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tooluniverse-pharmacogenomics

Pharmacogenomics (PGx) research — drug-gene interactions (CPIC, PharmGKB), CPIC dosing guidelines, variant-drug-response associations, ethnic-allele-frequency considerations, and metabolizer-status scoring. Use for PGx-informed dosing recommendations, CYP/HLA pharmacogenomic allele interpretation, and clinically-actionable PGx report generation.

Quality

88%

Does it follow best practices?

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SKILL.md
Quality
Evals
Security

Quality

Content

78%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.

The body is highly actionable and well-sequenced: a 7-phase pipeline with concrete tool calls, return-shape documentation, gotchas, fallback strategies, and three worked example workflows covering the main entry points. Its main weaknesses are the fully inlined API catalog in a monolithic single file (no progressive disclosure into reference files) and minor over-explanation of pharmacology concepts Claude already knows.

Suggestions

Split the per-tool parameter/return-shape documentation (Phases 0-5 tool entries) into a references/ file (e.g., references/tool-catalog.md), keeping SKILL.md as a concise workflow overview with per-phase pointers — this would move progressive_disclosure from inline monolith to a well-signaled one-level-deep structure.

Trim the 'Metabolizer Status Reasoning' active-vs-prodrug explanation and the PharmVar paragraph to the non-obvious operational facts (e.g., which tool requires which ID format, the PHARMVAR_API_KEY requirement), cutting restatements of standard pharmacology Claude already knows.

Add explicit verification checkpoints between phases (e.g., after Phase 2, confirm the retrieved guideline's cpiclevel is A/B before proceeding to dosing interpretation) to close the minor workflow_clarity validation gaps.

DimensionReasoningScore

Conciseness

The body is dense with non-obvious operational knowledge (PostgREST auto-normalization, clinpgxid vs pharmgkbid, warfarin's 0-row exception, limit=1000 for FDA queries) and largely avoids explaining general concepts. However, the 'Metabolizer Status Reasoning' active-vs-prodrug explanation and the lengthy PharmVar paragraph restate pharmacology Claude largely knows, and phrases like 'Get it right before interpreting any metabolizer phenotype' are padding — minor over-explanation that could be trimmed, matching the 4 anchor.

4 / 5

Actionability

Every tool is documented with required parameters, return shapes, and concrete values, and the Example Workflows section gives literal copy-paste invocations covering the three common entry points: drug-first ('CPIC_get_recommendations(drug="codeine", limit=50)' → filter phenotypes), gene-first ('CPIC_search_gene_drug_pairs(gene_symbol="CYP2C19", cpiclevel="A")'), and variant-first ('PharmGKB_search_variants(query="rs1799853")'). Specific examples cover the common cases, matching the 5 anchor.

5 / 5

Workflow Clarity

A clear 7-phase pipeline with an ASCII overview diagram, per-phase Gotchas, and an explicit Fallback Strategies section providing error-recovery loops (e.g., 'drug auto-resolve fails → CPIC_get_drug_info + manual guideline_id extraction'). This is a read-only retrieval skill so the destructive/batch validation cap does not apply, but explicit verification checkpoints between phases are absent — a clear sequence with most checkpoints present and minor validation gaps, matching the 4 anchor rather than 5.

4 / 5

Progressive Disclosure

No bundle files exist (references/, scripts/, assets/ are all absent), so the full tool-by-tool API catalog — per-tool parameter schemas, return shapes, and gotchas for ~30 tools across ~280 lines — is inlined in SKILL.md. Section structure itself is good, but content that clearly belongs in a separate reference file is inline with no external split at all, matching the 3 anchor ('some structure but... content that should be separate is inline') rather than the 4 anchor, which requires most content to be appropriately placed across files.

3 / 5

Total

16

/

20

Passed

Description

92%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.

A strong description: it names the domain comprehensively with multiple concrete capabilities, includes an explicit 'Use for...' trigger clause with specific scenarios, and occupies a distinct niche with domain-specific terminology. Voice is third-person imperative throughout, consistent with the good examples. Only minor improvement possible by adding common user synonyms like 'star allele' or 'genotype' to the trigger terms.

DimensionReasoningScore

Specificity

The description lists multiple concrete, comprehensive actions within the PGx niche: 'drug-gene interactions (CPIC, PharmGKB)', 'CPIC dosing guidelines', 'variant-drug-response associations', 'metabolizer-status scoring', 'CYP/HLA pharmacogenomic allele interpretation', and 'clinically-actionable PGx report generation'. Coverage is comprehensive rather than leaving minor gaps, matching the 5 anchor rather than the 4 anchor.

5 / 5

Completeness

It clearly answers 'what' (interaction retrieval, dosing guidelines, variant associations, metabolizer-status scoring) and explicitly answers 'when' with an explicit 'Use for...' clause naming concrete trigger scenarios ('PGx-informed dosing recommendations', 'CYP/HLA pharmacogenomic allele interpretation', 'clinically-actionable PGx report generation'). This matches the 5 anchor; the 'when' is explicit and specific, not merely present.

5 / 5

Trigger Term Quality

Good keyword coverage with natural domain terms users would say ('Pharmacogenomics', 'PGx', 'CPIC', 'PharmGKB', 'dosing recommendations', 'CYP/HLA', 'allele interpretation') plus the full-name/abbreviation synonym pair. A few natural terms are missing (e.g., 'star allele', 'genotype', 'drug response'), so it fits the 4 anchor rather than comprehensive 5 coverage.

4 / 5

Distinctiveness Conflict Risk

A clear niche with distinct triggers: CPIC, PharmGKB, CYP/HLA, PGx, and metabolizer-status terminology would not naturally trigger any other skill. Minimal conflict risk.

5 / 5

Total

19

/

20

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.

Validation — 16 / 16 Passed

Validation for skill structure

No warnings or errors.

Repository

mims-harvard/ToolUniverse

Path

plugin/skills/tooluniverse-pharmacogenomics/SKILL.md

Reviewed

Table of Contents

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