DGIdb MCP Server

Overview

The DGIdb MCP server bridges the gap between natural‑language queries and a rich, curated resource of drug–gene interactions. By exposing the Drug Gene Interaction Database (DGIdb) through the Model Context Protocol, it turns a static web API into an interactive tool that Claude Desktop can invoke on demand. This eliminates the need for developers to write custom HTTP requests or parse JSON responses, allowing them to focus on higher‑level scientific reasoning.

At its core, the server accepts high‑level commands such as “search for drug interactions” or “list genes linked to a specific compound.” It translates these requests into the appropriate DGIdb API calls, handles authentication and pagination, and streams the results back to Claude. The integration is lightweight: a single configuration entry in the section of Claude Desktop’s settings points to the server’s URL, and the assistant automatically discovers and uses the tool when a user asks a relevant question. This seamless discovery makes it feel as if Claude has native knowledge of drug–gene relationships, even though the data lives in an external database.

Key capabilities include:

• Querying by drug name or gene symbol – return interaction types, evidence scores, and source references.
• Filtering by therapeutic class or target pathway – useful for hypothesis generation in translational research.
• Retrieving drug attributes such as approvals, indications, and mechanism of action.
• Streaming results in real time, allowing Claude to present partial answers while the full dataset loads.

Typical use cases span drug discovery, precision medicine, and academic research. A researcher can ask Claude to “list all FDA‑approved drugs that target the EGFR gene” and receive a concise table of candidates, complete with links to supporting literature. Clinicians might query “are there known interactions between Drug X and Gene Y” to inform off‑label prescribing decisions. Because the server is protocol‑agnostic, it can be deployed on any platform that supports MCP—Cloudflare Workers, Docker containers, or a private Kubernetes cluster—providing flexibility for both open‑source and commercial environments.

The main advantage of this MCP server is its zero‑touch integration. Developers and scientists need only configure a URL; no additional SDKs or data pipelines are required. The server handles all the intricacies of the DGIdb API, such as rate limiting and data normalization, ensuring that Claude’s responses are accurate and up‑to‑date. By turning complex biomedical data into a conversational tool, the DGIdb MCP server empowers AI assistants to support evidence‑based decision making in real time.