sviatkh/flybase-mcp-server

FlyBase MCP

MCP server for FlyBase integration

This MCP server allows accessing and retrieving information from FlyBase, a comprehensive database for the genetics and molecular biology of Drosophila melanogaster.

Installation

• Local setup with Claude Desktop:

Add the following to your claude_desktop_config.json file. To locate this file, click your name in Claude Desktop, go to “Settings,” then “Developer.” Under “Local MCP servers,” select “Edit Config.”

{
  "mcpServers": {
    "flybase": {
      "command": "uvx",
      "args": [
        "flybase-mcp-server@latest"
      ],
      "env": {
        "UV_PYTHON": "3.11"
      }
    }
  }
}

Features

• Retrieving a concise summary for a specific gene from FlyBase using its unique gene ID.
• Fetching Gene Ontology (GO) slim terms for a gene by specifying the GO domain, such as biological_process, cellular_component, or molecular_function.

API reference

Tools

1. get_flybase_gene_summary

   • This tool retrieves a concise summary for a specific gene from FlyBase.
   • Requires: the unique FlyBase gene ID (e.g., FBgn0003362).

2. get_flybase_gene_ontology

   • This tool fetches Gene Ontology (GO) slim terms for a gene, categorized by a specific GO domain.
   • Requires: the unique FlyBase gene ID (e.g., FBgn0003362).

     • gene_ontology_domain (str): The specific GO domain to query.

       • Available values for GO: biological_process, cellular_component, molecular_function