Unofficial bioRxiv MCP Server

Model Context Protocol (MCP) server for accessing bioRxiv and medRxiv preprint servers (Cold Spring Harbor Laboratory). Provides access to 260,000+ preprints across 27 biological and 51 medical science categories.

Features

• Single unified tool (biorxiv_info) with 7 methods
• No API key required — uses the public bioRxiv API
• Keyword search with client-side filtering over date-range browsing
• Full preprint metadata retrieval by DOI (all versions)
• Published preprint tracking (preprint → journal mapping)
• Funder search by ROR ID (NIH, NSF, Wellcome, etc.)
• Content and usage statistics (submissions, views, downloads)
• Subject category listings for both bioRxiv and medRxiv

Installation

cd biorxiv-mcp-server
npm install
npm run build

Usage

{
  "mcpServers": {
    "biorxiv-mcp-server": {
      "command": "node",
      "args": ["/path/to/biorxiv-mcp-server/build/index.js"]
    }
  }
}

Tool: biorxiv_info

Single unified tool with multiple methods accessed via the method parameter.

Methods

1. search_preprints

Search preprints by keywords. Uses client-side filtering over the bioRxiv date-range API (no native keyword search endpoint). Scans up to 300 results across the date range.

{
  "method": "search_preprints",
  "query": "CRISPR gene editing",
  "server": "biorxiv",
  "date_from": "2025-01-01",
  "date_to": "2025-12-31",
  "category": "genetics",
  "limit": 30
}

Returns: doi, title, authors, abstract (500 chars), date, category, version, published status.

2. get_preprint_details

Get complete metadata for a specific preprint by DOI, including all versions.

{
  "method": "get_preprint_details",
  "doi": "10.1101/2024.01.15.575123",
  "server": "biorxiv"
}

Returns: all versions with doi, title, authors, full abstract, date, category, license, published status.

3. get_categories

List all available subject categories for bioRxiv (27) and medRxiv (51).

{
  "method": "get_categories"
}

4. search_published_preprints

Find preprints that have been formally published in peer-reviewed journals.

{
  "method": "search_published_preprints",
  "date_from": "2025-01-01",
  "publisher": "10.1038",
  "server": "biorxiv",
  "limit": 30
}

Common publisher DOI prefixes: 10.1038 (Nature), 10.1126 (Science), 10.1016 (Elsevier), 10.1371 (PLOS), 10.7554 (eLife), 10.1073 (PNAS).

5. search_by_funder

Find preprints by funding organization using ROR IDs. Data available from 2025-04-10 onwards.

{
  "method": "search_by_funder",
  "funder_ror_id": "021nxhr62",
  "server": "biorxiv",
  "limit": 30
}

Common ROR IDs: 021nxhr62 (NIH), 01cwqze88 (NSF), 02mhbdp94 (European Commission), 029chgv08 (Wellcome Trust), 05a28rw58 (HHMI), 006wxqw41 (MRC).

6. get_content_statistics

Get submission statistics (new papers, revisions, authors).

{
  "method": "get_content_statistics",
  "interval": "m"
}

Interval: "m" (monthly) or "y" (yearly).

7. get_usage_statistics

Get engagement statistics (views, downloads).

{
  "method": "get_usage_statistics",
  "interval": "m",
  "server": "biorxiv"
}

Example Queries with Claude

Once configured, you can ask Claude:

• "Search bioRxiv for recent CRISPR preprints"
• "Get details for preprint DOI 10.1101/2024.01.15.575123"
• "What bioRxiv categories are available?"
• "Find preprints published in Nature this month"
• "Show NIH-funded preprints in cancer biology"
• "What are the monthly submission statistics for bioRxiv?"
• "Search medRxiv for COVID-19 vaccine preprints"

Important Notes

• Preprints are NOT peer-reviewed — results should not be cited as established fact
• Keyword search is client-side (bioRxiv API only supports date-range browsing), so narrow date ranges improve relevance
• DOI format: 10.1101/YYYY.MM.DD.NNNNNN (bioRxiv prefix is always 10.1101)
• Funder data only available from April 10, 2025 onwards

Data Source

• Database: bioRxiv / medRxiv (Cold Spring Harbor Laboratory)
• Preprints: 260,000+ across biology and medicine
• Categories: 27 bioRxiv + 51 medRxiv subject areas
• API: https://api.biorxiv.org/
• Rate limits: No published limits, respectful usage encouraged

License

MIT