geo-database

Access NCBI GEO for gene expression/genomics data. Search/download microarray and RNA-seq datasets (GSE, GSM, GPL), retrieve SOFT/Matrix files, for transcriptomics and expression analysis.

Quality

73%

Does it follow best practices?

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Securityby

Low

Low-risk findings worth noting

Fix and improve this skill with Tessl

tessl review fix ./bundled/skills/geo-database/SKILL.md

Quality

Content

65%

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 executable code and a well-signaled reference file, but it is verbose and monolithic rather than an overview pointing to detail, and it lacks validation checkpoints for its batch/bulk operations.

Suggestions

Trim repeated boilerplate (e.g. the repeated GEOparse.get_GEO setup) and remove concept explanations Claude already knows to reduce token cost.

Move the long analysis/processing examples into references/geo_reference.md so SKILL.md is a concise overview pointing to detail.

Add explicit validation/verification checkpoints to batch-download and differential-expression workflows (e.g. verify file integrity, check sample counts, confirm QC before proceeding).

Dimension	Reasoning	Score
Conciseness	The ~800-line body repeats boilerplate (GEOparse.get_GEO called ~8 times) and explains concepts Claude already knows (what GEO is, basic library purpose); mostly accurate and useful but padded and could be tightened.	2 / 3
Actionability	Provides fully executable Python throughout — GEOparse, Bio.Entrez, ftplib, scipy/statsmodels differential expression — with concrete, copy-paste-ready examples.	3 / 3
Workflow Clarity	Sections are task-organized but lack explicit sequenced workflows with validation checkpoints; batch and bulk-download operations have no verify/validate step, which caps workflow clarity at 2.	2 / 3
Progressive Disclosure	A real one-level reference (references/geo_reference.md) is clearly signaled, but the SKILL.md body itself is a monolithic wall with content that should live in the reference kept inline.	2 / 3
	Total	9 / 12 Passed

Description

82%

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 specific and well-targeted to a clear niche, with strong concrete actions and natural trigger terms. Its main weakness is the absence of an explicit "Use when..." trigger clause, leaving the activation context only implied.

Suggestions

Add an explicit 'Use when...' trigger clause, e.g. 'Use when searching for or downloading gene expression datasets, retrieving GSE/GSM/GPL records, or working with NCBI GEO data.'

Dimension	Reasoning	Score
Specificity	Lists multiple specific concrete actions — "Access NCBI GEO", "Search/download microarray and RNA-seq datasets (GSE, GSM, GPL)", "retrieve SOFT/Matrix files" — rather than vague language.	3 / 3
Completeness	Clearly states what the skill does, but "when" is only implied via "for transcriptomics and expression analysis" with no explicit "Use when..." trigger, which caps completeness at 2.	2 / 3
Trigger Term Quality	Covers natural domain terms users would say: "microarray and RNA-seq datasets", "GSE, GSM, GPL", "SOFT/Matrix files", "transcriptomics and expression analysis".	3 / 3
Distinctiveness Conflict Risk	Highly specific niche (NCBI GEO, GSE/GSM/GPL accessions, SOFT/Matrix formats) with distinct triggers unlikely to conflict with other skills.	3 / 3
	Total	11 / 12 Passed

Validation

87%

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 — 14 / 16 Passed

Validation for skill structure

Criteria	Description	Result
skill_md_line_count	SKILL.md is long (813 lines); consider splitting into references/ and linking	Warning
metadata_version	'metadata.version' is missing	Warning

	Total	14 / 16 Passed

Repository: foryourhealth111-pixel/Vibe-Skills
Path: bundled/skills/geo-database/SKILL.md
Commit: f627ab5

Reviewed: about 9 hours ago

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