# biorxiv-mcp-server [Health: Active] **Category:** 💻 Developer Tools **Repository:** https://github.com/cyanheads/biorxiv-mcp-server **GitHub Stars:** 4 **Views:** 0 **Installs:** 0 **Upvotes:** 0 **Directory Page:** https://allmcps.com/mcp/biorxiv-mcp-server ## Description Search and retrieve bioRxiv and medRxiv preprints — by DOI, date interval, or keyword — via MCP. ## Claude Desktop Quick Installation Install path detected from listing signals. Uses `bunx` (confidence: high): ```json "mcpServers": { "biorxiv-mcp-server": { "command": "bunx", "args": ["@cyanheads/biorxiv-mcp-server@latest"] } } ``` ## Documentation & README

@cyanheads/biorxiv-mcp-server

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

6 Tools

[![Version](https://img.shields.io/badge/Version-0.2.6-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/)
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--- ## Tools Six tools for working with bioRxiv and medRxiv preprint data: | Tool | Description | |:---|:---| | `biorxiv_get_preprint` | Fetch full metadata, abstract, revision history, and journal crosswalk for one or more preprints by DOI | | `biorxiv_list_recent` | List preprints posted or updated within a date interval, with optional server and category filters | | `biorxiv_search_preprints` | Search preprints by keyword and/or author via EuropePMC for relevance ranking, enriched with bioRxiv/medRxiv metadata | | `biorxiv_get_published_version` | Resolve a preprint DOI to its journal publication record (journal DOI, name, published date) | | `biorxiv_get_fulltext` | Retrieve a preprint's full text as best-effort Markdown extracted from its rendered HTML article page | | `biorxiv_list_categories` | List valid subject category strings for bioRxiv and medRxiv | ### `biorxiv_get_preprint` Fetch preprint metadata by DOI — all revisions in one call. - Batch fetch up to 10 DOIs in a single request - Each DOI returns the full revision history in `collection[]` — one API call per DOI, no enumeration loop - Includes title, authors, abstract, category, license, JATS XML full-text link (`jatsxml`), and published journal DOI when the preprint has been accepted - Scope to `biorxiv`, `medrxiv`, or `both`; when `both`, each DOI fans out in parallel and partial failures report per-DOI in `failed[]` - Each `failed[]` entry carries a `reason` (`not_found`, `invalid_doi_format`, `upstream_unavailable`, `rate_limited`) and a `retryable` flag — a DOI is only reported as not found when every attempted server answered - A lookup the origin rate-limited (HTTP 429) reports as `rate_limited` rather than folding into `upstream_unavailable`, and carries `retryAfter` — the wait in seconds `api.biorxiv.org` asked for --- ### `biorxiv_list_recent` Page through preprints in a date interval. - Server-side category filtering via `?category=…` — pass a value from `biorxiv_list_categories` - Fixed page size of 30 (API constraint); advance with integer `cursor` (0, 30, 60, …) - Response includes `total` count per server for calculating remaining pages - When `server="both"`, each server paginates independently; response surfaces per-server pagination state (`{ biorxiv: { cursor, total }, medrxiv: { cursor, total } }`) - A server whose cursor is past its last page is marked `exhausted: true` — the API reports `total: 0` for an out-of-range cursor, so that count is an artifact rather than the interval total - One server not answering under `server="both"` is named in `failed[]` rather than dropped; the other server's page is still returned, and a non-empty `failed[]` marks the result set as partial - Every attempted server failing raises a retryable `upstream_unavailable` (or `rate_limited`) error instead of returning an empty page — nothing answered, so an empty interval was never established --- ### `biorxiv_search_preprints` Keyword and/or author search with relevance ranking. - EuropePMC powers relevance ranking (indexes new preprints within 1–2 days of posting); bioRxiv/medRxiv API provides canonical metadata enrichment - Optional `author` maps to an EuropePMC `AUTH:"…"` field query, ANDed with the keyword query — supply `query`, `author`, or both - Covers both servers by default; scope down with `server` - Optional date range filters (`date_from`, `date_to`) - Enriched results carry the same latest-revision fields `biorxiv_get_preprint` returns — including `type`, `license`, `funder`, and `authorCorrespondingInstitution` - Enrichment failures degrade gracefully to EuropePMC-only metadata, surfaced via `partial_results` and a per-record `enrichment_error` (`service_error`, `rate_limited`, or `not_found`) - A EuropePMC rate limit (HTTP 429) raises a retryable `rate_limited` error carrying the origin's `Retry-After` wait — the search is the primary call and has no metadata to fall back on, unlike the enrichment step --- ### `biorxiv_get_published_version` Resolve a preprint DOI to its journal publication crosswalk. - Uses the `/pubs/{server}/{doi}` endpoint for richer metadata than the `publishedJournalDoi` field in `biorxiv_get_preprint` - Returns journal DOI, journal name, published date, and corresponding author institution - Use when the preprint's `publishedJournalDoi` field is present and you need the full crosswalk record - Scope to `biorxiv`, `medrxiv`, or `both`; `both` is the default because the two servers share the `10.1101/` DOI prefix, and the output `server` field names the one that answered - No server answering raises a retryable `upstream_unavailable`, or `rate_limited` with the origin's wait when the failure was an HTTP 429 — never `doi_not_found`, which would assert an absence nothing established --- ### `biorxiv_get_fulltext` Retrieve a preprint's full text as best-effort Markdown. - Fetches the rendered HTML article page (`www.{server}.org/content/{doi}v{N}.full`) and extracts Markdown — there is no keyless JATS source - Resolves the latest version via the details API first, for the URL version and clean not-found handling - Scope to `biorxiv`, `medrxiv`, or `both`; `both` is the default because the two servers share the `10.1101/` DOI prefix. Only the DOI resolution fans out — the full-text fetch targets the single server that answered, named in the output `server` field - Long articles page via `offset`/`limit` character chunking (`totalChars`, `remainingChars`, `hasMore`); the extracted article is cached per version, so paging costs one origin fetch rather than one per chunk - PDF-only preprints and blocked/challenge pages return a typed `fulltext_unavailable` error routing to `biorxiv_get_preprint` - An origin rate limit (HTTP 429) returns a retryable `rate_limited` error carrying the origin's `Retry-After` wait, rather than a bare fetch failure. Both origins this tool touches can hit it — the article page during the full-text fetch, `api.biorxiv.org` during version resolution — and the recovery hint names which of them are limiting, since `biorxiv_get_preprint` is only a useful fallback while the metadata origin is answering --- ### `biorxiv_list_categories` Return the static subject category taxonomy for both servers. - No API call — hardcoded static list (~30 bioRxiv + ~50 medRxiv categories) - Use to validate category strings before passing to `biorxiv_list_recent` ## Features Built on [`@cyanheads/mcp-ts-core`](https://www.npmjs.com/package/@cyanheads/mcp-ts-core): - Declarative tool definitions — single file per tool, framework handles registration and validation - Unified error handling across all tools - Pluggable auth (`none`, `jwt`, `oauth`) - Swappable storage backends: `in-memory`, `filesystem`, `Supabase`, `Cloudflare KV/R2/D1` - Structured logging with optional OpenTelemetry tracing - STDIO and Streamable HTTP transports bioRxiv-specific: - `BiorxivApiService` wraps `api.biorxiv.org` — details, publications, and crosswalk endpoints with retry and exponential backoff. An origin rate limit (HTTP 429) is classified as a retryable `rate_limited` error carrying the parsed `Retry-After` wait; the upstream response body never reaches the error payload - `EuropePmcService` wraps the EuropePMC search endpoint for relevance-ranked keyword and/or author results. An origin rate limit (HTTP 429) is classified the same way as the JSON API's — a retryable `rate_limited` error carrying the parsed `Retry-After` wait, with the upstream response body kept out of the error payload - `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 - Two-server fan-out via `Promise.allSettled` — both `biorxiv` and `medrxiv` queried in parallel when `server="both"`, results merged and deduplicated by DOI - Polite `User-Agent` header including a mailto address (`BIORXIV_MAILTO` env var) per Cold Spring Harbor Lab API guidelines - Pairs with **pubmed-mcp-server** (post-publication), **openalex-mcp-server** (citation analytics), and **crossref-mcp-server** (DOI metadata) ## Getting started Add the following to your MCP client configuration file. ```json { "mcpServers": { "biorxiv-mcp-server": { "type": "stdio", "command": "bunx", "args": ["@cyanheads/biorxiv-mcp-server@latest"], "env": { "MCP_TRANSPORT_TYPE": "stdio", "MCP_LOG_LEVEL": "info", "BIORXIV_MAILTO": "your@email.com" } } } } ``` Or