DOI and per-server failures land in `failed[]` with a typed `reason` and `retryable` flag instead of aborting the whole batch or listing call\n- Rate-limit transparency — a 429 from any upstream surfaces as `reason: \"rate_limited\"` carrying the origin's parsed `retryAfter` wait, distinguished from a generic `upstream_unavailable`\n- Discriminated enrichment outputs — `biorxiv_search_preprints` results carry `enriched` plus a typed `enrichment_error` (`service_error` / `rate_limited` / `not_found`) so callers branch on data, not string parsing\n- Paging and pagination state — `exhausted` cursors are flagged as an out-of-range artifact rather than an empty interval, and `biorxiv_get_fulltext` reports `totalChars` / `remainingChars` / `hasMore` for chunked reads\n- Clean titles and abstracts — Highwire export markup is resolved to plain text on both surfaces: symbol placeholders (`{beta}`, `{+/-}`, `[≥]`) become their characters, structured-abstract headings read `Results: …`, list items read `• …`, and figure and table blocks are dropped. The Markdown in `content[]` escapes upstream text so it renders as written\n\n## Getting started\n\n### Public Hosted Instance\n\nA public instance is available at `https://biorxiv.caseyjhand.com/mcp` — no installation required. Point any MCP client at it via Streamable HTTP:\n\n```json\n{\n \"mcpServers\": {\n \"biorxiv-mcp-server\": {\n \"type\": \"streamable-http\",\n \"url\": \"https://biorxiv.caseyjhand.com/mcp\"\n }\n }\n}\n```\n\n### Self-Hosted / Local\n\nAdd the following to your MCP client configuration file.\n\n```json\n{\n \"mcpServers\": {\n \"biorxiv-mcp-server\": {\n \"type\": \"stdio\",\n \"command\": \"bunx\",\n \"args\": [\"@cyanheads/biorxiv-mcp-server@latest\"],\n \"env\": {\n \"MCP_TRANSPORT_TYPE\": \"stdio\",\n \"MCP_LOG_LEVEL\": \"info\",\n \"BIORXIV_MAILTO\": \"your@email.com\"\n }\n }\n }\n}\n```\n\nOr with npx (no Bun required):\n\n```json\n{\n \"mcpServers\": {\n \"biorxiv-mcp-server\": {\n \"type\": \"stdio\",\n \"command\": \"npx\",\n \"args\": [\"-y\", \"@cyanheads/biorxiv-mcp-server@latest\"],\n \"env\": {\n \"MCP_TRANSPORT_TYPE\": \"stdio\",\n \"MCP_LOG_LEVEL\": \"info\",\n \"BIORXIV_MAILTO\": \"your@email.com\"\n }\n }\n }\n}\n```\n\nOr with Docker:\n\n```json\n{\n \"mcpServers\": {\n \"biorxiv-mcp-server\": {\n \"type\": \"stdio\",\n \"command\": \"docker\",\n \"args\": [\"run\", \"-i\", \"--rm\", \"-e\", \"MCP_TRANSPORT_TYPE=stdio\", \"-e\", \"BIORXIV_MAILTO=your@email.com\", \"ghcr.io/cyanheads/biorxiv-mcp-server:latest\"]\n }\n }\n}\n```\n\nFor Streamable HTTP, set the transport and start the server:\n\n```sh\nMCP_TRANSPORT_TYPE=http MCP_HTTP_PORT=3010 BIORXIV_MAILTO=your@email.com bun run start:http\n# Server listens at http://localhost:3010/mcp\n```\n\n### Prerequisites\n\n- [Bun v1.4.0](https://bun.sh/) or higher (or Node.js v24+).\n\n### Installation\n\n1. **Clone the repository:**\n\n```sh\ngit clone https://github.com/cyanheads/biorxiv-mcp-server.git\n```\n\n2. **Navigate into the directory:**\n\n```sh\ncd biorxiv-mcp-server\n```\n\n3. **Install dependencies:**\n\n```sh\nbun install\n```\n\n4. **Configure environment:**\n\n```sh\ncp .env.example .env\n# optionally set BIORXIV_MAILTO for polite API access\n```\n\n## Configuration\n\nAll configuration is validated at startup via Zod schemas in `src/config/server-config.ts`.