gwas-database
Query NHGRI-EBI GWAS Catalog for SNP-trait associations. Search variants by rs ID, disease/trait, gene, retrieve p-values and summary statistics, for genetic epidemiology and polygenic risk scores.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill gwas-database --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
What it does
Guides an AI agent to query the GWAS Catalog for SNP-trait associations, search by rs ID, disease/trait, or gene, and retrieve p-values and summary statistics for genetic epidemiology and polygenic risk scores.
How it works
- The skill describes the GWAS Catalog data structure with four core entities: Studies, Associations, Variants, and Traits, and identifies key identifiers (GCST IDs, rs numbers, EFO/trait IDs, HGNC gene symbols).
- It lists multiple web interface search modes (Variant rsID, Disease/Trait, Gene, Chromosomal Region, Publication) and provides REST API endpoints and example Python requests for Studies, Associations, Variants, and Traits.
- It includes example workflows: exploring disease associations via trait queries, retrieving variant information and associations, accessing summary statistics via the Summary Statistics API, and following related resources via _links in API responses.
- It specifies common data fields found in responses (rsId, strongestAllele, pvalue, orPerCopyNum, betaNum, efoTrait, accessionId, pubmedId, sampleSize) and notes about pagination, rate limits, and data quality.
- It emphasizes best practices for queries (start with web interface for trait IDs, use API for bulk data, handle pagination, cache results), and data interpretation guidance (p-value thresholds, ancestry, replication, winner’s curse).
When to use it
Use this skill for:
- Genetic variant associations: finding SNPs linked to diseases/traits
- SNP lookups: retrieving data about rs IDs
- Trait/disease searches: discovering genetic associations for phenotypes
- Gene associations: variants near specific genes
- GWAS summary statistics access: full data for analyses
- Study metadata: publication and cohort details
- Population genetics considerations and polygenic risk score variant selection
- Functional genomics and systematic reviews of genetic associations
What it can touch
- The skill references REST API endpoints at https://www.ebi.ac.uk/gwas/rest/api and the Summary Statistics API at https://www.ebi.ac.uk/gwas/summary-statistics/api, and demonstrates using HTTP requests to: /studies/{accessionID}, /singleNucleotidePolymorphisms/{rsID}, /singleNucleotidePolymorphisms/{rsID}/associations, /efoTraits/{efoID}, and related endpoints. It also shows an ftp download path for summary statistics. Commands and code samples use standard Python requests to access these endpoints.
Caveats
- Data comes from published GWAS associations and may contain inconsistencies; effect sizes are those reported in published studies and may require harmonization.
- Genome-wide significance is commonly p ≤ 5×10⁻⁸; results should be interpreted with consideration of ancestry, sample size, and potential biases.
- Rate limiting and ethical use guidelines apply to API usage; responses are paginated and require handling of _links for navigation.
- The skill describes workflows and code patterns but does not guarantee availability or stability of external APIs or data.
# GWAS Catalog Database ## Overview The GWAS Catalog is a comprehensive repository of published genome-wide association studies maintained by the National Human Genome Research Institute (NHGRI) and the European Bioinformatics Institute (EBI). The catalog contains curated SNP-trait associations from thousands of GWAS publications, including genetic variants, associated traits and diseases, p-values, effect sizes, and full summary statistics for many studies. ## When to Use This Skill This skill should be used when queries involve: - **Genetic variant associations**: Finding SNPs associated with diseases or traits - **SNP lookups**: Retrieving information about specific genetic variants (rs IDs) - **Trait/disease searches**: Discovering genetic associations for phenotypes - **Gene associations**: Finding variants in or near specific genes - **GWAS summary statistics**: Accessing complete genome-wide association data - **Study metadata**: Retrieving publication and cohort information - **Population genetics**: Exploring ancestry-specific associations - **Polygenic risk scores**: Identifying variants for risk prediction models - **Functional genomics**: Understanding variant effects a
- Overview
- When to Use This Skill
- Core Capabilities
- 1. Understanding GWAS Catalog Data Structure
- 2. Web Interface Searches
- 3. REST API Access
- 4. Query Examples and Patterns
- 5. Working with Summary Statistics
- 6. Data Integration and Cross-referencing
- Query Workflows
- Workflow 1: Exploring Genetic Associations for a Disease
- Workflow 2: Investigating a Specific Genetic Variant
- Workflow 3: Gene-Centric Association Analysis
- Workflow 4: Systematic Review of Genetic Evidence
wget ftp://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/GCSTXXXXXX/harmonised/GCSTXXXXXX-harmonised.tsv.gz
What does the gwas-database skill do?
Query NHGRI-EBI GWAS Catalog for SNP-trait associations. Search variants by rs ID, disease/trait, gene, retrieve p-values and summary statistics, for genetic epidemiology and polygenic risk scores.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill gwas-database --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From FreedomIntelligence/OpenClaw-Medical-Skills, a repository with 2,909 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.