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tooluniverse-metabolomics-pathway

Metabolomics pathway analysis — metabolite identification (HMDB, KEGG, ChEBI), pathway mapping (Reactome, KEGG, MetaCyc), disease associations, enzyme/gene linkage. Use for metabolite-to-pathway-to-disease connections, BridgeDb-based ID conversion, and integrating metabolomics with gene-level pathway analyses.

71

Quality

86%

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SKILL.md
Quality
Evals
Security

Quality

Content

85%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 a dense, well-structured reference of tool calls organized into a clear phased workflow with fallback and evidence-grading sections. It is highly concise and actionable, with only minor gaps in explicit validation checkpoints and runnable code blocks.

Suggestions

Add explicit validation/verification checkpoints between phases (e.g., 'verify metabolite identity resolves to a single structure before proceeding to Phase 1') to strengthen workflow feedback loops.

For batch metabolite-list enrichment, add a concrete code example or explicit validate-fix-retry step since enrichment is a batch operation.

DimensionReasoningScore

Conciseness

Lean reference-style content: tool names with required parameters and short notes, no padding or explanation of concepts Claude already knows; every line earns its place.

5 / 5

Actionability

Provides concrete tool calls with required parameters and examples of valid IDs, but most entries are tool signatures rather than fully copy-paste runnable code blocks; minor gaps in complete invocation syntax.

4 / 5

Workflow Clarity

Clear phased sequence (Phase 0–5 → Report) with per-phase tool lists and a 'Common Mistakes' table, plus fallback strategies; validation checkpoints are implicit (verify identity first) rather than explicit validate-fix-retry loops.

4 / 5

Progressive Disclosure

Well-organized sectioned structure with clear headers and no bundle files; for a self-contained reference skill this is appropriate, though some dense tool tables could theoretically be split into reference files.

4 / 5

Total

17

/

20

Passed

Description

88%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.

The description is specific, complete, and distinctive, explicitly stating both capabilities and use-conditions with named databases. Trigger term coverage is strong but could add a few more natural synonyms.

Suggestions

Add natural user-facing synonyms or phrasings (e.g., 'metabolite ID mapping', 'compound-to-pathway') to broaden trigger-term coverage.

Consider mentioning common file formats or input types users would cite (e.g., metabolite lists, HMDB/KEGG IDs) to strengthen trigger terms.

DimensionReasoningScore

Specificity

Lists multiple concrete actions (metabolite identification, pathway mapping, disease associations, enzyme/gene linkage, BridgeDb ID conversion) across named databases — comprehensive coverage matching the score-5 anchor.

5 / 5

Completeness

Explicitly answers 'what' (identification, mapping, disease, linkage, ID conversion) and 'when' ('Use for metabolite-to-pathway-to-disease connections...'), matching the clear what-and-when anchor.

5 / 5

Trigger Term Quality

Includes natural domain terms (metabolomics, pathway, metabolite, disease, enzyme/gene) and database names, but lacks common synonyms and file-extension-style triggers a user would naturally say.

4 / 5

Distinctiveness Conflict Risk

A clear niche (metabolomics pathway analysis with named DBs and BridgeDb ID conversion) with distinct triggers and minimal overlap risk with other skills.

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.

Validation16 / 16 Passed

Validation for skill structure

No warnings or errors.

Repository
mims-harvard/ToolUniverse
Reviewed

Table of Contents

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