Searching the Druggable Genome using Large Language Models

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ID: 326082
2026
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Abstract
Summary: The druggable genome encompasses the genes that are known or predicted to interact with drugs. The Drug-Gene Interaction Database (DGIdb) provides an integrated resource for discovering and contextualizing these interactions, supporting a broad range of research and clinical applications. DGIdb is currently accessed through structured web interfaces and API calls, requiring users to translate natural-language questions into database-specific query patterns. To allow for the use of DGIdb through natural language, we developed the DGIdb Model Context Protocol (MCP) server, which allows large language models (LLMs) access to up-to-date information through the DGIdb API. We demonstrate that the MCP server greatly enhances an LLM's ability to answer questions requiring accurate, up-to-date biomedical knowledge drawn from structured external resources. Availability and implementation: The DGIdb MCP server is detailed at https://github.com/griffithlab/dgidb-mcp-server and includes instructions for accessing the server through the Claude desktop app.
Reference Key
openalex_W7125503801 Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Lars Schimmelpfennig, Matthew Cannon, Quentin Cody, Joshua McMichael, Adam Coffman, Susanna Kiwala, Kilannin J Krysiak, Alex H. Wagner, Malachi Griffith, Obi L Griffith
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Journal BMC Bioinformatics
Year 2026
DOI
10.1093/bioinformatics/btag632
URL
https://doi.org/10.1093/bioinformatics/btag632
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