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MCP server

The GWAS Catalog Model Context Protocol (MCP) server allows compatible AI agents to query GWAS Catalog data directly.

Instead of constructing REST API requests yourself, you can ask questions in natural language or allow an agent to make structured queries on your behalf.

MCP server: https://ebi.ac.uk/gwas/mcp

Use the REST API when building software or making reproducible programmatic queries. Use the MCP server when working with an MCP-compatible AI agent that should discover and query GWAS Catalog data on your behalf.

Available data​

The MCP server provides tools for querying:

  • Traits — EFO traits (diseases and phenotypes) by name, gene or publication
  • Studies — GWAS studies by trait, ancestry label, gene or accession
  • Associations — variant-trait associations and statistics such as p-values and odds ratios

It also provides reference data, including ancestry labels, cohort IDs and variant consequences, which agents can use to interpret results.

Example questions​

You do not need to call the tools directly. Ask your MCP-compatible agent questions such as:

  • “What EFO trait covers type 2 diabetes?”
  • “Find GWAS studies of type 2 diabetes in East Asian cohorts.”
  • “What variants are associated with LDL cholesterol near the APOE gene?”
  • “Show the strongest associations for study accession GCST000001.”