BioMCP
by genomoncology
BioMCP is an open-source toolkit for biomedical research AI assistants and agents, built following the Model Context Protocol (MCP). It supports searching and retrieving clinical trials, PubMed articles, and genomic variants.
Last updated: N/A
What is BioMCP?
BioMCP is an open-source toolkit designed to facilitate biomedical research by providing AI assistants and agents with access to relevant data sources like PubMed, ClinicalTrials.gov, and MyVariant.info.
How to use BioMCP?
BioMCP can be installed via pip or uv using the package name biomcp-python. It can be used through a command-line interface (CLI) or integrated with Claude Desktop. The CLI allows users to search and retrieve information from various biomedical databases. For Claude Desktop, it can be configured as an MCP server.
Key features of BioMCP
PubMed article search and full-text retrieval
Clinical trial advanced search (ClinicalTrials.gov)
Genomic variant search and annotation (MyVariant.info)
Command-line interface for direct database interaction
Integration with Claude Desktop via MCP
Access to curated knowledge base (OncoMCP commercial version)
Use cases of BioMCP
Assisting researchers in finding relevant publications
Identifying suitable clinical trials for patients
Annotating genomic variants for clinical interpretation
Integrating biomedical knowledge into AI-powered tools
Building AI assistants for biomedical research
Facilitating precision oncology workflows (OncoMCP commercial version)
FAQ from BioMCP
What is the license for BioMCP?
What is the license for BioMCP?
BioMCP is licensed under the MIT License.
How do I install BioMCP?
How do I install BioMCP?
BioMCP can be installed using pip or uv with the package name biomcp-python.
Can I use BioMCP commercially?
Can I use BioMCP commercially?
Yes, but users must comply with the terms of service for each data source integrated by BioMCP.
Does BioMCP handle PHI or PII?
Does BioMCP handle PHI or PII?
No, BioMCP does not handle or provide access to protected health information (PHI) or personally identifiable information (PII).
What databases does BioMCP integrate?
What databases does BioMCP integrate?
BioMCP integrates data from PubTator3/PubMed, ClinicalTrials.gov, and MyVariant.info.