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gwas-database

Retrieve SNP-trait associations from the NHGRI-EBI GWAS Catalog via REST API.

Updated Aug 23, 2026
Search Tags:#data-extraction#rest-api#variant#snp#gwas-catalog#genetic-associations
One-click install
npx skills add https://github.com/Org-GAgent/result-interpreter --skill gwas-database-org-gagent
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: gwas-database
Source: https://github.com/Org-GAgent/result-interpreter/tree/main/.skills/scientific-skills/gwas-database
Command: npx skills add https://github.com/Org-GAgent/result-interpreter --skill gwas-database-org-gagent

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

This skill enables researchers to programmatically discover SNP-trait associations from the NHGRI-EBI GWAS Catalog, retrieving variants, associated traits, p-values, and study metadata for genetic epidemiology and downstream analyses.

Core Features & Use Cases

  • Programmatic access to studies, associations, variants, and traits via the GWAS Catalog REST APIs.
  • Trait- and variant-centric queries (e.g., by EFO terms or rs IDs) with pagination and HAL navigation.
  • Cross-study comparisons, filtering by significance thresholds, and extraction of key fields (rsId, strongestAllele, pvalue, orPerCopyNum, betaNum, studyId, pubmedId).
  • Optional integration with summary statistics API to access full study data where available.

Quick Start

Query the GWAS Catalog for a trait or variant and print the top associations.

Frequently Asked Questions about gwas-database

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I retrieve SNP-trait associations from the GWAS Catalog via REST API?▼

Retrieve SNP-trait associations from the GWAS Catalog by querying its REST API endpoints for studies, associations, variants, and traits, using pagination and HAL links to navigate large result sets.

Can I query the GWAS Catalog by EFO trait terms or rs IDs?▼

Yes, GWAS Catalog queries support both trait-centered searches using EFO terms and variant-centered searches using rs IDs, returning matching associations with p-values and study metadata.

What data fields are available when extracting GWAS Catalog associations?▼

Available extraction fields include rsId, strongestAllele, pvalue, orPerCopyNum, betaNum, studyId, and pubmedId, enabling detailed cross-study comparisons and downstream genetic epidemiology analyses.

Does the GWAS Catalog REST API support downloading summary statistics?▼

Yes, the GWAS Catalog REST API offers optional integration with a summary statistics API, allowing users to access and download full study data where available for complete datasets.

How do I filter GWAS Catalog associations by significance thresholds for large-scale data extraction?▼

Filter GWAS Catalog associations by applying significance thresholds to p-values during extraction, enabling cross-study comparisons and large-scale data retrieval tailored to specific genetic association criteria.

What is the best way to perform cross-study comparisons of genetic associations from the GWAS Catalog?▼

Perform cross-study comparisons by querying GWAS Catalog associations for specific traits or variants, retrieving study metadata and p-values, and filtering results by significance thresholds to identify consistent genetic associations.

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