mcp-registry/biomcp

    ==================
      
       /// MCP ///
      /// BIO ///
        
    ==================
        
    [server:online]
    [protocol:ready]

biomcp

by genomoncology

BioMCP: Biomedical Model Context Protocol – an MCP server that exposes biomedical search/fetch tools for literature, clinical trials and genomic variants.

230
32
Open Source
GitHubWebsiteDocumentation

Installation

1. Prerequisites
• Python >= 3.9
• Git (to clone the repository)
• Optional: NCBI and/or OpenAI keys for extended retrieval/LLM functions
2. Clone the repo
git clone https://github.com/genomoncology/biomcp.git cd biomcp
3. Create and activate a virtual environment (recommended)
python -m venv .venv source .venv/bin/activate
4. Install BioMCP and its dependencies
pip install -e . # or: pip install biomcp if published on PyPI
5. (Optional) Set environment variables for external services
export BIOMCP_OPENAI_API_KEY="<your-openai-key>" export BIOMCP_NCBI_API_KEY="<your-ncbi-key>" # increases PubMed rate-limits
6. Launch the MCP server locally
uvicorn biomcp.server:app --host 0.0.0.0 --port 8000
7. Verify
Navigate to http://localhost:8000/health or open the auto-generated Swagger UI at http://localhost:8000/docs to confirm the server is running.
8. Production deployment
• Behind a reverse proxy (nginx, Traefik, etc.)
• Set `--workers` equal to CPU cores, e.g. `uvicorn biomcp.server:app --workers 4`
• Configure HTTPS/TLS at the proxy layer.

Documentation

License: MIT License
Updated 7/30/2025

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