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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.

77

Quality

96%

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SecuritybySnyk

Passed

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SKILL.md
Quality
Evals
Security

Quality

Content

92%

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

A concise, highly actionable orchestration skill with a clear phased workflow and built-in quality tiers. Its main gap is progressive disclosure: everything lives inline in one file with no reference structure for the sizable tool/evidence detail.

Suggestions

Move the Tool Parameter Reference and Evidence Grading tables into a short REFERENCE.md and link to it from the body so the main SKILL.md stays a lean overview.

Add one concrete Python example under "COMPUTE, DON'T DESCRIBE" (e.g. grouping PTM sites by modification type with pandas) to back the directive with executable guidance.

Add an explicit validate-and-retry note for the compute step (e.g. re-query iPTMnet if a UniProt accession returns empty) to make the workflow's error-recovery loop explicit.

DimensionReasoningScore

Conciseness

Lean bullet/table format with no padding or explanations of concepts Claude already knows; directives like "LOOK UP DON'T GUESS" and "COMPUTE, DON'T DESCRIBE" assume competence and every token earns its place.

3 / 3

Actionability

Concrete, copy-paste-ready tool calls with real parameters (e.g. `iPTMnet_get_ptm_sites(operation="get_ptm_sites", uniprot_id="P04637")`) plus a Tool Parameter Reference table and fallback matrix.

3 / 3

Workflow Clarity

Clearly sequenced Phase 0→5 pipeline with a disambiguation checkpoint in Phase 0 ("Select human entry if multiple hits") and a tiered Evidence Grading table that functions as a quality checklist for synthesis.

3 / 3

Progressive Disclosure

Content is well-organized into labeled sections but the skill is a single monolithic file over 50 lines with no external references or one-level-deep navigation to split out the tool catalog or evidence-grading detail.

2 / 3

Total

11

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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.

A strong, third-person description that names concrete actions, data sources, and natural trigger terms with an explicit "Use for" clause. It answers both what and when without verbosity or over-claiming.

DimensionReasoningScore

Specificity

Names the PTM types ("phosphorylation, ubiquitination, acetylation, glycosylation, methylation") and concrete actions ("PTM site annotation, kinase-substrate identification, and PTM-disease associations"), plus the specific data sources used for each.

3 / 3

Completeness

Explicitly answers what it does (PTM analysis across named sources) and when to use it via the "Use for PTM site annotation, kinase-substrate identification, and PTM-disease associations" trigger clause.

3 / 3

Trigger Term Quality

Uses natural domain terms a user would actually say ("phosphorylation", "kinase-substrate", "PTM-disease associations", individual modification names) rather than opaque jargon.

3 / 3

Distinctiveness Conflict Risk

The PTM-analysis niche with these specific triggers (kinase-substrate, PTM-disease) is clearly distinguishable from other bioinformatics skills and unlikely to fire for the wrong skill.

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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