Is this skill useful for calculating Polygenic Risk Scores (PRS)?

Absolutely; it helps identify relevant variants and retrieve the necessary statistical evidence, such as odds ratios and beta coefficients, required for risk prediction models.

Can I access full summary statistics with this skill?

Yes, the skill provides specific implementation patterns for accessing full summary statistics via the GWAS Catalog REST API and FTP servers for studies that provide them.

What identifiers are used for searching the database?

You can search using variant rs IDs, study accession numbers (GCST IDs), Experimental Factor Ontology (EFO) terms for traits, and HGNC symbols for genes.

Does it support programmatic API integration?

Yes, it includes detailed Python code examples for interacting with both the main GWAS Catalog REST API and the dedicated Summary Statistics API.

What is the GWAS Catalog?

The GWAS Catalog is a comprehensive, curated repository of all published genome-wide association studies, providing data on SNP-trait associations, p-values, and effect sizes.

GWAS Catalog Explorer

Name: GWAS Catalog Explorer
Author: Zehong-Wang

byZehong-Wang

0•

Data Science & ML

Queries the NHGRI-EBI GWAS Catalog to retrieve genetic variant associations, study metadata, and comprehensive summary statistics for genomic research.

This skill provides specialized knowledge and implementation patterns for interacting with the GWAS Catalog, the premier repository of curated genome-wide association studies. It enables users to programmatically or manually search for SNP-trait associations, retrieve study-specific summary statistics, and map genetic variants to diseases or phenotypes using EFO ontology. Whether performing a systematic review of genetic evidence or building polygenic risk score models, this skill streamlines the process of extracting high-quality genomic data and metadata from NHGRI-EBI APIs and web interfaces.

Key Features

010 GitHub stars

02Access comprehensive GWAS summary statistics via REST API and FTP links.

03Cross-reference data with external resources like Ensembl, dbSNP, and Open Targets.

04Extract study metadata including publication details, cohort sizes, and ancestry information.

05Retrieve SNP-trait associations using rs IDs, gene symbols, or chromosomal regions.

06Search for phenotype associations using standardized EFO trait terms.

Use Cases

01Genetic Epidemiology: Identifying variants associated with specific diseases for association studies.

02Functional Genomics: Investigating the genomic context and potential regulatory effects of specific SNPs near target genes.

03Polygenic Risk Scores (PRS): Gathering effect sizes and p-values to construct predictive genomic models.

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add zehong-wang/kosmos gwas-database

For use in Claude.ai and ChatGPT

Download Skill