Gwas Mcp
GWAS Catalog Model Context Protocol server, supporting natural language queries of associations, studies, and traits
Install
$ agentstack add mcp-ebispot-gwas-mcp ✓ scanned · ✓ verified, works with Claude Code, Cursor, and more.
Security review
✓ PassedNo issues found. Passed automated security review. · v0.1.0 How review works →
- ✓ Prompt-injection patterns
- ✓ Secret / credential exfiltration
- ✓ Dangerous shell & filesystem operations
- ✓ Untrusted network calls
- ✓ Known-malicious package signatures
What it can access
- ✓ Network access No
- ✓ Filesystem access No
- ✓ Shell / process execution No
- ✓ Environment & secrets No
- ✓ Dynamic code execution No
From automated source analysis of v0.1.0. “Used” means the capability is present in the source — more access means more to trust, not that it’s unsafe.
Verified badge
Passed review? Show it. Paste this badge into your README, it links to the public security report.
Links to your public security report.[](https://agentstack.voostack.com/security/report/mcp-ebispot-gwas-mcp) Reliability & compatibility
Declared compatibility
Compatibility is declared by the source manifest. End-to-end runtime verification is coming, see below.
We're building live execution health for every listing: tool-call success rate, median latency, uptime, and last-checked timestamps, measured, not self-reported. It isn't live yet, so we don't show numbers we can't stand behind.
How agent discovery & health will work →About
GWAS Catalog MCP
A Model Context Protocol (MCP) server that lets AI agents and agentic IDEs query the GWAS Catalog 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://ebi.ac.uk/gwas/mcpConnect
Claude Code
claude mcp add --transport http gwas-mcp https://ebi.ac.uk/gwas/mcpAdd --scope user to make it available in all your projects.
Codex
Add this to ~/.codex/config.toml:
[mcp_servers.gwas-mcp]
url = "https://ebi.ac.uk/gwas/mcp"Any MCP client that supports remote (streamable HTTP) servers can connect using the same URL.
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 in STDIO mode.
License
Apache-2.0
Source & license
This open-source MCP server is cataloged on AgentStack and links to its original source — we do not rehost the code.
- Author: EBISPOT
- Source: EBISPOT/gwas-mcp
- License: Apache-2.0
- Homepage: https://ebi.ac.uk/gwas/mcp
Install and usage instructions live in the source repository linked above.
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Versions
- v0.1.0 Imported from the upstream source.