Gwas Catalog

mcp-gwas-catalog

GWAS Catalog (EBI/NHGRI) MCP — curated catalog of genome-wide association studies. Look up a SNP (rsID) and its mapped genes, get trait associations + p-values/effect sizes for a SNP, or find studies for a disease/trait. Keyless REST API.

Part of Pipeworx — an MCP gateway connecting AI agents to 1881+ live data sources. This is an independent, unofficial integration — not affiliated with, endorsed by, or published by the upstream provider.

Tools

Tool	Description
get_snp	GWAS Catalog: look up a single-nucleotide polymorphism (SNP) by rsID. Returns functional class, chromosome/region locations, and mapped genes (with up/downstream + distance). Keyless, from EBI/NHGRI.
snp_associations	GWAS Catalog: get trait/disease associations for a SNP (rsID) — risk allele, p-value, odds ratio per copy, beta/effect size, and risk allele frequency. Keyless, from EBI/NHGRI.
studies_by_trait	GWAS Catalog: find genome-wide association studies for a disease/trait (EFO trait, e.g. "asthma" or "type 2 diabetes"). Returns accession, PubMed ID, title, journal, date, sample size. Keyless, from EBI/NHGRI.

Quick Start

Add to your MCP client (Claude Desktop, Cursor, Windsurf, etc.):

{
  "mcpServers": {
    "gwas-catalog": {
      "url": "https://gateway.pipeworx.io/gwas-catalog/mcp"
    }
  }
}

What this endpoint actually serves

tools/list at https://gateway.pipeworx.io/gwas-catalog/mcp returns the tools in the table above plus the shared Pipeworx meta-tools — ask_pipeworx, discover_tools, search_within, remember/recall and the rest of the gateway-wide set. So the tool count you see is larger than this table: a single-pack endpoint currently lists roughly 30 shared tools alongside the pack's own. The connection's initialize response states its exact scope, and is the authoritative answer for a given day.

This is deliberate, not multiplexing by accident. The meta-tools are what let a scoped connection answer a question this pack does not cover — via ask_pipeworx, which routes across the whole catalog — without you adding a second MCP server. There is currently no way to mount a pack endpoint without them; if the extra schemas cost you more context than the routing is worth, connect to the full gateway once rather than to several pack endpoints.

Or connect to the full Pipeworx gateway to get every pack's tools listed directly, instead of just this one's:

{
  "mcpServers": {
    "pipeworx": {
      "url": "https://gateway.pipeworx.io/mcp"
    }
  }
}

Both URLs reach the same gateway and the same 1881+ data sources. The only difference is which pack's tools are listed directly; ask_pipeworx reaches all of them from either one.

No MCP client? Call it over HTTP

curl -X POST https://gateway.pipeworx.io/v1/tools/get_snp \
  -H 'Content-Type: application/json' \
  -d '{"rsid":"rs7329174"}'

No account needed for the first calls. Inspect any tool: GET https://gateway.pipeworx.io/v1/tools/get_snp. Find one: POST https://gateway.pipeworx.io/v1/tools/search_packs with {"query":"..."}.

Standalone (no gateway account)

This package also runs as a local stdio MCP server — no Pipeworx account, no gateway round-trip:

{
  "mcpServers": {
    "gwas-catalog": {
      "command": "npx",
      "args": ["-y", "@pipeworx/mcp-gwas-catalog"]
    }
  }
}

Or run it directly to confirm it starts:

npx -y @pipeworx/mcp-gwas-catalog

It speaks MCP over stdin/stdout and answers initialize/tools/list/tools/call for only this pack's tools — none of the shared meta-tools the gateway connection above adds. Same source, same tools, no ask_pipeworx routing.

Using with ask_pipeworx

Instead of calling tools directly, you can ask questions in plain English — this works on the pack endpoint above as well as on the full gateway:

ask_pipeworx({ question: "your question about Gwas Catalog data" })

The gateway picks the right tool and fills the arguments automatically.

More

• Docs and guides
• pipeworx.io

License

MIT