mcp

# GWAS Catalog MCP A Model Context Protocol (MCP) server that lets AI agents and agentic IDEs query the [GWAS Catalog](https://www.ebi.ac.uk/gwas/) in plain language — searching traits, studies, and variant–trait associations from published genome-wide association studies. You don't need to install anything. A hosted server is live at: ``` https://www.ebi.ac.uk/gwas/mcp ``` The server is also listed in the [BioContext registry](https://biocontext.ai/registry/gwas-catalog/mcp). ## Connect The server uses MCP's Streamable HTTP transport. Connect to the hosted endpoint with an MCP 2.x-compatible client. ### Codex ```bash codex mcp add gwas-mcp --url https://www.ebi.ac.uk/gwas/mcp ``` Use `codex mcp list` to check the configured servers. ### Claude Code For MCP 2.x, use Claude Code's `http` transport for the hosted Streamable HTTP endpoint: ```bash claude mcp add --transport http gwas-mcp https://www.ebi.ac.uk/gwas/mcp ``` Add `--scope user` to make it available in all your projects. ### ChatGPT desktop app Open Settings → MCP Servers → Add server, choose Streamable HTTP, and enter: ``` https://www.ebi.ac.uk/gwas/mcp ``` Save the server and restart the app. Other MCP clients that support remote Streamable HTTP servers can connect using the same URL. Clients that only support local STDIO servers can use the `mcp-remote` bridge. ## What you can ask The server gives your agent three tools: | Tool | What it finds | |------|---------------| | Traits | EFO traits (diseases, phenotypes) by name, gene, or publication | | Studies | GWAS studies by trait, ancestry, gene, or accession | | Associations | Variant–trait associations with statistics (p-value, odds ratio, …) | It also exposes reference data (ancestry labels, cohort IDs, variant consequences) that agents use to interpret results. You don't call these directly — just ask your agent questions like: - "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." ## Run it yourself Most people should use the server hosted above. The best way to test and develop the server locally is to run [MCP Inspector](https://github.com/modelcontextprotocol/inspector) in STDIO mode. The development endpoint is `https://wwwdev.ebi.ac.uk/gwas/mcp`. Both development Helm paths are `/gwas/mcp`; an older deployed path containing `/api` requires a Helm release update using the current values. ## License Apache-2.0