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tooluniverse-protein-modification-analysis

Post-translational modification (PTM) analysis — phosphorylation, ubiquitination, acetylation, glycosylation, methylation. Uses iPTMnet (sites + enzymes), ProtVar (functional consequences), UniProt (baseline), STRING, ELM (linear motifs), MassIVE/ProteomeXchange (experimental). Use for PTM site annotation, kinase-substrate identification, and PTM-disease associations.

68

Quality

81%

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SKILL.md
Quality
Evals
Security

Quality

Content

75%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 well-structured, actionable skill body with a clear phased workflow, concrete tool calls, and useful grading/fallback tables. Adding explicit validation checkpoints and trimming minor redundancy would push it higher.

Suggestions

Add explicit validation/verification checkpoints between phases (e.g., confirm UniProt accession resolved before proceeding to Phase 1) to strengthen workflow_clarity.

Tighten redundant framing — "LOOK UP DON'T GUESS", "COMPUTE, DON'T DESCRIBE", and "KEY PRINCIPLES" overlap; consolidate to reduce token use.

Provide one complete end-to-end runnable Python example that chains ToolUniverse retrieval with pandas/scipy analysis to lift actionability toward copy-paste readiness.

DimensionReasoningScore

Conciseness

Lean, table-driven body that assumes Claude's competence and avoids explaining basic PTM concepts; a few section headings and the brief "Domain Reasoning" could be trimmed but overall efficient.

4 / 5

Actionability

Concrete tool invocations with parameters (e.g. `iPTMnet_get_ptm_sites(operation="get_ptm_sites", uniprot_id="P04637")`) and a parameter reference table give mostly executable guidance, with minor gaps in full end-to-end runnable examples.

4 / 5

Workflow Clarity

Clear Phase 0–5 sequence with an evidence-grading scheme and fallbacks, but lacks explicit validate-then-proceed feedback loops; this is analysis (not destructive/batch), so the destructive cap does not apply.

4 / 5

Progressive Disclosure

Single self-contained file with well-organized sections and no nested external references; no bundle files exist, so it scores on structure alone, which is good but not the exemplar of one-level-deep external references.

4 / 5

Total

16

/

20

Passed

Description

87%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 in third person that clearly states both capability and use-case triggers with concrete domain terms. Minor room only for broader action/synonym coverage.

DimensionReasoningScore

Specificity

Names the PTM domain and several concrete actions ("PTM site annotation, kinase-substrate identification, and PTM-disease associations") plus specific tools, but coverage of actions is slightly less exhaustive than the 5-anchor.

4 / 5

Completeness

Explicitly answers "what" (PTM analysis with named tools and modification types) and "when" ("Use for PTM site annotation, kinase-substrate identification, and PTM-disease associations") with concrete trigger phrases.

5 / 5

Trigger Term Quality

Strong natural keyword coverage (phosphorylation, ubiquitination, kinase-substrate, PTM) that specialists would actually say, missing only a few common synonyms/variations for a perfect score.

4 / 5

Distinctiveness Conflict Risk

Clear niche (PTM analysis) with distinct, specialized triggers unlikely to fire for unrelated skills; minimal conflict risk.

5 / 5

Total

18

/

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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