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OpenTargets MCP Server

by Augmented-Nature
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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.

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:

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}
Deploy Server
A
security – no known vulnerabilities
F
license - not found
A
quality - confirmed to work

How are these scores calculated?

remote-capable server

The server can be hosted and run remotely because it primarily relies on remote services or has no dependency on the local environment.

Tools

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

  1. ✅ Verified Features
    1. 🚀 Quick Start
      1. 📋 MCP Client Configuration
        1. Claude Desktop
        2. Other MCP Clients
      2. 🛠️ Available Tools
        1. 🎯 search_targets
        2. 🦠 search_diseases
        3. 🔗 get_target_disease_associations
        4. 📊 get_disease_targets_summary
        5. 🧬 get_target_details
        6. 🎭 get_disease_details
      3. 📚 Resource Templates
        1. 🧪 Real-World Examples
          1. Cancer Research Workflow
          2. Drug Discovery Pipeline
        2. 🔬 Data Sources & Standards
          1. 🏗️ Architecture
            1. 📊 API Information
              1. 🤝 Contributing
                1. Support
                  1. Citation

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