OpenTargets-MCP-Server

Unofficial Open Targets MCP Server 🧬

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

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

🚀 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:

• MCP Server: Check the server logs and error outputs
• Open Targets API: Visit platform.opentargets.org
• GraphQL Queries: Use the Open Targets GraphQL browser

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}