Menú
Compare candidate rsIDs against GWAS Catalog phenotype associations. Use association evidence with source and ancestry limitations.
Instalar con Codex o Claude Copia este prompt, pégalo en Codex, Claude u otro asistente, y deja que revise la página de la skill y la instale por ti.
Basado en la clasificación ocupacional SOC
| 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 |
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.
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.
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.
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.
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.
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.
variant.resolve as context-only follow-up after the GWAS
source ranking is chosen.mapped_genes as source gene-field association
context, not causal-gene evidence.Use this skill for genetics, genome source, variant, gene, phenotype, disease, screen, pharmacogenomics, and Genomi install/setup maintenance questions.
Build and inspect ClinVar exact-match evidence and candidate inventories. Use for clinical labels, VUS/conflict, carrier context, and drug-response rows.
Activate this skill for "/genomi decode", "decode my genome", "decode my DNA", "show me the dashboard", "the Genomi dashboard", "one-shot rundown", or any all-at-once request that asks Genomi to compose every capability's findings into a single artifact. This is the whole-genome dashboard kicker — it sweeps every relevant Genomi capability in one shot, not a per-target lookup. Composes evidence from every relevant Genomi capability into a single self-contained Genomi Dashboard.html and returns localhost serve metadata. Active genome required.
Answer drug-response, medication, PharmGKB-style, PGxDB, ATC, DrugBank, gene-drug, and variant-drug questions using public PGx evidence plus local sample genotype support when an Active Genome Index is selected.
Plan rare disease, hereditary disease, cancer risk, carrier-relevance, and observed-condition source investigation from public targets or selected active genome evidence.
Answer specific rsID, allele, gene, region, genotype, and absence/callability questions using explicit session context or public evidence.