gwas-database

Name: gwas-database
Availability: InStock
Author: Org-GAgent

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

Ready to run

npx skills add https://github.com/Org-GAgent/result-interpreter --skill gwas-database-org-gagent

💬 Prompt for ChatGPT / Claude Chat▼

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.