biothings-mcp

MCP (Model Context Protocol) server for Biothings.io

This server implements the Model Context Protocol (MCP) for BioThings, providing a standardized interface for accessing and manipulating biomedical data. MCP enables AI assistants and agents to access specialized biomedical knowledge through structured interfaces to authoritative data sources. Supported BioThings data sources include:

mygene.info — Gene annotation and query service
myvariant.info — Variant annotation and query service
mychem.info — Chemical compound annotation and query service

About MCP (Model Context Protocol)

MCP is a protocol that bridges the gap between AI systems and specialized domain knowledge. It enables:

Structured Access: Direct connection to authoritative biomedical data sources
Natural Language Queries: Simplified interaction with specialized databases
Type Safety: Strong typing and validation through biothings-typed-client
AI Integration: Seamless integration with AI assistants and agents

Available API Interfaces

This server provides dedicated API interfaces for different BioThings data types, leveraging the biothings-typed-client library. These interfaces are implemented using the following mixins:

Gene Interface: GeneRoutesMixin (wraps GeneClientAsync)
Variant Interface: VariantsRoutesMixin (wraps VariantClientAsync)
Chemical Interface: ChemRoutesMixin (wraps ChemClientAsync)
Taxon Interface: TaxonRoutesMixin (wraps TaxonClientAsync)

Quick Start

Installing uv

# Download and install uv
curl -LsSf https://astral.sh/uv/install.sh | sh

# Verify installation
uv --version

Setup

# Clone the repository
git clone git@github.com:longevity-genie/biothings-mcp.git
cd biothings-mcp
uv sync

Running the MCP Server

# Start the MCP server locally
uv run server

Docker Deployment

The easiest way to run the MCP server is using Docker. The project provides a pre-built Docker image available on GitHub Container Registry.

Using Docker Compose (recommended):

# Clone the repository
git clone git@github.com:longevity-genie/biothings-mcp.git
cd biothings-mcp

# Start the services
docker-compose up

This will start:

The MCP server on port 3001
The MCP Inspector on port 6277

Using Docker directly:

# Pull the latest image
docker pull ghcr.io/longevity-genie/biothings-mcp:latest

# Run the container
docker run -p 3001:3001 -e MCP_PORT=3001 ghcr.io/longevity-genie/biothings-mcp:latest

The MCP server will be available at http://localhost:3001/mcp (with docs at http://localhost:3001/docs).

A publicly hosted version of this server is also available at https://biothings.longevity-genie.info/mcp (with docs at https://biothings.longevity-genie.info/docs)

Integration with AI Systems

To integrate this server with your MCP-compatible AI client, you can use one of the preconfigured JSON files provided in this repository:

For connecting to a locally running server: Use mcp-config.json. Ensure the server is running first, either via uv run server (see Running the MCP Server) or docker-compose up (see Docker Deployment).
For connecting to the publicly hosted server: Use mcp-config-remote.json. This connects to https://biothings.longevity-genie.info/mcp and doesn't require you to run anything locally.

Simply point your AI client (like Cursor, Windserve, ClaudeDesktop, VS Code with Copilot, or others) to use the appropriate configuration file.

Here's an example of how the tools might appear in an MCP client like Cursor after configuration:

Cursor Usage Example

KNOWN ISSUES

The library is alpha-quality. The major problem right now is that LLM-s are often stupid and do not know how to put valid gene and gene variant symbols. We plan to mitigrate it by extending comments and providing additional method for entetity resolution.

Testing & Verification

Run tests for the API endpoint:

uv run pytest -vvv -s

Test your MCP setup with the MCP Inspector:

npx @modelcontextprotocol/inspector --config mcp-config.json --server biothings-mcp

Note: Using the MCP Inspector is optional. Most MCP clients (like Cursor, Windsurv, etc.) will automatically display the available tools from this server once configured. However, the Inspector can be useful for detailed testing and exploration.

If you choose to use the Inspector via npx, ensure you have Node.js and npm installed. Using nvm (Node Version Manager) is recommended for managing Node.js versions.

This opens a web interface where you can explore and test all available tools.

Documentation

For detailed documentation about the MCP protocol and its implementation, refer to:

MCP Protocol Documentation
biothings-typed-client Documentation
FastAPI-MCP Documentation

License

This project is licensed under the MIT License.

Acknowledgments

BioThings for the REST API and original client library
MCP Protocol for the protocol specification
Pydantic for the data validation framework
FastAPI-MCP for the MCP server implementation
This project is part of the Longevity Genie organization, which develops open-source AI assistants and libraries for health, genetics, and longevity research.

We are supported by:

HEALES - Healthy Life Extension Society

and

IBIMA - Institute for Biostatistics and Informatics in Medicine and Ageing Research

Categories

Current Category: biothings

biothings-mcp