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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).

80

Quality

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SKILL.md
Quality
Evals
Security

Quality

Content

100%

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

A tightly written, highly actionable skill body: concrete tool calls, a sequenced workflow with explicit verification checkpoints, and dense domain-specific caveats Claude could not derive itself. Organization into labeled sections is clear with no reference indirection.

DimensionReasoningScore

Conciseness

The body is dense with non-obvious operational knowledge Claude would not know (FinnGen's rsID exception, GRCh37/GRCh38 build handling, pval:0.0 underflow, BBJ meta-analysis double-counting) and does not pad with basic explanations; nearly every token earns its place, fitting the level-3 lean-and-efficient anchor.

3 / 3

Actionability

Provides copy-paste-ready calls with real tool names and parameters (e.g. UKBTOPMed_phewas_by_variant(rsid="rs7903146", max_pval=5e-8, limit=25), exact "10:112998590:C:T" coordinate format, burden_set="pLoF") plus a concrete report template, matching the level-3 executable-guidance anchor.

3 / 3

Workflow Clarity

A clear 5-step sequence (decide variant/gene → parallel query → align phenotypes → judge replication → report) with explicit verification checkpoints — check af/num_cases before calling biology, verify ref/alt allele on opposite beta signs — matching the level-3 anchor for explicit validation steps.

3 / 3

Progressive Disclosure

No bundle files exist, but the single SKILL.md is well-organized into clearly signaled sections (biobank panel table, workflow, interpretation table, report structure, worked example, limitations) with no nested-reference indirection, satisfying the guideline that skills with no external references can score 3 with well-organized sections.

3 / 3

Total

12

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12

Passed

Description

100%

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

A high-quality description: concrete capabilities, natural quoted trigger phrases, explicit when-to-use guidance, and clear negative boundaries that separate it from neighboring GWAS skills. It uses third-person voice throughout with no fluff.

DimensionReasoningScore

Specificity

Names multiple concrete actions — "look up every phenotype it associates with across [four named biobanks]", "plus exome-wide gene-burden PheWAS (Genebass)", "then judge whether an association replicates across ancestries or is population-specific" — matching the level-3 anchor for multiple specific concrete actions.

3 / 3

Completeness

Explicitly answers both what (cross-biobank PheWAS + replication judgment) and when via a clear "Use whenever the user asks..." clause with multiple triggers, satisfying the level-3 requirement for both what AND when; it is not the level-2 case where 'when' is only implied.

3 / 3

Trigger Term Quality

Quoted natural user phrasings — "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" — give good coverage of terms a user would actually say, beyond level 2's partial coverage.

3 / 3

Distinctiveness Conflict Risk

A clear niche (variant/gene → cross-ancestry phenome scan) plus explicit "NOT for... use the gwas-* skills / tooluniverse-gwas-finemapping / tooluniverse-gwas-snp-interpretation" boundaries make it unlikely to trigger for the wrong skill.

3 / 3

Total

12

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12

Passed

Validation

100%

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

Validation16 / 16 Passed

Validation for skill structure

No warnings or errors.

Repository
mims-harvard/ToolUniverse
Reviewed

Table of Contents

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