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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.

68

Quality

81%

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SecuritybySnyk

Low

Low-risk findings worth noting

SKILL.md
Quality
Evals
Security

Quality

Content

62%

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

A well-organized, actionable workflow body with a clear phased sequence and error recovery, weakened by repeated quality-criteria prose and placeholder-based code examples. Progressive disclosure is structure-only with no file-level split.

Suggestions

De-duplicate the biological-replicate/metadata quality criteria that appears in both 'Domain Reasoning' and 'Reasoning Framework' into a single canonical statement.

Replace placeholder code (e.g. accession=accession, keywords="[gene/disease]") with concrete, runnable examples or clearly mark the values to substitute.

Move the dense 'Tool Reference' and 'Search Parameters' sections into a reference file referenced from SKILL.md to improve progressive disclosure.

DimensionReasoningScore

Conciseness

Mostly lean and table-driven, but quality criteria ('Prioritize >=3 biological replicates, complete annotations, both raw+processed data') and the RNA-seq/microarray comparison are restated across 'Domain Reasoning' and 'Reasoning Framework', offering tightening room.

2 / 3

Actionability

Provides concrete tool-call signatures, fallback chains, and search parameters, but the code blocks use placeholders (keywords="[gene/disease]", accession=accession) making them templates rather than fully executable copy-paste examples.

2 / 3

Workflow Clarity

Clear Phase 0→1→2→3 sequence with a diagram, an error-handling table supplying recovery feedback loops, and quality tiers plus synthesis questions acting as a checklist for a non-destructive retrieval task.

3 / 3

Progressive Disclosure

Well-sectioned with clear headers, but ~145 lines are entirely inline with no bundle files or reference split; the dense Tool Reference and Search Parameters sections could be separated for cleaner disclosure.

2 / 3

Total

9

/

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, specific description that states concrete capabilities, natural trigger terms, an explicit use-clause, and a distinct niche, all in third-person voice. It cleanly satisfies all four dimensions.

DimensionReasoningScore

Specificity

Lists multiple concrete actions ('Retrieve gene expression and omics datasets', 'gene disambiguation', 'quality assessment', 'comparing across studies', 'assessing dataset suitability') rather than vague language, matching the comprehensive-actions anchor.

3 / 3

Completeness

Explicitly answers both what (retrieve + disambiguate + quality-assess) and when via the 'Use for finding...' trigger clause, an equivalent of 'Use when...', so it is not capped at 2.

3 / 3

Trigger Term Quality

Covers natural user terms a bioinformatician would say — 'RNA-seq/microarray datasets', 'organism/tissue/condition', 'case-control, time-series, dose-response', 'ArrayExpress', 'BioStudies' — with good variation coverage.

3 / 3

Distinctiveness Conflict Risk

Occupies a clear niche — gene-expression/omics retrieval from two named databases — with distinct triggers unlikely to overlap with other skills.

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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