interopdb-mcp

MCP server for the Interop DB, enabling LLMs like Claude Desktop to search and query genes, strains, and gene-strain pairs across multiple biological databases through natural language.

Interop DB is a federated registry that assigns unified identifiers to genes and strains across multiple biological databases. It integrates data from:

• ALEdb -- Adaptive Laboratory Evolution Database
• BiGGr -- Knowledgebase of genome-scale metabolic network reconstructions
• PanKB -- Pangenome Knowledge Base
• PMkbase -- Phenotype MicroArray Knowledge Base

Interop DB also has a Python client and CLI for programmatic use. This MCP package wraps the client using FastMCP. For developers who prefer coding directly, install the interopdb package instead.

Installation

pip install interopdb-mcp

Usage with Claude Desktop

interopdb-mcp runs as a local MCP server over stdio hosted by Claude Desktop. First, find the absolute path to the installed package:

which interopdb-mcp

Copy and add the path to your claude_desktop_config.json:

{
  "mcpServers": {
    "interopdb-mcp": {
      "command": "/full/path/to/interopdb-mcp"
    }
  }
}

Then restart Claude Desktop. You can now ask Claude questions like:

• "Find data for gene rpoB"
• "Look up strain 511145 across all databases"
• "What data is available for gene thrL in strain 511145?"
• "Search for dnaA in the registry"
• "What gene-strain relationships exist for GCF_031662355.1 in the registry?"

Available Tools