tooluniverse-phewas

Cross-ancestry / cross-biobank phenome-wide association (PheWAS) and replication. Given ONE variant (rsID) or ONE gene, look up every phenotype it associates with across European/UK (UKB-TOPMed), Finnish (FinnGen), Japanese (BioBank Japan), and Taiwanese (TPMI) biobanks, plus exome-wide gene-burden PheWAS (Genebass), then judge whether an association replicates across ancestries or is population-specific. Use whenever the user asks "what else is this variant/gene associated with", "does this association replicate in other ancestries / biobanks", "is this effect East-Asian-specific", "pleiotropy of rsXXX", "phenome scan", or wants to compare effect sizes/allele frequencies of a variant across populations. NOT for the forward direction (trait → which SNPs: use the gwas-* skills), NOT for fine-mapping a locus (use tooluniverse-gwas-finemapping), and NOT for single-SNP mechanism tracing in one population (use tooluniverse-gwas-snp-interpretation).

Quality

94%

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Passed

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Quality

Content

88%Weight 40%Scale 1-5

Reviews the quality of instructions and guidance provided to agents. Good implementation is clear, handles edge cases, and produces reliable results.

A strong, highly actionable skill body with concrete tool calls, a sequenced workflow, interpretive checkpoints, and a worked example; the only weaknesses are minor narrative padding in the worked example and a dense single-file layout.

Suggestions

Tighten the worked example: drop editorializing like "textbook replicated association" and "a good sanity check that the panel is working" to recover token budget without losing the demonstration.

Consider trimming the opening PheWAS-vs-GWAS definition, which restates a concept Claude already knows, or compressing it to a single clause.

If the interpretation table or worked example grows further, consider splitting them into a reference file referenced one level deep from SKILL.md to keep the overview lean.

Dimension	Reasoning	Score
Conciseness	Mostly efficient and dense with non-obvious domain specifics, but the opening PheWAS-vs-GWAS definition and editorializing in the worked example ("textbook replicated association", "a good sanity check that the panel is working") are minor over-explanation that could be trimmed.	4 / 5
Actionability	Provides copy-paste-ready tool calls with concrete parameters (e.g. UKBTOPMed_phewas_by_variant(rsid="rs7903146", max_pval=5e-8, limit=25), Genebass_gene_burden_phewas(gene="PCSK9", burden_set="pLoF")), a report template, and a fully worked example covering the common cases.	5 / 5
Workflow Clarity	A clear 5-step sequence (decide variant/gene → query in parallel → align phenotypes → judge replication → report) with explicit interpretive checkpoints (check af/num_cases before concluding ancestry-specific, verify ref/alt on opposite beta signs, treat pval:0.0 as underflow) and a checklist-style interpretation table.	5 / 5
Progressive Disclosure	Well-organized into clearly headed sections (biobank panel, workflow, interpretation, report, worked example, limitations) with easy navigation and content appropriately placed in one self-contained file; no external references are needed, though the dense single-file form is a minor organization consideration.	4 / 5
	Total	18 / 20 Passed

Description

100%Weight 40%Scale 1-5

Based on the skill's description, can an agent find and select it at the right time? Clear, specific descriptions lead to better discovery.

An exemplary description: concrete actions, natural trigger phrases, explicit what/when, and sharp boundaries against sibling skills, all in third-person imperative voice with no fluff.

Dimension	Reasoning	Score
Specificity	Lists multiple concrete actions — "look up every phenotype it associates with", "judge whether an association replicates", "compare effect sizes/allele frequencies" — across five named biobanks, matching the comprehensive-coverage anchor.	5 / 5
Completeness	Explicitly answers what (cross-biobank PheWAS lookup + replication judgment) and when ("Use whenever the user asks...") with concrete trigger phrases, satisfying the top anchor.	5 / 5
Trigger Term Quality	Embeds natural user phrases ("what else is this variant/gene associated with", "does this association replicate in other ancestries / biobanks", "is this effect East-Asian-specific", "pleiotropy of rsXXX", "phenome scan") plus synonyms, matching comprehensive natural-term coverage.	5 / 5
Distinctiveness Conflict Risk	Clear niche (cross-biobank PheWAS replication) with explicit NOT-for boundaries naming three competing skills (gwas-*, tooluniverse-gwas-finemapping, tooluniverse-gwas-snp-interpretation), giving minimal conflict risk.	5 / 5
	Total	20 / 20 Passed

Validation

100%

Warnings & errors only

Checks the skill against the spec for correct structure and formatting. All validation checks must pass before discovery and implementation can be scored.

Validation — 16 / 16 Passed

Validation for skill structure

No warnings or errors.

Repository: mims-harvard/ToolUniverse
Path: plugins/tooluniverse/skills/tooluniverse-phewas/SKILL.md
Commit: 1b02920

Reviewed: 1 day ago

Table of Contents

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