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[]

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 } })

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)
• Enrichment failures degrade gracefully to EuropePMC-only metadata, surfaced via partial_results

biorxiv_get_published_version

Resolve a preprint DOI to its journal publication crosswalk.

• Uses the /pubs/{server}/{doi} endpoint for richer metadata than the published field in biorxiv_get_preprint
• Returns journal DOI, journal name, published date, and corresponding author institution
• Use when the preprint's published field is non-null and you need the full crosswalk record

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
• Long articles page via offset/limit character chunking (totalChars, remainingChars, hasMore)
• PDF-only preprints and blocked/challenge pages return a typed fulltext_unavailable error routing to biorxiv_get_preprint

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
• EuropePmcService wraps the EuropePMC search endpoint for relevance-ranked keyword and/or author results
• 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": "[email protected]"
      }
    }
  }
}

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": "[email protected]"
      }
    }
  }
}

Or with Docker:

{
  "mcpServers": {
    "biorxiv-mcp-server": {
      "type": "stdio",
      "command": "docker",
      "args": ["run", "-i", "--rm", "-e", "MCP_TRANSPORT_TYPE=stdio", "-e", "[email protected]", "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 [email protected] bun run start:http
# Server listens at http://localhost:3010/mcp

Prerequisites

• Bun v1.3.2 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 [email protected] -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.