MCP server for Interop DB
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# interopdb-mcp MCP server for the [Interop DB](https://interopdb-staging-f-ca.salmonpebble-cac1724c.northeurope.azurecontainerapps.io/), 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](https://aledb.org)** -- Adaptive Laboratory Evolution Database - **[BiGGr](https://biggr.org)** -- Knowledgebase of genome-scale metabolic network reconstructions - **[PanKB](https://pankb.org)** -- Pangenome Knowledge Base - **[PMkbase](https://www.pmkbase.com)** -- Phenotype MicroArray Knowledge Base Interop DB also has a [Python client and CLI](https://pypi.org/project/interopdb/) for programmatic use. This MCP package wraps the client using FastMCP. For developers who prefer coding directly, install the `interopdb` package instead. ## Installation ```bash 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: ```bash which interopdb-mcp ``` Copy and add the path to your `claude_desktop_config.json`: ```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 | Tool | Description | |---|---| | `get_gene` | Query a gene by local ID or UID | | `get_strain` | Query a strain by local ID or UID | | `get_pair` | Query a gene-strain pair by local ID | | `se…
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