Opengenes

opengenes-mcp

MCP (Model Context Protocol) server for OpenGenes database

This server implements the Model Context Protocol (MCP) for OpenGenes, providing a standardized interface for accessing aging and longevity research data. MCP enables AI assistants and agents to query comprehensive biomedical datasets through structured interfaces.

The server automatically downloads the latest OpenGenes database and documentation from Hugging Face Hub (specifically from the opengenes folder), ensuring you always have access to the most up-to-date data without manual file management.

The OpenGenes database contains:

• lifespan_change: Experimental data about genetic interventions and their effects on lifespan across model organisms
• gene_criteria: Criteria classifications for aging-related genes (12 different categories)
• gene_hallmarks: Hallmarks of aging associated with specific genes
• longevity_associations: Genetic variants associated with longevity from population studies

If you want to understand more about what the Model Context Protocol is and how to use it more efficiently, you can take the DeepLearning AI Course or search for MCP videos on YouTube.

🏆 Part of Holy Bio MCP Framework

This MCP server is part of the Holy Bio MCP project - a unified framework for bioinformatics research that won the Bio x AI Hackathon 2025 and continues to be actively developed and extended after the victory.

The Holy Bio MCP framework brings together multiple specialized MCP servers into a cohesive ecosystem for advanced biological research:

• gget-mcp - Genomics & sequence analysis toolkit
• opengenes-mcp - Aging & longevity genetics (this server)
• synergy-age-mcp - Synergistic genetic interactions in longevity
• biothings-mcp - Foundational biological data from BioThings.io
• pharmacology-mcp - Drug, target & ligand data

Together, these servers provide 50+ specialized bioinformatics functions that can work seamlessly together in AI-driven research workflows. Learn more about the complete framework at github.com/longevity-genie/holy-bio-mcp.

Usage Example

Here's how the OpenGenes MCP server works in practice with AI assistants:

Example showing how to query the OpenGenes database through an AI assistant using natural language, which gets translated to SQL queries via the MCP server. You can use this database both in chat interfaces for research questions and in AI-based development tools (like Cursor, Windsurf, VS Code with Copilot) to significantly improve your bioinformatics productivity by having direct access to aging and longevity research data while coding.

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 aging and longevity research data
• Natural Language Queries: Simplified interaction with specialized databases through SQL
• Type Safety: Strong typing and validation through FastMCP
• AI Integration: Seamless integration with AI assistants and agents

Data Source and Updates

The OpenGenes MCP server automatically downloads data from the longevity-genie/bio-mcp-data repository on Hugging Face Hub. This ensures:

• Always Up-to-Date: Automatic access to the latest OpenGenes database without manual updates
• Reliable Distribution: Centralized data hosting with version control and change tracking
• Efficient Caching: Downloaded files are cached locally to minimize network requests
• Fallback Support: Local fallback files are supported for development and offline use

The data files are stored in the opengenes subfolder of the Hugging Face repository and include:

• open_genes.sqlite - The complete OpenGenes database
• prompt.txt - Database schema documentation and usage guidelines

Available Tools

This server provides three main tools for interacting with the OpenGenes database:

1. opengenes_db_query(sql: str) - Execute read-only SQL queries against the OpenGenes database
2. opengenes_get_schema_info() - Get detailed schema information including tables, columns, and enumerations
3. opengenes_example_queries() - Get a list of example SQL queries with descriptions

Available Resources

1. resource://db-prompt - Complete database schema documentation and usage guidelines
2. resource://schema-summary - Formatted summary of tables and their purposes

Quick Start

Installing uv

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

# Verify installation
uv --version
uvx --version

uvx is a very nice tool that can run a python package installing it if needed.

Running with uvx

You can run the opengenes-mcp server directly using uvx without cloning the repository:

# Run the server in streamed http mode (default)
uvx opengenes-mcp

STDIO Mode (for MCP clients that require stdio, can be useful when you want to save files)

# Or explicitly specify stdio mode
uvx opengenes-mcp stdio

HTTP Mode (Web Server)

# Run the server in streamable HTTP mode on default (3001) port
uvx opengenes-mcp server

# Run on a specific port
uvx opengenes-mcp server --port 8000

SSE Mode (Server-Sent Events)

# Run the server in SSE mode
uvx opengenes-mcp sse

In cases when there are problems with uvx often they can be caused by clenaing uv cache:

uv cache clean

The HTTP mode will start a web server that you can access at http://localhost:3001/mcp (with documentation at http://localhost:3001/docs). The STDIO mode is designed for MCP clients that communicate via standard input/output, while SSE mode uses Server-Sent Events for real-time communication.

