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OpenTargets MCP Server

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Unofficial Open Targets MCP Server 🧬

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

API

Developed by Augmented Nature

✅ Verified Features

All 6 tools working with live Open Targets API data:

  • 🎯 Target Search - Gene symbols, names, descriptions (BRCA1, TP53, etc.)

  • 🦠 Disease Search - Names, synonyms, descriptions (cancer, diabetes, etc.)

  • 🔗 Target-Disease Associations - Evidence scores from 20+ databases

  • 📊 Disease Target Summaries - Prioritized therapeutic targets

  • 🧬 Target Details - Comprehensive gene/protein information

  • 🎭 Disease Details - Complete disease profiles with ontologies

Related MCP server: Zenn MCP Server

🚀 Quick Start

# Install and build npm install npm run build # Run the server node build/index.js

📋 MCP Client Configuration

Claude Desktop

{ "mcpServers": { "opentargets-server": { "command": "node", "args": ["/path/to/opentargets-server/build/index.js"] } } }

Other MCP Clients

node /path/to/opentargets-server/build/index.js

🛠️ Available Tools

🎯 search_targets

Search therapeutic targets by gene symbol, name, or description

{ "name": "search_targets", "arguments": { "query": "BRCA1", // Gene symbol, name, or description "size": 10 // Optional: 1-500 results (default: 25) } }

Example Results:

  • BRCA1 (ENSG00000012048) - BRCA1 DNA repair associated

  • BRCA2 (ENSG00000139618) - BRCA2 DNA repair associated

  • BRIP1 (ENSG00000136492) - BRCA1 interacting DNA helicase 1

🦠 search_diseases

Search diseases by name, synonym, or description

{ "name": "search_diseases", "arguments": { "query": "breast cancer", // Disease name, synonym, or description "size": 10 // Optional: 1-500 results (default: 25) } }

🔗 get_target_disease_associations

Get target-disease associations with evidence scores

{ "name": "get_target_disease_associations", "arguments": { "targetId": "ENSG00000012048", // Target Ensembl ID "size": 10 // Optional: 1-500 results } }

OR

{ "name": "get_target_disease_associations", "arguments": { "diseaseId": "EFO_0000305", // Disease EFO ID "size": 10 // Optional: 1-500 results } }

📊 get_disease_targets_summary

Get prioritized targets associated with a disease

{ "name": "get_disease_targets_summary", "arguments": { "diseaseId": "EFO_0000305", // Disease EFO ID (required) "size": 20 // Optional: 1-500 targets (default: 50) } }

🧬 get_target_details

Get comprehensive target information

{ "name": "get_target_details", "arguments": { "id": "ENSG00000012048" // Target Ensembl gene ID } }

🎭 get_disease_details

Get comprehensive disease information

{ "name": "get_disease_details", "arguments": { "id": "EFO_0000305" // Disease EFO ID } }

📚 Resource Templates

Access Open Targets data through standardized URIs:

  • opentargets://target/{ensemblId} - Complete target information

  • opentargets://disease/{efoId} - Complete disease information

  • opentargets://drug/{chemblId} - Drug information

  • opentargets://association/{targetId}/{diseaseId} - Association evidence

  • opentargets://search/{query} - Search results

🧪 Real-World Examples

Cancer Research Workflow

# 1. Search for cancer-related targets {"name": "search_targets", "arguments": {"query": "oncogene", "size": 10}} # 2. Get detailed info for specific target {"name": "get_target_details", "arguments": {"id": "ENSG00000012048"}} # 3. Find all diseases associated with BRCA1 {"name": "get_target_disease_associations", "arguments": {"targetId": "ENSG00000012048"}} # 4. Get top targets for breast cancer {"name": "get_disease_targets_summary", "arguments": {"diseaseId": "EFO_0000305", "size": 20}}

Drug Discovery Pipeline

# 1. Search for Alzheimer's disease {"name": "search_diseases", "arguments": {"query": "Alzheimer", "size": 5}} # 2. Get disease details {"name": "get_disease_details", "arguments": {"id": "EFO_0000249"}} # 3. Find prioritized therapeutic targets {"name": "get_disease_targets_summary", "arguments": {"diseaseId": "EFO_0000249", "size": 30}}

🔬 Data Sources & Standards

Open Targets integrates 20+ databases:

  • ChEMBL - Drug & compound data

  • Ensembl - Gene & protein annotations

  • EFO - Experimental Factor Ontology

  • ClinVar - Clinical variant data

  • GWAS Catalog - Genome-wide association studies

  • UniProt - Protein sequences & functions

  • Reactome - Biological pathways

  • And many more...

Standardized Identifiers:

  • Targets: Ensembl gene IDs (e.g., ENSG00000012048)

  • Diseases: EFO IDs (e.g., EFO_0000305)

  • Drugs: ChEMBL IDs (e.g., CHEMBL1234)

🏗️ Architecture

  • TypeScript implementation with robust type safety

  • GraphQL queries for efficient data retrieval

  • MCP Protocol compliant JSON-RPC communication

  • Error Handling with comprehensive validation

  • Production Ready with 30s timeouts and proper logging

📊 API Information

  • Base URL: https://api.platform.opentargets.org/api/v4/graphql

  • Version: Open Targets v25.0.1

  • Rate Limits: Generous for research use

  • Authentication: None required

  • Format: GraphQL queries, JSON responses

🤝 Contributing

This server is developed and maintained by Augmented Nature. For enhancements:

  1. Fork the repository

  2. Make your changes

  3. Submit a pull request

Support

For issues with:

Citation

If you use this project in your research or publications, please cite it as follows:

author = {Moudather Chelbi}, title = {OpenTargets MCP Server}, year = {2025}, howpublished = {https://github.com/Augmented-Nature/OpenTargets-MCP-Server}, note = {Accessed: 2025-06-29}
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