Unofficial Open Targets MCP Server 🧬

Name: Unofficial Open Targets MCP Server 🧬
Author: Augmented-Nature

@Augmented-Nature

About Unofficial Open Targets MCP Server 🧬

Unofficial Model Context Protocol server for accessing Open Targets platform data for gene-drug-disease associations research.

#gene-drug-disease #open-targets #mcp-server

Basic information

Config

Add this server to your MCP-compatible client using the configuration below.

{
  "mcpServers": {
    "Augmented-Nature-OpenTargets-MCP-Server": {
      "command": "node",
      "args": [
        "build/index.js"
      ]
    }
  }
}

Tools

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Overview

What is Unofficial Open Targets MCP Server?

An unofficial Model Context Protocol server that provides access to Open Targets platform data for gene‑drug‑disease associations research. It is developed by Augmented Nature and uses the Open Targets v25.0.1 API.

How to use Unofficial Open Targets MCP Server?

Install and build the server with npm install and npm run build, then run it with node build/index.js. Configure it as an MCP client (e.g., Claude Desktop) by adding the server to the mcpServers object with the node command and path to the built index.js.

Key features of Unofficial Open Targets MCP Server

Six verified tools: target search, disease search, target‑disease associations, disease target summaries, target details, disease details
Access 20+ integrated databases including ChEMBL, Ensembl, EFO, ClinVar, GWAS Catalog, UniProt, and Reactome
Resource templates using standardized URIs (e.g., opentargets://target/{ensemblId})
No authentication required; generous rate limits for research use
TypeScript implementation with GraphQL queries and JSON‑RPC communication
Error handling, 30‑second timeouts, and proper logging

Use cases of Unofficial Open Targets MCP Server

Cancer research workflow: search for oncogenes, get target details, find associated diseases, and retrieve prioritized targets for a specific cancer
Drug discovery pipeline: search for a disease, get its details, and find prioritized therapeutic targets
Retrieve comprehensive gene/protein information for a given Ensembl ID
Obtain disease profiles with ontologies and evidence scores from multiple databases

FAQ from Unofficial Open Targets MCP Server

What is the Open Targets platform?

Open Targets is a platform that integrates data from 20+ databases to provide evidence‑based target‑disease associations for drug discovery.

What identifiers are used for targets, diseases, and drugs?

Targets use Ensembl gene IDs (e.g., ENSG00000012048), diseases use EFO IDs (e.g., EFO_0000305), and drugs use ChEMBL IDs (e.g., CHEMBL1234).

Is authentication required to use the server?

No, the Open Targets API requires no authentication and is freely accessible for research.

What are the rate limits?

Rate limits are described as generous for research use, though no specific numbers are provided.

What data sources are integrated?

The server queries the Open Targets platform, which combines data from 20+ databases including ChEMBL, Ensembl, EFO, ClinVar, GWAS Catalog, UniProt, and Reactome.