Note: Currently, we do not have a Swagger/OpenAPI interface, so accessing the server directly in your browser will not show much useful information. To explore the available tools and capabilities, you should either use the MCP Inspector (see below) or connect through an MCP client to see the available tools.

Configuring your AI Client (Anthropic Claude Desktop, Cursor, Windsurf, etc.)

Quick Configuration Example

Here's what you can copy directly into your Claude Desktop or Cursor MCP configuration:

{
  "mcpServers": {
    "opengenes-mcp": {
      "command": "uvx",
      "args": ["opengenes-mcp"],
      "env": {
        "MCP_TRANSPORT": "stdio"
      }
    }
  }
}

Alternative: Using Preconfigured Files

We also provide preconfigured JSON files for different use cases:

• For STDIO mode (recommended): Use mcp-config-stdio.json
• For HTTP mode: Use mcp-config.json
• For local development: Use mcp-config-stdio-debug.json

Configuration Video Tutorial

For a visual guide on how to configure MCP servers with AI clients, check out our configuration tutorial video for our sister MCP server (biothings-mcp). The configuration principles are exactly the same for the OpenGenes MCP server - just use the appropriate JSON configuration files provided above.

Inspecting OpenGenes MCP server

If you want to inspect the methods provided by the MCP server, use npx (you may need to install nodejs and npm):

For STDIO mode with uvx:

npx @modelcontextprotocol/inspector --config mcp-config-stdio.json --server opengenes-mcp

For HTTP mode (ensure server is running first):

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

For local development:

npx @modelcontextprotocol/inspector --config mcp-config-stdio-debug.json --server opengenes-mcp

You can also run the inspector manually and configure it through the interface:

npx @modelcontextprotocol/inspector

After that you can explore the tools and resources with MCP Inspector at http://127.0.0.1:6274 (note, if you run inspector several times it can change port)

Integration with AI Systems

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

Repository setup

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

Running the MCP Server

If you already cloned the repo you can run the server with uv:

# Start the MCP server locally (HTTP mode)
uv run server

# Or start in STDIO mode  
uv run stdio

# Or start in SSE mode
uv run sse

Database Schema

Main Tables

• lifespan_change (47 columns): Experimental lifespan data with intervention details across model organisms
• gene_criteria (2 columns): Gene classifications by aging criteria (12 different categories)
• gene_hallmarks (2 columns): Hallmarks of aging mappings for genes
• longevity_associations (11 columns): Population genetics longevity data from human studies

Key Fields

• HGNC: Gene symbol (primary identifier across all tables)
• model_organism: Research organism (mouse, C. elegans, fly, etc.)
• effect_on_lifespan: Direction of lifespan change (increases/decreases/no change)
• intervention_method: Method of genetic intervention (knockout, overexpression, etc.)
• criteria: Aging-related gene classification (12 categories)
• hallmarks of aging: Biological aging processes associated with genes

Example Queries

-- Get top genes with most lifespan experiments
SELECT HGNC, COUNT(*) as experiment_count 
FROM lifespan_change 
WHERE HGNC IS NOT NULL 
GROUP BY HGNC 
ORDER BY experiment_count DESC 
LIMIT 10;

-- Find genes that increase lifespan in mice
SELECT DISTINCT HGNC, effect_on_lifespan 
FROM lifespan_change 
WHERE model_organism = 'mouse' 
AND effect_on_lifespan = 'increases lifespan' 
AND HGNC IS NOT NULL;

-- Get hallmarks of aging for genes
SELECT HGNC, "hallmarks of aging" 
FROM gene_hallmarks 
WHERE "hallmarks of aging" LIKE '%mitochondrial%';

-- Find longevity associations by ethnicity
SELECT HGNC, "polymorphism type", "nucleotide substitution", ethnicity 
FROM longevity_associations 
WHERE ethnicity LIKE '%Italian%';

-- Find genes with both lifespan effects and longevity associations
SELECT DISTINCT lc.HGNC 
FROM lifespan_change lc 
INNER JOIN longevi

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