longevity-genie/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