Open Targets MCP Server

A Model Context Protocol (MCP) server that exposes the Open Targets Platform GraphQL API as a set of tools for use with Claude Desktop and other MCP-compatible clients.

Quick Install

Option 1: Run once with uvx (no install)

uvx --from git+https://github.com/nickzren/opentargets-mcp opentargets-mcp

Option 2: Claude Desktop (MCPM)

# Install mcpm package manager
pip install mcpm

# Install the server
mcpm install opentargets

Option 3: Local install (dev or self-host)

git clone https://github.com/nickzren/opentargets-mcp
cd opentargets-mcp
pip install uv
uv sync

# Run (stdio transport by default)
uv run python -m opentargets_mcp.server

Option 4: Docker

git clone https://github.com/nickzren/opentargets-mcp
cd opentargets-mcp

# Build and run with Docker Compose
docker-compose up -d --build

Note: the default transport is http for docker deployments.

See the configuration section below for details and how to set ports and other environment variables.

Claude Desktop Manual Import (optional)

mcpm import stdio opentargets \
  --command "$(uv run which python)" \
  --args "-m opentargets_mcp.server --transport stdio"

Then restart Claude Desktop to start using the Open Targets tools.

Features

Core Capabilities

• Target Analysis: Search genes/proteins by Ensembl ID or symbol. Access expression data, genetic constraints, pathways, protein interactions, safety profiles, and mouse phenotypes
• Disease Analysis: Query diseases by EFO ID. Find associated targets, phenotypes (HPO), and research projects
• Drug Discovery: Search drugs by ChEMBL ID. Access safety data, adverse events, indications, and mechanism of action
• Evidence Mining: Explore target-disease associations with scored evidence from multiple sources
• Variant Analysis: Query genetic variants, GWAS credible sets, and pharmacogenomics data
• Study Exploration: Access GWAS studies with L2G predictions and fine-mapped loci
• Smart Search: Entity resolution with synonym handling, autocomplete, and ID mapping
• Cross-Entity Workflows: Multi-hop tools that chain disease, target, and drug evidence for prioritization
• Raw GraphQL Power Tools: Run single and batch raw GraphQL operations with structured status envelopes

Why This Server

This implementation is designed for practical Open Targets workflows:

• Curated breadth: 65 curated tools plus 3 advanced GraphQL tools (68 total), spanning target, disease, drug, evidence, variant, study, metadata, and cross-entity workflow tasks.
• Safer automation: strict ID resolution, typed parameter handling, and resilient retry behavior.
• Lower token overhead: optional fields filters on core domain tools to return only what you need.
• Flexible power mode: raw GraphQL tools are available for edge cases.

Data Sources

The Open Targets Platform integrates evidence from 22+ primary data sources:

• Genetics: Open Targets Genetics, ClinVar, UK Biobank, FinnGen, Gene2Phenotype, Orphanet, COSMIC
• Functional: CRISPR screens, DepMap, GeneBass
• Drugs: ChEMB

... View full README on GitHub