gwas-catalog

name	gwas-catalog
description	Compare candidate rsIDs against GWAS Catalog phenotype associations. Use association evidence with source and ancestry limitations.
tools	["gwas.compare_variant_associations","gwas.compare_gene_associations","phenotype.retrieve_trait_gene_records","variant.resolve","active_genome_index.classify_genotype_support","research.record"]
mutating	true

GWAS Catalog Association Evidence

Use GWAS Catalog association records for supplied phenotypes plus candidate variants or genes.

For phenotype plus candidate genes, gwas.compare_gene_associations returns GWAS Catalog reported_gene, mapped_gene, or source gene-field association evidence. phenotype.retrieve_trait_gene_records retrieves native trait-to-gene records from integrated public sources, optionally filtered by gene. If another source prior is relevant, call that source-specific tool separately and keep the evidence regimes separate. HPO or single-subject phenotype matching belongs outside this skill.

Goal

Retrieve and compare GWAS Catalog association evidence with explicit source-field and phenotype-match limitations. Personal interpretation requires separate sample support and careful wording.

Convention: See skills/conventions/evidence-quality.md.

Cross-Capability Synthesis

A scope-limited result from this capability is not a final user-facing answer when other Genomi capabilities can contribute orthogonal evidence to the same question. Returning "cannot answer" while applicable capabilities remain unexamined is a host-agent failure mode.

Tools

gwas.compare_gene_associations

Compare candidate genes using GWAS Catalog reported_gene and mapped_gene trait-association evidence.

Use when: The user gives a phenotype or trait plus candidate genes and asks for GWAS Catalog gene-field association support.

Why necessary: GWAS Catalog gene fields are source annotations for population-trait associations; they should stay separate from causal-gene, HPO, or drug-target evidence.

Not for: causal-gene claims unless separate causal evidence is supplied.

Result semantics: Returns source-local GWAS Catalog gene-field association evidence only. reported_gene and mapped_gene are source annotations and are not causal-gene evidence. Causal-gene or effector-gene wording returns wrong_evidence_regime with a routing hint.

gwas.compare_variant_associations

Compare candidate rsIDs by population-trait GWAS Catalog association evidence.

Use when: Returns GWAS Catalog population-trait association records for candidate rsIDs, ranked by trait match and p-value.

Why necessary: Population-trait rsID ranking needs GWAS Catalog evidence, not ClinVar or personal genotype evidence.

Not for: clinical disease diagnosis or personal genotype support.

Example prompts: Compare these rsIDs for LDL cholesterol GWAS evidence.

Result semantics: Returns public GWAS association evidence rows ranked by source trait match and p-value. For population-trait lead-variant tasks, GWAS Catalog evidence rows are the ranking source. Personal interpretation uses separate sample genotype evidence tools only after the source-ranked rsID decision.

Boundary

GWAS prioritization answers “which candidate has public association support for this phenotype?” Personal risk interpretation requires sample support, phenotype context, ancestry/source limitations, and careful claim wording.

For phenotype-plus-rsID questions, call gwas.compare_variant_associations directly. If personal context exists, choose follow-up rsIDs from the returned association evidence before checking sample support. Keep ClinVar, Mendelian, sample genotype, same-gene, or pathway context as follow-up context beside the GWAS Catalog population-trait ranking.

For phenotype-plus-gene-list questions, call gwas.compare_gene_associations only when GWAS Catalog reported_gene/mapped_gene/source gene-field association is the intended prior. If a trait-to-gene source record is needed, retrieve native trait-to-gene records with phenotype.retrieve_trait_gene_records. If it returns only association_only_not_causal records, do not answer from those records alone. Call separate source-specific tools when drug-target, curated association, or locus-to-gene evidence also matters; do not collapse those priors into the GWAS Catalog association result. HPO or single-subject phenotype matching belongs to phenotype.compare_gene_hpo_evidence.

For GWAS variant prioritization, exact GWAS Catalog trait matches outrank nearby trait matches. P-value breaks ties inside the same evidence level; ClinVar, Mendelian disease, same-gene, pathway, or sample context does not rerank the population-trait lead-variant result.

Routing Checks

• Present GWAS associations as association evidence.
• Preserve ancestry/source limitations.
• Check whether the selected rsID is present in the Active Genome Index before personal interpretation.
• Preserve which phenotype/query produced the ranking.
• Prefer direct GWAS Catalog records over inferring a winner from prose.
• Treat variant.resolve as context-only follow-up after the GWAS source ranking is chosen.
• Interpret GWAS Catalog mapped_genes as source gene-field association context, not causal-gene evidence.
• If the selected candidate is not direct-source supported, say the result is lower-support adjacent GWAS evidence.