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

```bibtex @misc{opentargetsmcp2025,
author = {Moudather Chelbi},
title = {OpenTargets MCP Server},
year = {2025},
howpublished = {https://github.com/Augmented-Nature/OpenTargets-MCP-Server},
note = {Accessed: 2025-06-29}