Gwas Database

What it does

This skill allows an AI agent to access and query the GWAS Catalog, a comprehensive repository of genome-wide association studies. It enables retrieval of genetic variant associations with traits or diseases, information about specific genetic variants (SNPs), summary statistics from studies, and study metadata. The skill leverages both the web interface and REST APIs provided by the GWAS Catalog for data access.

When to use it

• Finding SNPs associated with a particular disease or trait (e.g., "What genes are linked to Alzheimer's?").
• Looking up information about a specific genetic variant using its rs ID (e.g., "Tell me about rs7903146").
• Discovering genetic variants associated with a phenotype (e.g., "What SNPs are related to body mass index?").
• Identifying variants located near or within a specific gene (e.g., "Show me variants near the APOE gene").
• Accessing complete genome-wide association data for a published study.

Key capabilities

• Data Structure Understanding: Knowledge of GWAS Catalog entities: Studies, Associations, Variants, and Traits.
• Web Interface Search: Ability to perform searches using the web interface by Variant (rs ID), Disease/Trait, Gene, Chromosomal Region, or Publication details (PMID, Author, GCST ID).
• REST API Access: Utilizes both the GWAS Catalog API and Summary Statistics API for programmatic data retrieval.
• Identifier Recognition: Understands key identifiers such as rs numbers, EFO terms, gene symbols, and GCST IDs.

Example prompts

• "Find SNPs associated with type 2 diabetes."
• "What is the significance of rs7903146?"
• "Show me all studies related to the TCF7L2 gene."

Tips & gotchas

• The skill relies on identifiers like rs IDs and GCST IDs for precise queries. Ensure these are accurate.
• Familiarize yourself with the GWAS Catalog's data structure (Studies, Associations, Variants, Traits) for more targeted searches.
• The skill accesses external APIs; availability depends on the GWAS Catalog’s service status.