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tooluniverse-expression-data-retrieval

Retrieve gene expression and omics datasets from ArrayExpress and BioStudies with gene disambiguation and quality assessment. Use for finding RNA-seq/microarray datasets by organism/tissue/condition, comparing across studies (case-control, time-series, dose-response), and assessing dataset suitability before downloading. Always uses English search terms.

72

Quality

87%

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SecuritybySnyk

Low

Low-risk findings worth noting

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, largely actionable skill body with clear phased workflow, fallback handling, and a quality-assessment checkpoint. Main weaknesses are mild over-explanation of known concepts and reference material that could be offloaded to separate files.

Suggestions

Trim 'Domain Reasoning' and 'Reasoning Framework' to decision criteria only, dropping general knowledge Claude already has (e.g., RNA-seq dynamic range, batch correction need).

Make code examples more copy-paste ready by replacing '[gene/disease]' placeholders with concrete example values or clearly typed parameter descriptions.

Consider moving the Tool Reference and Search Parameters sections into a references/ file to improve progressive disclosure and keep SKILL.md a lean overview.

DimensionReasoningScore

Conciseness

Mostly efficient action-oriented tables and code, but 'Domain Reasoning' and 'Reasoning Framework' restate known concepts (RNA-seq dynamic range, batch correction) that could be trimmed.

4 / 5

Actionability

Concrete tool calls with parameters, a full Tool Reference, fallback chains, and an error table give mostly executable guidance; template placeholders like '[gene/disease]' and 'accession=accession' stop just short of copy-paste readiness.

4 / 5

Workflow Clarity

Clear Phase 0→3 sequence with an explicit clarify/skip gate, fallback chains, and quality tiers as an assessment checkpoint; a few validation steps are implicit rather than spelled out.

4 / 5

Progressive Disclosure

Well-organized section headers and no nested references, but at ~145 lines with reference material (Tool Reference, Search Parameters, Data Quality Tiers) inlined and no separate bundle files, some content could be split out.

4 / 5

Total

16

/

20

Passed

Description

100%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, third-person description that concretely states both capabilities and explicit use-when triggers with domain-natural keywords. It is distinguishable, complete, and free of vague fluff or over-claims.

DimensionReasoningScore

Specificity

Lists multiple concrete actions — 'Retrieve gene expression and omics datasets', 'gene disambiguation', 'quality assessment', 'comparing across studies', 'assessing dataset suitability' — giving comprehensive coverage of capabilities.

5 / 5

Completeness

Explicitly answers 'what' (retrieve datasets with disambiguation and QA from named databases) and 'when' via a concrete 'Use for finding…comparing…assessing…before downloading' trigger clause.

5 / 5

Trigger Term Quality

Comprehensive natural researcher terms including synonyms — 'gene expression', 'RNA-seq/microarray', 'organism/tissue/condition', 'case-control', 'time-series', 'dose-response' — phrases users would naturally say.

5 / 5

Distinctiveness Conflict Risk

Clear niche (gene expression/omics retrieval) anchored to specific databases (ArrayExpress, BioStudies) with distinct trigger phrases, minimizing overlap with other skills.

5 / 5

Total

20

/

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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