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tooluniverse-pathway-disease-genetics

Connect GWAS variants to biological pathways and druggable targets. Maps GWAS hits to causal genes (via fine-mapping/eQTL), then to pathways (Reactome, KEGG, WikiPathways), then to existing drugs hitting those pathways. Use for pathway-level disease mechanisms, druggable-pathway prioritization from GWAS, SNP-to-pathway-to-target tracing, and tissue-specific eQTL evidence for drug target hypotheses.

72

Quality

88%

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SKILL.md
Quality
Evals
Security

Quality

Content

77%

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 with concrete tool signatures, exact parameter gotchas, and a clearly sequenced three-step workflow backed by cross-database validation and evidence tiers. Its main weaknesses are some prose reasoning that could be tightened for conciseness and a monolithic single-file structure with no progressive disclosure to external reference files.

Suggestions

Tighten the 'Core Reasoning Principles' section: convert the TCF7L2 and NF-kB worked prose into terse bullet guidance to cut tokens while keeping the reasoning intent.

Externalize the detailed 'Tool Selection Guide' parameter reference into a references/ file (e.g. TOOL_REFERENCE.md) and keep SKILL.md as an overview pointing to it, adding one-level-deep progressive disclosure.

Add explicit error-recovery feedback loops for common tool failures (e.g., 'if GTEx eQTL returns empty, fall back to GTEx_get_expression_summary across tissues') to harden the workflow checkpoints.

DimensionReasoningScore

Conciseness

The body is mostly efficient and focused on ToolUniverse-specific knowledge Claude lacks (tool signatures, parameter gotchas), but the 'Core Reasoning Principles' section carries illustrative prose ('TCF7L2 is the strongest T2D GWAS gene. It participates in the Wnt signaling pathway...') that could be tightened. It is not score 3 because some explanatory worked examples pad the token budget; it is not score 1 because it avoids explaining basic concepts Claude already knows (no 'what is a pathway/SNP').

2 / 3

Actionability

Concrete tool invocations with exact parameter names and values are given throughout, e.g. `gwas_get_variants_for_trait(trait=<trait>, p_value_threshold=5e-8)` and `ReactomeAnalysis_pathway_enrichment(identifiers="P04637 P38398 ...")`, plus a 'COMPUTE, DON'T DESCRIBE' directive to run Python. The per-tool gotchas make the calls actually executable correctly, satisfying copy-paste-ready concrete guidance rather than the pseudocode/vague score-2 case.

3 / 3

Workflow Clarity

A clearly sequenced Three-Step Workflow (GWAS→causal gene; gene set→pathway enrichment; pathway→drug target) with explicit validation checkpoints: multi-database convergence ('pathways appearing across multiple databases = stronger evidence'), High/Medium/Low evidence tiers as a checklist, and 'Cross-reference pathway genes with GWAS genes: overlap = top candidate.' It is not score 2 because checkpoints are explicit rather than implicit; the destructive/batch feedback-loop cap does not apply to this analytical retrieval workflow.

3 / 3

Progressive Disclosure

The body is well-organized into clear sections (When to Use, Core Reasoning Principles, Tool Selection Guide, Three-Step Workflow, Key Parameter Gotchas, Limitations), but it is a monolithic single SKILL.md with no bundle files (no references/, scripts/, assets/) and substantial reference-style content (full tool parameter listings) kept inline. It is not score 1 because sectioning and header navigation are good; it is not score 3 because there is no one-level-deep file split and API-reference-style detail is not externalized.

2 / 3

Total

10

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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.

The description is specific, third-person, and explicitly pairs concrete multi-step capabilities with a 'Use for' trigger clause covering natural domain terms. It clearly answers both what the skill does and when to invoke it, with a distinct niche that minimizes conflict risk.

DimensionReasoningScore

Specificity

Lists multiple concrete actions chained end-to-end: 'Connect GWAS variants to biological pathways and druggable targets. Maps GWAS hits to causal genes (via fine-mapping/eQTL), then to pathways (Reactome, KEGG, WikiPathways), then to existing drugs hitting those pathways.' This matches the score-3 anchor of listing several specific concrete actions; it is not the score-2 level because the actions are comprehensive and named with concrete data sources rather than a single partial capability.

3 / 3

Completeness

Explicitly answers both what ('Connect GWAS variants ... Maps GWAS hits to causal genes ... then to pathways ... then to existing drugs') and when ('Use for pathway-level disease mechanisms, druggable-pathway prioritization from GWAS, SNP-to-pathway-to-target tracing ...'). The explicit 'Use for' trigger clause satisfies the score-3 requirement and avoids the score-2 cap where 'when' is only implied.

3 / 3

Trigger Term Quality

The 'Use for' clause surfaces natural domain terms a genomics user would actually say — 'pathway-level disease mechanisms', 'druggable-pathway prioritization from GWAS', 'SNP-to-pathway-to-target tracing', 'tissue-specific eQTL evidence for drug target hypotheses' — alongside concrete keywords GWAS, eQTL, pathways, drug targets. Good coverage of natural terms rather than the sparse single-keyword score-2 case.

3 / 3

Distinctiveness Conflict Risk

A highly specific niche — GWAS → causal genes → pathways → druggable targets via named databases — with distinct triggers unlikely to fire for unrelated skills. It is far from the generic score-1/score-2 examples ('Works with document files') and forms a clear, non-overlapping niche.

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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