tooluniverse-polygenic-risk-score

Build and interpret polygenic risk scores (PRS) for complex diseases using GWAS summary statistics. Covers PRS construction (clumping/thresholding, PRS-CS), validation in independent cohorts, ancestry-aware adjustment, and clinical interpretation (population-relative risk, not absolute prediction). Use for PRS-based risk stratification.

Quality

70%

Does it follow best practices?

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Securityby

Low

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tessl review fix ./plugin/skills/tooluniverse-polygenic-risk-score/SKILL.md

Quality

Content

57%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 knowledgeable, well-structured skill body with concrete tools and a clear workflow, weakened by over-explanation of basic genomics concepts, missing validation checkpoints in a batch workflow, and a monolithic structure with no progressive disclosure to reference files.

Suggestions

Cut or externalize the 'Key Concepts' section — Claude already knows GWAS, beta/OR, LD, and population stratification; keep only the skill-specific guidance such as the ancestry transferability numbers and 'LOOK UP DON'T GUESS' directive.

Add an explicit validation/verification checkpoint to the workflow (e.g., sanity-check SNP count and effect-size distribution against a PGS Catalog model, and re-query if the association set is unexpectedly small) to satisfy the batch-operation feedback-loop requirement.

Split detailed reference material (Data Sources tool catalog, Applications, Limitations) into one-level-deep files like DATA_SOURCES.md and LIMITATIONS.md, leaving SKILL.md a concise overview that links out with clearly signaled references.

Dimension	Reasoning	Score
Conciseness	Mostly efficient with valuable skill-specific material (tool names, QC thresholds, ancestry caveats), but the 'Key Concepts' section extensively explains genomics concepts Claude already knows (GWAS study design, beta/OR basics, LD, population stratification) and could be trimmed.	3 / 5
Actionability	Provides mostly concrete, executable guidance — named ToolUniverse tools with parameters, the PRS/z-score formulas, QC filters, and percentile risk categories — with the minor gap that the workflow's headline functions (build_polygenic_risk_score, calculate_personal_prs) are not listed among the documented tools.	4 / 5
Workflow Clarity	A clear six-step sequence is present, but validation/verification checkpoints are missing; because PRS construction is a batch operation over many variants, the rubric caps workflow clarity at 3 absent explicit validate-fix-retry feedback loops.	3 / 5
Progressive Disclosure	Well-organized with clear section headers, but it is a 282-line monolithic file with no external references; conceptual exposition (Key Concepts) and detailed Applications/Limitations sections are inlined that could be split into one-level-deep reference files.	3 / 5
	Total	13 / 20 Passed

Description

83%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, specific description that clearly conveys a distinct genomics niche and concrete capabilities with an explicit 'Use for' trigger. Its main weakness is a narrow trigger clause that omits natural user synonyms like 'genetic risk' or 'genetic predisposition'.

Dimension	Reasoning	Score
Specificity	Lists multiple specific concrete actions with comprehensive coverage — 'Build and interpret polygenic risk scores (PRS)', 'PRS construction (clumping/thresholding, PRS-CS)', 'validation in independent cohorts', 'ancestry-aware adjustment', and 'clinical interpretation (population-relative risk, not absolute prediction)'.	5 / 5
Completeness	Clearly answers 'what' (build/interpret PRS with enumerated sub-tasks) and includes an explicit 'Use for PRS-based risk stratification' trigger clause, but the 'when' is a single narrow phrase and could be more explicit with concrete user trigger phrasings.	4 / 5
Trigger Term Quality	Good keyword coverage with 'polygenic risk scores (PRS)', 'GWAS summary statistics', and 'PRS-based risk stratification', but missing natural lay synonyms a user might say such as 'genetic risk', 'genetic predisposition', or 'genetic risk score'.	4 / 5
Distinctiveness Conflict Risk	Occupies a clear, highly specialized niche (polygenic risk scores from GWAS summary statistics) with distinct triggers, making conflict with other skills minimal.	5 / 5
	Total	18 / 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: plugin/skills/tooluniverse-polygenic-risk-score/SKILL.md
Commit: 1b02920

Reviewed: 1 day ago

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