\n\n| Variable | Description | Default |\n|:---|:---|:---|\n| `BIORXIV_MAILTO` | Email address included in the `User-Agent` header for polite API access per Cold Spring Harbor Lab guidelines. Optional, but recommended. | — |\n| `BIORXIV_API_BASE_URL` | Override the bioRxiv API base URL. | `https://api.biorxiv.org` |\n| `EUROPEPMC_API_BASE_URL` | Override the EuropePMC base URL. | `https://www.ebi.ac.uk/europepmc/webservices/rest` |\n| `BIORXIV_WEB_BASE_URL` | Override the bioRxiv website base URL (full-text HTML source for `biorxiv_get_fulltext`). | `https://www.biorxiv.org` |\n| `MEDRXIV_WEB_BASE_URL` | Override the medRxiv website base URL (full-text HTML source for `biorxiv_get_fulltext`). | `https://www.medrxiv.org` |\n| `MCP_TRANSPORT_TYPE` | Transport: `stdio` or `http`. | `stdio` |\n| `MCP_HTTP_PORT` | HTTP server port. | `3010` |\n| `MCP_HTTP_ENDPOINT_PATH` | HTTP endpoint path. | `/mcp` |\n| `MCP_AUTH_MODE` | Auth mode: `none`, `jwt`, or `oauth`. | `none` |\n| `MCP_LOG_LEVEL` | Log level (`debug`, `info`, `warning`, `error`, etc.). | `info` |\n| `LOGS_DIR` | Directory for log files (Node.js only). | `/logs` |\n| `OTEL_ENABLED` | Enable OpenTelemetry instrumentation. | `false` |\n\nSee [`.env.example`](./.env.example) for the full list of optional overrides.\n\n## Running the server\n\n### Local development\n\n- **Build and run:**\n\n ```sh\n # One-time build\n bun run rebuild\n\n # Run the built server\n bun run start:stdio\n # or\n bun run start:http\n ```\n\n- **Run checks and tests:**\n\n ```sh\n bun run devcheck # Lint, format, typecheck, security\n bun run test # Vitest test suite\n bun run lint:mcp # Validate MCP definitions against spec\n ```\n\n### Docker\n\n```sh\ndocker build -t biorxiv-mcp-server .\ndocker run --rm -e BIORXIV_MAILTO=your@email.com -p 3010:3010 biorxiv-mcp-server\n```\n\nThe Dockerfile defaults to HTTP transport, stateless session mode, and logs to `/var/log/biorxiv-mcp-server`. OpenTelemetry peer dependencies are installed by default — build with `--build-arg OTEL_ENABLED=false` to omit them.\n\n## Project structure\n\n| Directory | Purpose |\n|:---|:---|\n| `src/index.ts` | `createApp()` entry point — registers tools and initializes services. |\n| `src/config` | Server-specific environment variable parsing and validation with Zod. |\n| `src/mcp-server/tools` | Tool definitions (`*.tool.ts`). Six tools across bioRxiv and medRxiv. |\n| `src/services/biorxiv` | `BiorxivApiService` — details, publications, and crosswalk endpoint wrappers with retry. |\n| `src/services/biorxiv-fulltext` | `BiorxivFullTextService` — rendered HTML article page fetch and Markdown extraction. |\n| `src/services/europe-pmc` | `EuropePmcService` — preprint keyword/author search endpoint wrapper. |\n| `tests/` | Unit and integration tests mirroring the `src/` structure. |\n\n## Development guide\n\nSee [`CLAUDE.md`](./CLAUDE.md) for development guidelines and architectural rules. The short version:\n\n- Handlers throw, framework catches — no `try/catch` in tool logic\n- Use `ctx.log` for request-scoped logging, `ctx.state` for tenant-scoped storage\n- Register new tools via the barrel in `src/mcp-server/tools/definitions/index.ts`\n- Wrap external API calls: validate raw → normalize to domain type → return output schema; never fabricate missing fields\n\n## Contributing\n\nIssues are welcome. Run checks and tests before submitting:\n\n```sh\nbun run devcheck\nbun run test\n```\n\n## License\n\nApache-2.0 — see [LICENSE](./LICENSE) for details.\n","readmeFilename":"README.md"}