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tooluniverse-gwas-trait-to-gene

Discover causal genes for diseases/traits from GWAS data using Open Targets L2G (locus-to-gene) scoring — integrates eQTL, chromatin interaction, and distance evidence. Use for trait-to-gene mapping, drug-target hypothesis generation from GWAS, and replacing the 'nearest gene' heuristic with multi-evidence L2G scores.

68

Quality

82%

Does it follow best practices?

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SecuritybySnyk

Low

Low-risk findings worth noting

SKILL.md
Quality
Evals
Security

Quality

Content

65%

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

Highly actionable content with concrete tools, executable code, and a clear output schema, but it is verbose for a context-loaded skill: it re-explains basic genetics concepts and keeps a large monolithic body instead of offloading detail to bundle files. The workflow is sequenced but lacks validation checkpoints.

Suggestions

Trim or remove sections that restate knowledge Claude already has (genome-wide significance threshold, linkage disequilibrium, 'association ≠ causation') to reclaim context tokens.

Move the full tool catalog, programmatic-access code blocks, and citation list into separate reference files and link to them one level deep, keeping SKILL.md as an overview.

Tighten the workflow into concrete, ordered commands with an explicit verification step (e.g., confirm significant SNP count and L2G scores before ranking genes).

DimensionReasoningScore

Conciseness

Mostly efficient and skill-specific (tool lists, broken-tool flags, parameter renames), but spends tokens explaining concepts Claude already knows — the genome-wide significance threshold, linkage disequilibrium, and 'association ≠ causation' are restated across the intro, Key Concepts, and Best Practices sections.

2 / 3

Actionability

Provides named tools with exact parameters, copy-paste-ready Python (requests/pandas bulk download), a concrete output schema, and worked example results — fully executable guidance.

3 / 3

Workflow Clarity

A 5-step workflow is present and sequenced, but the steps are conceptual ('Evidence Ranking → Score by p-value, replication, fine-mapping') with no explicit validation checkpoints or feedback loops; it reads as a high-level flow rather than a checklist.

2 / 3

Progressive Disclosure

Sections are well-labeled, but no bundle files exist and the ~300-line body is monolithic — the full tool catalog, programmatic-access code, and citations are inlined where separate reference files would reduce token load.

2 / 3

Total

9

/

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 strong, third-person description that clearly states capabilities, integrates specific evidence types, and provides an explicit 'Use for' trigger covering several natural use cases. It is specific, complete, and distinct with no over-claims.

DimensionReasoningScore

Specificity

Lists multiple concrete actions — 'Discover causal genes', 'integrates eQTL, chromatin interaction, and distance evidence', 'replacing the nearest gene heuristic with multi-evidence L2G scores' — rather than vague language.

3 / 3

Completeness

Explicitly states what it does ('Discover causal genes... using Open Targets L2G scoring') and when to use it via the 'Use for...' clause covering three trigger scenarios.

3 / 3

Trigger Term Quality

Covers natural domain terms a user would say — 'trait-to-gene mapping', 'drug-target hypothesis generation from GWAS', 'GWAS data' — alongside the domain shorthand, giving good coverage.

3 / 3

Distinctiveness Conflict Risk

Occupies a clear niche (GWAS trait-to-gene via Open Targets L2G) with distinct triggers unlikely to fire for unrelated skills.

3 / 3

Total

12

/

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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