with npx (no Bun required): ```json { "mcpServers": { "biorxiv-mcp-server": { "type": "stdio", "command": "npx", "args": ["-y", "@cyanheads/biorxiv-mcp-server@latest"], "env": { "MCP_TRANSPORT_TYPE": "stdio", "MCP_LOG_LEVEL": "info", "BIORXIV_MAILTO": "your@email.com" } } } } ``` Or with Docker: ```json { "mcpServers": { "biorxiv-mcp-server": { "type": "stdio", "command": "docker", "args": ["run", "-i", "--rm", "-e", "MCP_TRANSPORT_TYPE=stdio", "-e", "BIORXIV_MAILTO=your@email.com", "ghcr.io/cyanheads/biorxiv-mcp-server:latest"] } } } ``` For Streamable HTTP, set the transport and start the server: ```sh MCP_TRANSPORT_TYPE=http MCP_HTTP_PORT=3010 BIORXIV_MAILTO=your@email.com bun run start:http # Server listens at http://localhost:3010/mcp ``` ### Prerequisites - [Bun v1.3.0](https://bun.sh/) or higher (or Node.js v24+). ### Installation 1. **Clone the repository:** ```sh git clone https://github.com/cyanheads/biorxiv-mcp-server.git ``` 2. **Navigate into the directory:** ```sh cd biorxiv-mcp-server ``` 3. **Install dependencies:** ```sh bun install ``` 4. **Configure environment:** ```sh cp .env.example .env # optionally set BIORXIV_MAILTO for polite API access ``` ## Configuration All configuration is validated at startup via Zod schemas in `src/config/server-config.ts`. | Variable | Description | Default | |:---|:---|:---| | `BIORXIV_MAILTO` | Email address included in the `User-Agent` header for polite API access per Cold Spring Harbor Lab guidelines. Optional, but recommended. | — | | `BIORXIV_API_BASE_URL` | Override the bioRxiv API base URL. | `https://api.biorxiv.org` | | `EUROPEPMC_API_BASE_URL` | Override the EuropePMC base URL. | `https://www.ebi.ac.uk/europepmc/webservices/rest` | | `BIORXIV_WEB_BASE_URL` | Override the bioRxiv website base URL (full-text HTML source for `biorxiv_get_fulltext`). | `https://www.biorxiv.org` | | `MEDRXIV_WEB_BASE_URL` | Override the medRxiv website base URL (full-text HTML source for `biorxiv_get_fulltext`). | `https://www.medrxiv.org` | | `MCP_TRANSPORT_TYPE` | Transport: `stdio` or `http`. | `stdio` | | `MCP_HTTP_PORT` | HTTP server port. | `3010` | | `MCP_HTTP_ENDPOINT_PATH` | HTTP endpoint path. | `/mcp` | | `MCP_AUTH_MODE` | Auth mode: `none`, `jwt`, or `oauth`. | `none` | | `MCP_LOG_LEVEL` | Log level (`debug`, `info`, `warning`, `error`, etc.). | `info` | | `LOGS_DIR` | Directory for log files (Node.js only). | `/logs` | | `OTEL_ENABLED` | Enable OpenTelemetry instrumentation. | `false` | ## Running the server ### Local development - **Build and run:** ```sh # One-time build bun run rebuild # Run the built server bun run start:stdio # or bun run start:http ``` - **Run checks and tests:** ```sh bun run devcheck # Lint, format, typecheck, security bun run test # Vitest test suite bun run lint:mcp # Validate MCP definitions against spec ``` ### Docker ```sh docker build -t biorxiv-mcp-server . docker run --rm -e BIORXIV_MAILTO=your@email.com -p 3010:3010 biorxiv-mcp-server ``` The 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. ## Project structure | Directory | Purpose | |:---|:---| | `src/index.ts` | `createApp()` entry point — registers tools and initializes services. | | `src/config` | Server-specific environment variable parsing and validation with Zod. | | `src/mcp-server/tools` | Tool definitions (`*.tool.ts`). Six tools across bioRxiv and medRxiv. | | `src/services/biorxiv` | `BiorxivApiService` — details, publications, and crosswalk endpoint wrappers with retry. | | `src/services/biorxiv-fulltext` | `BiorxivFullTextService` — rendered HTML article page fetch and Markdown extraction. | | `src/services/europe-pmc` | `EuropePmcService` — preprint keyword/author search endpoint wrapper. | | `tests/` | Unit and integration tests mirroring the `src/` structure. | ## Development guide See [`CLAUDE.md`](https://github.com/cyanheads/biorxiv-mcp-server/blob/HEAD/CLAUDE.md) for development guidelines and architectural rules. The short version: - Handlers throw, framework catches — no `try/catch` in tool logic - Use `ctx.log` for request-scoped logging, `ctx.state` for tenant-scoped storage - Register new tools via the barrel in `src/mcp-server/tools/definitions/index.ts` - Wrap external API calls: validate raw → normalize to domain type → return output schema; never fabricate missing fields ## Contributing Issues and pull requests are welcome. Run checks and tests before submitting: ```sh bun run devcheck bun run test ``` ## License Apache-2.0 — see [LICENSE](https://github.com/cyanheads/biorxiv-mcp-server/blob/HEAD/LICENSE) for details.