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biothings-mcp

@longevity-genie

Repository

About biothings-mcp

MCP (Model Context Protocol) server for biothings

#bioinformatics#genetics#genetic-variants#biothings#mcp-server

Config

Add this server to your MCP-compatible client using the configuration below.

{
  "mcpServers": {
    "biothings-mcp": {
      "command": "uvx",
      "args": [
        "biothings-mcp"
      ]
    }
  }
}

Tools

No tools detected

We auto-extract tools from the README. The maintainer can list them under a ## Tools heading to populate this section.

Overview

What is biothings-mcp?

biothings-mcp is a Model Context Protocol (MCP) server that provides a standardized interface for accessing and manipulating biomedical data from the BioThings platform, including gene annotation (mygene.info), variant annotation (myvariant.info), and chemical compound annotation (mychem.info). It is designed for AI assistants and agents that require specialized biomedical knowledge.

How to use biothings-mcp?

Install and run the server using uvx (no cloning required) or by cloning the repository. For STDIO mode, use uvx biothings-mcp; for HTTP streamable mode, use uvx --from biothings-mcp server run; for SSE mode, use uvx --from biothings-mcp sse. Optionally specify a custom output directory with --output-dir. Configure your MCP‑compatible AI client using the provided JSON configuration files (e.g., mcp-config.json for local servers, mcp-config-remote.json for the public hosted server).

Key features of biothings-mcp

  • Standard MCP interface for BioThings biomedical data
  • Supports gene, variant, chemical, taxon, and download tools
  • Local file saving with automatic directory creation and unique filenames
  • Supports STDIO, HTTP streamable, and SSE transport modes
  • Type safety via the biothings-typed-client library
  • Ready-to-use configuration for AI clients like Cursor and Claude Desktop

Use cases of biothings-mcp

  • AI assistants querying gene annotations from mygene.info
  • Analyzing genetic variants via myvariant.info
  • Chemical compound lookup from mychem.info
  • Downloading NCBI Entrez data (sequences, GenBank) for analysis
  • Integrating specialized biomedical knowledge into MCP-compatible AI clients

FAQ from biothings-mcp

What biomedical data sources does biothings-mcp provide access to?

It supports mygene.info (gene annotation), myvariant.info (variant annotation), and mychem.info (chemical compound annotation), all accessed via BioThings REST APIs.

How do I run biothings-mcp?

You can run it with uvx without cloning: uvx biothings-mcp for STDIO mode, uvx --from biothings-mcp server run for HTTP streamable mode, or uvx --from biothings-mcp sse for

Frequently asked questions

What biomedical data sources does biothings-mcp provide access to?

It supports mygene.info (gene annotation), myvariant.info (variant annotation), and mychem.info (chemical compound annotation), all accessed via BioThings REST APIs.

How do I run biothings-mcp?

You can run it with uvx without cloning: `uvx biothings-mcp` for STDIO mode, `uvx --from biothings-mcp server run` for HTTP streamable mode, or `uvx --from biothings-mcp sse` for

Comments

Basic information

Category

Other

License

MIT

Transports

stdio

Author

longevity-genie

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