BioMCP is an open-source toolkit designed to equip AI assistants and agents with specialized biomedical knowledge, enabling precise answers on clinical trials, literature, and genomic variants. It acts as an MCP server, connecting AI systems to authoritative data sources like PubTator, ClinicalTrials.gov, and various BioThings APIs, bridging the gap left by general-purpose LLMs.

How It Works

BioMCP implements the Model Context Protocol (MCP) to provide structured access to diverse biomedical data. It offers a unified query language and domain-specific search capabilities across literature, clinical trials, and genomic variants. A core "Think Tool" facilitates systematic problem decomposition and multi-step research planning, enhancing AI reasoning. The system supports both direct tool access and a comprehensive CLI for database interaction.

Quick Start & Requirements

• Installation: pip install biomcp-python or uv pip install biomcp-python.
• Local Execution: uv run --with biomcp-python biomcp run (STDIO mode).
• HTTP Server: biomcp run --mode streamable_http (recommended).
• Dependencies: Python, uv (recommended). Optional environment variables for cBioPortal API token.
• Docs: https://biomcp.org
• Examples: biomcp-examples

Highlighted Details

• MCPHub Certified for best practices in Model Context Protocol implementation.
• Integrates with over 20 biomedical data sources including PubTator, ClinicalTrials.gov, FDA data, and the BioThings Suite (MyVariant, MyGene, MyDisease, MyChem).
• Offers 24 specialized tools, including core "Think," "Search," and "Fetch" tools, plus individual domain-specific tools for articles, trials, variants, NCI data, genes, diseases, and drugs.
• Supports advanced search features like field-specific queries, wildcard patterns, and automatic synonym expansion for diseases.
• Includes direct integration with cBioPortal for gene-level mutation frequency and study-level occurrence data.

Maintenance & Community

• Developed by GenomOncology.
• Enterprise version "OncoMCP" offers HIPAA-compliant deployment, real-time trial matching, and healthcare integration.

Licensing & Compatibility

• Licensed under the MIT License, permitting commercial use and closed-source linking.

Limitations & Caveats

• Integration tests make live API calls and may be affected by network issues or rate limiting.
• NCI-specific tools and some advanced features may require an NCI API key.