Opengenes MCP

What longevity-genie/opengenes-mcp MCP server does

longevity-genie/opengenes-mcp MCP server provides an MCP interface to the OpenGenes database, a collection of aging and longevity research data. The database includes experimental lifespan effects of genetic interventions across model organisms, aging-related gene criteria, gene-to-hallmark associations, and population-study genetic variants linked with longevity.

The server is intended for research workflows where an AI assistant or agent needs structured access to these datasets. Queries are issued as read-only SQL rather than through a separate application-specific search syntax. The server also exposes schema guidance and example queries so a client can discover the available tables and construct suitable requests.

How it works

At startup or when data is needed, the application retrieves the OpenGenes files from the opengenes directory in the longevity-genie/bio-mcp-data repository on Hugging Face Hub. The relevant files include a SQLite database and documentation describing its schema and usage. Downloaded files are cached locally to reduce repeated network access, and local fallback files can be used for development or offline operation.

The MCP interface includes three tools:

• opengenes_db_query(sql: str) executes read-only SQL.
• opengenes_get_schema_info() returns table, column, and enumeration details.
• opengenes_example_queries() returns example SQL statements with descriptions.

Two resources provide additional context: resource://db-prompt contains database guidance, while resource://schema-summary summarizes the tables and their purposes.

Setup and configuration

longevity-genie/opengenes-mcp MCP server can be launched from PyPI with uvx, without cloning the repository. The explicit stdio command is uvx opengenes-mcp stdio. The project also documents streamable HTTP mode with uvx opengenes-mcp server, which uses port 3001 by default, and SSE mode with uvx opengenes-mcp sse. HTTP mode exposes the MCP endpoint at /mcp and documentation at /docs.

For MCP clients that use standard input and output, configure the command as uvx with opengenes-mcp and stdio arguments. The README also shows MCP_TRANSPORT=stdio in the environment configuration. Preconfigured JSON files are supplied for stdio, HTTP, and local debugging scenarios.

Tools and capabilities

The server supports structured database access for questions about aging genetics and longevity research. Clients can first request schema information or example queries, then submit a read-only SQL statement to retrieve relevant records. This makes it suitable for exploratory analysis, checking gene-related classifications, comparing lifespan intervention results, and examining longevity-associated variants, provided the requested information exists in the OpenGenes database.

Limitations and notes

The server does not provide a Swagger or OpenAPI interface for browsing its capabilities directly in a web browser. MCP Inspector or an MCP client is recommended for examining the available tools. Data access depends on the OpenGenes files distributed through Hugging Face unless suitable local fallback files are available. The database operations exposed by the documented query tool are read-only, so the server is not intended for modifying or administering the dataset.