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pyopenms-skill

Comprehensive tool for computational mass spectrometry using PyOpenMS; use when you need to read/write MS formats (mzML/mzXML/MGF), run signal processing (smoothing/peak picking), detect isotope features, or perform peptide identification in proteomics/metabolomics workflows.

62

Quality

74%

Does it follow best practices?

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SecuritybySnyk

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tessl review fix ./scientific-skills/Data Analysis/pyopenms-skill/SKILL.md
SKILL.md
Quality
Evals
Security

Quality

Content

61%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 well-structured with a runnable example and appropriately split one-level-deep references, but it loses points on restated/hedged content, missing validation checkpoints for batch MS processing, and slightly thin referenced files.

Suggestions

Add an explicit validation/verification checkpoint to the workflow (e.g., confirm spectra loaded and peaks detected before declaring success) to lift workflow_clarity above the batch-operation cap of 3.

Trim the 'Implementation Details' restatement of Load->Process->Analyze and replace the hedging comment about run_workflow's return value with the actual return contract (it returns a summary dict).

Convert reference pointers into markdown links and expand references/file_io.md and references/signal_processing.md so the deferred detail is actually substantive.

DimensionReasoningScore

Conciseness

Mostly efficient with clear sections, but the 'Implementation Details' section restates the Load->Process->Analyze pattern already shown in the example, and hedging comments ('The returned object depends on the implementation...', 'exact filters... should be documented in scripts/process_ms.py') add padding that could be trimmed.

3 / 5

Actionability

Provides a concrete runnable example calling run_workflow, an install command, and pointers to a real script and references, but the example hedges on its return value and defers specifics rather than being fully copy-paste ready.

4 / 5

Workflow Clarity

The Load->Process->Analyze sequence is listed, but because the skill explicitly targets batch-processing of MS files, the absence of explicit validation/verification checkpoints (only a FileNotFoundError and a no-spectra warning) caps this at 3 per the batch-operation rule.

3 / 5

Progressive Disclosure

SKILL.md is a concise overview that points to real one-level-deep references (references/file_io.md, references/signal_processing.md) and scripts/process_ms.py with clear signaling; minor gaps are that references are plain-text paths rather than links and the referenced files are thin.

4 / 5

Total

14

/

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.

The description is strong: it states concrete capabilities, includes a clear 'use when' trigger clause with natural domain keywords and file extensions, and occupies a distinctive niche. The only weakness is the slightly generic 'Comprehensive tool' opener and a few missing synonyms.

DimensionReasoningScore

Specificity

Lists several concrete actions ('read/write MS formats (mzML/mzXML/MGF), run signal processing (smoothing/peak picking), detect isotope features, or perform peptide identification'), but the opener 'Comprehensive tool' is mildly generic, leaving minor coverage gaps versus a fully comprehensive list.

4 / 5

Completeness

Explicitly answers both 'what' (a PyOpenMS tool for computational mass spectrometry performing the listed actions) and 'when' ('use when you need to...') with concrete trigger phrases.

5 / 5

Trigger Term Quality

Good keyword coverage including natural terms and file extensions ('mzML/mzXML/MGF', 'proteomics/metabolomics', 'peak picking'), though some common synonyms a user might say (e.g. 'mass spec') are absent.

4 / 5

Distinctiveness Conflict Risk

Occupies a clear niche (computational mass spectrometry via PyOpenMS) with distinctive triggers like mzML/proteomics/metabolomics, giving minimal overlap with other skills.

5 / 5

Total

18

/

20

Passed

Validation

93%

Checks the skill against the spec for correct structure and formatting. All validation checks must pass before discovery and implementation can be scored.

Validation15 / 16 Passed

Validation for skill structure

CriteriaDescriptionResult

frontmatter_unknown_keys

Unknown frontmatter key(s) found; consider removing or moving to metadata

Warning

Total

15

/

16

Passed

Repository
aipoch/medical-research-skills
Reviewed

Table of Contents

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