tooluniverse-expression-data-retrieval

Retrieves gene expression and omics datasets from ArrayExpress and BioStudies with gene disambiguation, experiment quality assessment, and structured reports. Creates comprehensive dataset profiles with metadata, sample information, and download links. Use when users need expression data, omics datasets, or mention ArrayExpress (E-MTAB, E-GEOD) or BioStudies (S-BSST) accessions.

Quality

88%

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Securityby

Low

Low-risk findings worth noting

Quality

Content

77%

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

The body is highly actionable with a clear phased workflow, checklists, and error-handling feedback, but it is lengthy for a single file and lacks progressive disclosure via separate reference files.

Suggestions

Move the full report output template and the Tool Reference / Search Parameters tables into a separate reference file (e.g. REPORT_TEMPLATE.md) and link to it from the main body to improve progressive disclosure.

Trim duplication between the inline code examples and the Tool Reference / Search Parameters tables to reduce token usage.

Consider extracting the Data Quality Tiers and Completeness Checklist into a reference document, keeping the main SKILL.md focused on the workflow overview.

Dimension	Reasoning	Score
Conciseness	The body is mostly efficient and free of basic-concept filler, but the ~110-line report template and the separate Tool Reference / Search Parameters tables duplicate information already shown in the code examples and could be tightened.	2 / 3
Actionability	Provides fully executable tool calls with real method names and parameters, plus fallback chains, error-handling tables, parameter references, and worked use-case examples that are copy-paste ready.	3 / 3
Workflow Clarity	A clear Phase 0–3 sequence with an overview diagram, plus feedback loops (error-handling table with retry/broaden-keyword guidance) and checklists (gene disambiguation, completeness) for the multi-step retrieval-and-report process.	3 / 3
Progressive Disclosure	No bundle files exist and the skill is a single monolithic ~385-line file; content that could be split out (the large output template, tool/parameter reference tables) is inline rather than referenced one level deep.	2 / 3
	Total	10 / 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.

The description is concise, specific, and uses third-person voice while clearly stating capabilities and explicit trigger conditions. It names concrete tools and accession patterns that make it highly distinguishable.

Dimension	Reasoning	Score
Specificity	Lists multiple concrete actions: 'Retrieves gene expression and omics datasets', 'gene disambiguation, experiment quality assessment, and structured reports', and 'Creates comprehensive dataset profiles with metadata, sample information, and download links'.	3 / 3
Completeness	Explicitly answers both what (retrieve/profile datasets with disambiguation and quality assessment) and when via a clear 'Use when users need...' clause with concrete trigger conditions.	3 / 3
Trigger Term Quality	Covers natural user terms including 'expression data', 'omics datasets', and accession patterns users would cite ('ArrayExpress (E-MTAB, E-GEOD)', 'BioStudies (S-BSST) accessions').	3 / 3
Distinctiveness Conflict Risk	Occupies a clear niche (ArrayExpress/BioStudies expression retrieval) with distinctive accession-based triggers unlikely to fire for unrelated skills.	3 / 3
	Total	12 / 12 Passed

Validation

93%

Warnings & errors only

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

Validation — 15 / 16 Passed

Validation for skill structure

Criteria	Description	Result
relative_links	Relative link issues: 2 missing	Warning

	Total	15 / 16 Passed

Repository: wu-yc/LabClaw
Path: skills/bio/tooluniverse-expression-data-retrieval/SKILL.md
Commit: df37802

Reviewed: 2 days ago

Table of Contents

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