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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.

Quality

91%

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SKILL.md
Quality
Evals
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Quality

Content

82%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 high-quality, highly actionable instruction skill: exact tool signatures, gotchas, evidence tiers, and a clear three-phase workflow. Weaknesses are mild — duplicated gotcha listings, absent error-recovery loops, and an inline tool catalog that could be split into a reference file.

Suggestions

De-duplicate the parameter gotchas: keep them only in the 'Key Parameter Gotchas' quick-reference section (or only inline in the Phase sections) rather than repeating them in both places.

Add brief error-recovery guidance in the workflow (e.g., if VEP returns {error} or enrichment returns no significant pathways, fall back to STRING/KEGG or relax the FDR threshold) to close the feedback-loop gap.

Move the per-tool parameter catalog (Phase 1–4 'Tool Selection Guide') into a references/tools.md file and keep a condensed tool-index in SKILL.md to improve progressive disclosure.

DimensionReasoningScore

Conciseness

The body is efficient — tool calls, gotchas, and evidence tiers with no padding — but parameter gotchas appear twice (inline in the Phase sections and again in the 'Key Parameter Gotchas' section), which is trimmable duplication. Not below anchor 4 since the domain reasoning (convergence, druggability tiers) is non-obvious guidance rather than over-explanation.

4 / 5

Actionability

Every tool is given with exact parameter names and value formats (e.g., "identifiers='P04637 P38398 ...'" space-separated string, "gwas_get_snps_for_gene(gene_symbol=<gene>)"), plus decision rules like evidence tiers and the ranking formula 'Genetic Evidence x Druggability x Pathway Centrality' — copy-paste-ready guidance covering common cases, matching the 5 anchor.

5 / 5

Workflow Clarity

The three-step workflow is clearly sequenced with prioritization criteria and explicit cross-validation checkpoints ("Cross-check with OpenTargets_target_disease_evidence", "Identify pathways appearing across multiple databases"), but there are no error-recovery feedback loops (e.g., what to do when a tool returns {error} or enrichment returns nothing) — anchor 4 rather than 5.

4 / 5

Progressive Disclosure

The body is well-organized with clear headed sections (reasoning principles, phased tool guide, workflow, gotchas, limitations), and no bundle files exist so nothing is misfiled. Minor gap: ~50 lines of per-tool parameter detail in the 'Tool Selection Guide' could live in a references/ file to keep SKILL.md an overview — good structure (anchor 4) rather than the fully split ideal (anchor 5).

4 / 5

Total

17

/

20

Passed

Description

96%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: specific, third-person, comprehensive trigger terms, and an explicit 'Use for' clause. The only minor weakness is overlap risk with adjacent GWAS/enrichment skills in the same family.

DimensionReasoningScore

Specificity

"Maps GWAS hits to causal genes (via fine-mapping/eQTL), then to pathways (Reactome, KEGG, WikiPathways), then to existing drugs hitting those pathways" lists multiple concrete, chained actions with comprehensive coverage of the skill's capabilities.

5 / 5

Completeness

It explicitly answers both what ("Connect GWAS variants to biological pathways and druggable targets... Maps... 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, and tissue-specific eQTL evidence for drug target hypotheses") with concrete trigger phrases, mirroring the 5-anchor exemplar.

5 / 5

Trigger Term Quality

Natural domain terms are comprehensively covered — GWAS, variants, SNP, pathways, druggable targets, eQTL, fine-mapping, drug target — matching the vocabulary a user of this domain would actually say (e.g., "SNP-to-pathway-to-target tracing", "tissue-specific eQTL evidence").

5 / 5

Distinctiveness Conflict Risk

The GWAS-to-pathway-to-drug-target pipeline is a clear niche with distinct triggers, but the description overlaps with closely related sibling skills (GWAS-to-gene mapping, gene enrichment) referenced in the body — anchor 4 rather than 5.

4 / 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-pathway-disease-genetics/SKILL.md

Reviewed

Table of Contents

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