Biorxiv Mcp Server

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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

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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

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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

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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

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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

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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:

• 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.

{
  "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):

{
  "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:

{
  "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:

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 or higher (or Node.js v24+).

Installation

1. Clone the repository:

git clone https://github.com/cyanheads/biorxiv-mcp-server.git

2. Navigate into the directory:

cd biorxiv-mcp-server

3. Install dependencies:

bun install

4. Configure environment:

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).	<project-root>/logs
OTEL_ENABLED	Enable OpenTelemetry instrumentation.	false

Running the server

Local development

• Build and run:

  # One-time build
  bun run rebuild
  
  # Run the built server
  bun run start:stdio
  # or
  bun run start:http
  

• Run checks and tests:

  bun run devcheck   # Lint, format, typecheck, security
  bun run test       # Vitest test suite
  bun run lint:mcp   # Validate MCP definitions against spec
  

Docker

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 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:

bun run devcheck
bun run test

License

Apache-2.0 — see LICENSE for details.