biomcp

# BioMCP: Biomedical Model Context Protocol [](https://smithery.ai/server/@genomoncology/biomcp) BioMCP provides LLMs with structured access to critical biomedical databases through the Model Context Protocol (MCP). ## Tools - PubTator3 (PubMed/PMC) - Article Search - Full Text - ClinicalTrials.gov - Clinical Trial Advanced Search - Protocols - Outcomes - Locations - Reference - MyVariant.info - Variant Search - Annotations (CIViC, ClinVar, COSMIC, dbSNP, etc.) ## Installation ### Installing via Smithery To install biomcp for Claude Desktop automatically via [Smithery](https://smithery.ai/server/@genomoncology/biomcp): ```bash npx -y @smithery/cli install @genomoncology/biomcp --client claude ``` To install the BioMCP package to use it as a Python package or Command Line Interface (CLI), run the following command: ```bash pip install biomcp-python ``` Or preferably: ```bash uv pip install biomcp-python ``` Or just run it: ```bash uvx --from biomcp-python biomcp trial search --condition "lung cancer" --intervention "pembro" ``` To install it as a MCP Server to Claude Desktop or similar "MCP Clients", try something like: ```json { "globalShortcut": "", "mcpServers": { "biomcp": { "command": "uv", "args": ["run", "--from", "biomcp-python", "biomcp", "run"] } } } ``` Note: If you get a `SPAWN ENOENT` warning, make sure your `uv` executable is in your PATH or provide a full path to it (e.g. /Users/name/.local/bin/uv). For comprehensive instructions on integrating BioMCP with Claude Desktop and other MCP clients, see the [MCP Integration Guide](docs/mcp_integration.md). To test the MCP Server, using the MCP Inspector, run the following command: ```bash npx @modelcontextprotocol/inspector uv run biomcp run ``` ## Command Line Interface BioMCP provides a comprehensive CLI for direct interaction with biomedical databases: ```bash # Get help biomcp --help # Run the MCP server biomcp run # Search for articles biomcp article search --gene BRAF --disease Melanoma # Get article details by PMID biomcp article get 21717063 --full # Search for clinical trials biomcp trial search --condition "Lung Cancer" --phase Phase_3 # Get trial details by NCT ID biomcp trial get NCT04280705 Protocol # Search for variants biomcp variant search --gene BRAF --significance Pathogenic # Get variant details biomcp variant get rs113488022 ``` ## Commercial Version: OncoMCP OncoMCP extends BioMCP with GenomOncology's enterprise-grade precision oncology platform (POP), providing healthcare organizations with: - On-premise deployment with full HIPAA compliance - Real-time clinical trial recruiting status and arm-level matching - Seamless EHR and clinical data warehouse integration - Curated knowledge base of 15,000+ clinical trials and FDA approvals - Patient-trial matching using integrated clinical and molecular profiles - Advanced NLP for structured data extraction and normalization - Comprehensive biomarker and mutation rule processing Find out more about GenomOncology and OncoMCP by visiting: [GenomOncology](https://genomoncology.com/). ## License This project is licensed under the MIT License. ## Sources Below are the sources leveraged in BioMCP and their individual Terms of Service. Please recognize that each of these services may aggregate from multiple underlying sources that may have their own Terms of Service. - MyVariant.info * [Terms of Service](https://myvariant.info/terms) * [Annotation Source](https://docs.myvariant.info/en/latest/doc/data.html)