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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), and the EBI Proteins API (mutagenesis, MS-proteomics/HPP peptide evidence, antigenic regions, genomic coordinates, protein-level variant lookup by accession/dbSNP/HGVS) as a cross-validation source. Use for PTM site annotation, kinase-substrate identification, and PTM-disease associations.

Quality

89%

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SecuritybySnyk

Passed

No findings from the security scan

The canonical home for this skill is tooluniverse-protein-modification-analysis in mims-harvard/ToolUniverse

SKILL.md
Quality
Evals
Security

Quality

Content

78%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 highly actionable, evidence-graded workflow with concrete tool invocations, real fallbacks, and valuable verified-live operational status. Its weaknesses are inlined API-reference content that should live in a separate file, some repetition around the broken rna_editing endpoint, and an undefined final synthesis phase.

Suggestions

Move the Phase 4d EBI Proteins tool tables and the Tool Parameter Reference rows for those tools into a references/ file (e.g. references/ebi-proteins.md), keeping a one-line-per-tool summary with when-to-use guidance in SKILL.md.

State the EBIProteins_get_rna_editing 404 finding once (e.g. under Limitations) instead of three times across Phase 4d, the Fallbacks table, and Limitations.

Define Phase 5: specify what the synthesis report must contain (e.g. evidence-tiered site table, enzyme assignments, PTM-disease links, explicit gaps such as unavailable proteoform data).

DimensionReasoningScore

Conciseness

The body is dense with non-obvious operational detail (verified outages, tool parameters, fallbacks) and assumes Claude's competence, but the EBIProteins_get_rna_editing 404 note is repeated three times (Phase 4d, Fallbacks, Limitations) and the Phase 4d prose (byte-for-byte shortcut comparison, insulin example) could be tightened.

4 / 5

Actionability

Every phase gives copy-paste-ready tool calls with real parameters and a consistent running example (e.g. iPTMnet_get_ptm_sites(operation="get_ptm_sites", uniprot_id="P04637"), plus an explicit 'write and run Python' directive for computation.

5 / 5

Workflow Clarity

Phases 0-5 are clearly sequenced with per-phase fallbacks and an explicit error-recovery checkpoint ('Try one call; if it is a 503, use the fallbacks'), but Phase 5 'Synthesis & Report' has no content and cross-phase validation of findings is implicit.

4 / 5

Progressive Disclosure

No bundle files exist and the body is well-sectioned, but the ~40-line EBI Proteins tool catalog in Phase 4d and the full Tool Parameter Reference are API-reference material inlined in SKILL.md that belongs in a separate references file.

3 / 5

Total

16

/

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: concrete, third-person, comprehensive on PTM types and tools, with an explicit 'Use for' trigger clause. The only weakness is that the variant-lookup and genomic-coordinate capabilities broaden it toward a neighboring variant-analysis skill.

Suggestions

Scope the variant-lookup mention to its PTM use case (e.g. 'protein-level variant context at PTM sites by accession/dbSNP/HGVS') so the description does not compete with a dedicated variant-analysis skill.

DimensionReasoningScore

Specificity

It lists multiple concrete actions ('PTM site annotation, kinase-substrate identification, and PTM-disease associations') plus all five major modification types and seven named data sources, giving comprehensive coverage in third-person voice.

5 / 5

Completeness

It explicitly answers both questions: what ('Post-translational modification (PTM) analysis' with named tools and cross-validation role) and when ('Use for PTM site annotation, kinase-substrate identification, and PTM-disease associations').

5 / 5

Trigger Term Quality

It covers the natural terms users would say — 'phosphorylation, ubiquitination, acetylation, glycosylation, methylation', 'PTM', 'post-translational modification', 'kinase-substrate' — including synonyms for the domain.

5 / 5

Distinctiveness Conflict Risk

The PTM niche is clear and distinct, but 'protein-level variant lookup by accession/dbSNP/HGVS' and genomic-coordinate mapping bleed into variant-analysis territory that a sibling skill already covers, creating minor overlap risk.

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

plugins/tooluniverse/skills/tooluniverse-protein-modification-analysis/SKILL.md

Revision

37bb81a

Reviewed

Table of Contents

DiscoveryImplementationValidation

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