Query Open Targets Biomedical Data via GraphQL
Query the Open Targets Platform via GraphQL - target-disease associations, drug discovery data, and genetic constraints.
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Why it matters
Access and query the Open Targets Platform API for comprehensive biomedical research data, including target-disease associations and drug discovery information, using GraphQL.
Outcomes
What it gets done
Execute GraphQL queries against the Open Targets Platform API.
Retrieve data on biological targets, diseases, and drugs using their respective IDs.
Explore schema introspection to understand available data types.
Utilize parameterized queries for specific data retrieval needs.
Install
Add it to your toolbox
Run in your project directory:
curl -fsSL https://spark.entire.vc/get/vb-open-targets | bash Capabilities
Tools your agent gets
Execute GraphQL queries against the Open Targets Platform API with optional variables
Overview
Open Targets MCP Server
Open Targets MCP Server provides GraphQL access to the Open Targets Platform for target-disease associations, drug data, and genetic evidence via a single opentargets_graphql_query tool, identified by Ensembl, EFO, and ChEMBL IDs. Use it for ad-hoc, conversational Open Targets queries. For large-scale or repeated bulk retrieval, use Open Targets' official data downloads or BigQuery instance instead.
What it does
Open Targets MCP Server gives an AI assistant GraphQL access to the Open Targets Platform, a biomedical research database covering target-disease associations, drug discovery data, and genetic evidence, identified via Ensembl IDs (targets), EFO IDs (diseases/phenotypes), and ChEMBL IDs (drugs/compounds).
When to use - and when NOT to
Use it when you want to look up biological targets by Ensembl ID, disease/phenotype data by EFO ID, or drug/compound data by ChEMBL ID, explore target tractability and genetic constraints, or introspect the GraphQL schema to discover available data types. Do not use it for large-scale or repeated bulk data retrieval - Open Targets itself recommends using their official data downloads or Google BigQuery instance instead of hammering the GraphQL API with many queries.
Capabilities
opentargets_graphql_query: execute a GraphQL query (with optional variables) against the Open Targets Platform API.
This single tool supports schema introspection, parameterized queries, and lookups across targets, diseases, and drugs. Example queries: retrieve details for gene target ENSG00000169083; list all available data types in the schema; query asthma via EFO_0000270; retrieve drug data for CHEMBL1201236; explore target tractability and genetic constraints. See the project's GRAPHQL_EXAMPLES.md for correct query patterns and common mistakes to avoid.
How to install
Connect to the hosted server via mcp-remote:
npx mcp-remote https://open-targets-mcp-server.quentincody.workers.dev/mcp
Claude Desktop configuration (recommended, Streamable HTTP):
"open-targets-worker": {
"command": "npx",
"args": ["mcp-remote", "https://open-targets-mcp-server.quentincody.workers.dev/mcp"]
}
Or legacy SSE transport, using the /sse endpoint instead of /mcp. No local deployment required.
Who it's for
Biomedical researchers and drug discovery teams who want conversational, ad-hoc access to Open Targets' target-disease-drug evidence graph, reserving bulk analysis for the official data downloads or BigQuery instance.
Source README
MCP server providing access to the Open Targets Platform API for querying target-disease associations, drug discovery data, and biomedical research information via GraphQL.
Installation
NPX with mcp-remote
npx mcp-remote https://open-targets-mcp-server.quentincody.workers.dev/mcp
Configuration
Claude Desktop (Recommended)
"open-targets-worker": {
"command": "npx",
"args": [
"mcp-remote",
"https://open-targets-mcp-server.quentincody.workers.dev/mcp"
]
}
Claude Desktop (Legacy SSE)
"open-targets-worker": {
"command": "npx",
"args": [
"mcp-remote",
"https://open-targets-mcp-server.quentincody.workers.dev/sse"
]
}
Available Tools
| Tool | Description |
|---|---|
opentargets_graphql_query |
Execute GraphQL queries against the Open Targets Platform API with optional variables |
Capabilities
- Access to Open Targets Platform API via GraphQL queries
- Information about biological targets, identified by Ensembl ID
- Data about diseases and phenotypes, identified by EFO ID
- Data about drugs and chemical compounds, identified by ChEMBL ID
- Schema introspection capabilities for exploring available data types
- Support for parameterized queries with variables
- Two transport protocols: Streamable HTTP (recommended) and SSE (legacy)
Usage Examples
Retrieve details for a specific gene target using Ensembl ID ENSG00000169083
List all available data types in the Open Targets schema
Query information about asthma using EFO ID EFO_0000270
Retrieve information about a drug using ChEMBL ID CHEMBL1201236
Explore data on target tractability and genetic constraints
Notes
Licensed under MIT License with academic citation requirements. For large-scale Open Targets data retrieval, Open Targets recommends using their official data downloads or Google BigQuery instance instead of repeated GraphQL queries. See GRAPHQL_EXAMPLES.md for correct query examples and avoiding common mistakes.
FAQ
Common questions
Discussion
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