openpharma-org/opentargets-mcp

Unofficial Open Targets MCP Server

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

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

MCP Client Configuration

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

Available Tools

search_targets

Search therapeutic targets by gene symbol, name, or description

{
  "name": "search_targets",
  "arguments": {
    "query": "BRCA1",
    "size": 10
  }
}

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",
    "size": 10
  }
}

get_target_disease_associations

Get target-disease associations with evidence scores

{
  "name": "get_target_disease_associations",
  "arguments": {
    "targetId": "ENSG00000012048",
    "size": 10
  }
}

OR

{
  "name": "get_target_disease_associations",
  "arguments": {
    "diseaseId": "EFO_0000305",
    "size": 10
  }
}

get_disease_targets_summary

Get prioritized targets associated with a disease

{
  "name": "get_disease_targets_summary",
  "arguments": {
    "diseaseId": "EFO_0000305",
    "size": 20
  }
}

get_target_details

Get comprehensive target information

{
  "name": "get_target_details",
  "arguments": {
    "id": "ENSG00000012048"
  }
}

get_disease_details

Get comprehensive disease information

{
  "name": "get_disease_details",
  "arguments": {
    "id": "EFO_0000305"
  }
}

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)

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