BioMCP: Biomedical Model Context Protocol
BioMCP is an open source (MIT License) toolkit that empowers AI assistants and
agents with specialized biomedical knowledge. Built following the Model Context
Protocol (MCP), it connects AI systems to authoritative biomedical data
sources, enabling them to answer questions about clinical trials, scientific
literature, and genomic variants with precision and depth.
Why BioMCP?
While Large Language Models have broad general knowledge, they often lack
specialized domain-specific information or access to up-to-date resources.
BioMCP bridges this gap for biomedicine by:
- Providing structured access to clinical trials, biomedical literature, and genomic variants
- Enabling natural language queries to specialized databases without requiring knowledge of their specific syntax
- Supporting biomedical research workflows through a consistent interface
- Functioning as an MCP server for AI assistants and agents
Biomedical Data Sources
BioMCP integrates with three key biomedical data sources:
- PubTator3/PubMed - Biomedical literature with entity annotations
- ClinicalTrials.gov - Clinical trial registry and results database
- MyVariant.info - Consolidated genetic variant annotation from multiple databases
Available MCP Tools
PubMed & PubTator3
article_searcher: Search for articles by genes, diseases, variants, or keywords
article_details: Get detailed article information including abstracts and full text
ClinicalTrials.gov
trial_searcher: Advanced trial search with filtering by condition, intervention, phase, etc.
trial_protocol: Detailed trial protocol information
trial_locations: Trial site locations and contact information
trial_outcomes: Results and outcome measures
trial_references: Related publications
MyVariant.info
variant_searcher: Search for genetic variants with sophisticated filtering
variant_details: Comprehensive annotations from multiple sources (CIViC, ClinVar, COSMIC, dbSNP, etc.)
Quick Start
For Claude Desktop Users
- Install `uv` if you don't have it (recommended):
- Configure Claude Desktop:
Python Package Installation
Command Line Interface
BioMCP provides a comprehensive CLI for direct database interaction:
Testing & Verification
Test your BioMCP setup with the MCP Inspector:
This opens a web interface where you can explore and test all available tools.
Enterprise Version: OncoMCP
OncoMCP extends BioMCP with GenomOncology's enterprise-grade precision oncology
platform (POP), providing:
- HIPAA-Compliant Deployment: Secure on-premise options
- Real-Time Trial Matching: Up-to-date status and arm-level matching
- Healthcare Integration: Seamless EHR and data warehouse connectivity
- Curated Knowledge Base: 15,000+ trials and FDA approvals
- Sophisticated Patient Matching: Using integrated clinical and molecular profiles
- Advanced NLP: Structured extraction from unstructured text
- Comprehensive Biomarker Processing: Mutation and rule processing
Learn more: GenomOncology
MCP Registries
Documentation
For comprehensive documentation, visit https://biomcp.org
BioMCP Examples Repo
Looking to see BioMCP in action?
Check out the companion repository:
[biomcp-examples](https://github.com/genomoncology/biomcp-examples)
It contains real prompts, AI-generated research briefs, and evaluation runs across different models.
Use it to explore capabilities, compare outputs, or benchmark your own setup.
Have a cool example of your own?
We d love for you to contribute! Just fork the repo and submit a PR with your experiment.
License
This project is licensed under the MIT License.
BioMCP: Biomedical Model Context Protocol
BioMCP is an open source (MIT License) toolkit that empowers AI assistants and
agents with specialized biomedical knowledge. Built following the Model Context
Protocol (MCP), it connects AI systems to authoritative biomedical data
sources, enabling them to answer questions about clinical trials, scientific
literature, and genomic variants with precision and depth.
Why BioMCP?
While Large Language Models have broad general knowledge, they often lack
specialized domain-specific information or access to up-to-date resources.
BioMCP bridges this gap for biomedicine by:
- Providing structured access to clinical trials, biomedical literature, and genomic variants
- Enabling natural language queries to specialized databases without requiring knowledge of their specific syntax
- Supporting biomedical research workflows through a consistent interface
- Functioning as an MCP server for AI assistants and agents
Biomedical Data Sources
BioMCP integrates with three key biomedical data sources:
- PubTator3/PubMed - Biomedical literature with entity annotations
- ClinicalTrials.gov - Clinical trial registry and results database
- MyVariant.info - Consolidated genetic variant annotation from multiple databases
Available MCP Tools
PubMed & PubTator3
article_searcher: Search for articles by genes, diseases, variants, or keywords
article_details: Get detailed article information including abstracts and full text
ClinicalTrials.gov
trial_searcher: Advanced trial search with filtering by condition, intervention, phase, etc.
trial_protocol: Detailed trial protocol information
trial_locations: Trial site locations and contact information
trial_outcomes: Results and outcome measures
trial_references: Related publications
MyVariant.info
variant_searcher: Search for genetic variants with sophisticated filtering
variant_details: Comprehensive annotations from multiple sources (CIViC, ClinVar, COSMIC, dbSNP, etc.)
Quick Start
For Claude Desktop Users
- Install `uv` if you don't have it (recommended):
- Configure Claude Desktop:
Python Package Installation
Command Line Interface
BioMCP provides a comprehensive CLI for direct database interaction:
Testing & Verification
Test your BioMCP setup with the MCP Inspector:
This opens a web interface where you can explore and test all available tools.
Enterprise Version: OncoMCP
OncoMCP extends BioMCP with GenomOncology's enterprise-grade precision oncology
platform (POP), providing:
- HIPAA-Compliant Deployment: Secure on-premise options
- Real-Time Trial Matching: Up-to-date status and arm-level matching
- Healthcare Integration: Seamless EHR and data warehouse connectivity
- Curated Knowledge Base: 15,000+ trials and FDA approvals
- Sophisticated Patient Matching: Using integrated clinical and molecular profiles
- Advanced NLP: Structured extraction from unstructured text
- Comprehensive Biomarker Processing: Mutation and rule processing
Learn more: GenomOncology
MCP Registries
Documentation
For comprehensive documentation, visit https://biomcp.org
BioMCP Examples Repo
Looking to see BioMCP in action?
Check out the companion repository:
[biomcp-examples](https://github.com/genomoncology/biomcp-examples)
It contains real prompts, AI-generated research briefs, and evaluation runs across different models.
Use it to explore capabilities, compare outputs, or benchmark your own setup.
Have a cool example of your own?
We d love for you to contribute! Just fork the repo and submit a PR with your experiment.
License
This project is licensed under the MIT License.