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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.

57

Quality

72%

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SecuritybySnyk

Low

Low-risk findings worth noting

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tessl review fix ./backend/cli/skills/databases/geo-database/SKILL.md
SKILL.md
Quality
Evals
Security

Quality

Content

65%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.

Highly actionable content with comprehensive, executable code for searching, downloading, and analyzing GEO data, undermined by verbosity and a monolithic structure that duplicates material already in the reference file. Batch workflows lack validation checkpoints, capping workflow clarity at 3. Moving detail into the existing reference and adding explicit verification steps would raise most dimensions.

Suggestions

Trim concept-explaining sections (Key Concepts, GEO2R, Common Use Cases) and time-sensitive counts, or move them to references/geo_reference.md.

Push the detailed E-utilities parameter-level and FTP material into the reference, keeping SKILL.md as a quick-start overview with one example per capability.

Add explicit validation checkpoints to the batch workflows (e.g., verify downloaded file size/format, retry on failure, confirm sample counts match metadata) so batch operations satisfy the workflow-clarity feedback-loop requirement.

DimensionReasoningScore

Conciseness

The bulk is domain-specific, executable code, but padded sections remain: "Key Concepts" defines SOFT/MINiML/MIAME, "Common Use Cases" and "GEO2R Web Tool" are generic prose, and time-sensitive counts ("264,928+ series", "2024[Publication Date]") are not isolated in a deprecated section. Mostly efficient with clear trim candidates, so above anchor 2 but below anchor 4.

3 / 5

Actionability

Every section gives copy-paste-ready, complete functions: Entrez esearch/esummary/efetch workflows, GEOparse get_GEO/pivot_samples/download_supplementary_files, FTP and wget download commands, and a full t-test with Benjamini-Hochberg correction pipeline. These cover the common cases end to end, matching the top anchor.

5 / 5

Workflow Clarity

Sections imply a search → retrieve → analyze progression but no explicit sequence is stated, and the batch operations (batch_download_geo, batch_fetch_geo_metadata) only print errors rather than validate or retry. Per the rubric guideline, batch operations lacking validation/verification steps cap workflow clarity at 3.

3 / 5

Progressive Disclosure

references/geo_reference.md exists, is one level deep, and is clearly signaled in the "## Resources" section — better than anchor 2. However, the ~820-line body inlines E-utilities and FTP detail that the reference also documents, so it is a full manual rather than the overview the rubric rationale calls for — not anchor 4's "most content appropriately placed".

3 / 5

Total

14

/

20

Passed

Description

70%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 specific, distinctive description with strong domain keywords, hampered by the missing explicit "Use when..." trigger clause, which caps completeness at 3. Adding a trigger sentence with natural phrases (e.g., "Use when the user mentions GEO, GSE/GSM accessions, or gene expression datasets") would lift it to the top anchors.

Suggestions

Append an explicit trigger clause, e.g., "Use when working with GEO datasets, GSE/GSM/GPL accessions, or NCBI gene expression data."

Include a few more natural synonyms and file extensions ("series matrix", ".soft", "differential expression") to strengthen trigger-term coverage.

Add one analysis-side action verb (e.g., "perform differential expression analysis") to round out the capability list.

DimensionReasoningScore

Specificity

"Search/download microarray and RNA-seq datasets (GSE, GSM, GPL), retrieve SOFT/Matrix files" names several concrete third-person actions with accession types and file formats. Falls short of anchor 5 because it lists only retrieval-side actions; analysis verbs appear only as the purpose clause "for transcriptomics and expression analysis".

4 / 5

Completeness

The "what" is clear (search/download GEO datasets, retrieve SOFT/Matrix files), but there is no "Use when..." clause or equivalent explicit trigger guidance — only the weakly implied purpose "for transcriptomics and expression analysis". Per the rubric guideline, a missing explicit trigger caps completeness at 3.

3 / 5

Trigger Term Quality

"gene expression", "RNA-seq", "microarray", "transcriptomics", "GSE, GSM, GPL", and "SOFT/Matrix files" are natural terms users would say. Between anchors 4 and 5: no file extensions and a few common synonyms (e.g., "GEO datasets", "differential expression") are missing, so it does not clearly match the comprehensive anchor 5.

4 / 5

Distinctiveness Conflict Risk

"Access NCBI GEO" plus the accession acronyms (GSE, GSM, GPL) and SOFT/Matrix file types carve out a clear niche with distinct triggers. Unlikely to fire for unrelated skills; not anchor 4 because no meaningful overlap risk exists.

5 / 5

Total

16

/

20

Passed

Validation

81%

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

Validation — 13 / 16 Passed

Validation for skill structure

CriteriaDescriptionResult

skill_md_line_count

SKILL.md is long (821 lines); consider splitting into references/ and linking

Warning

metadata_version

'metadata.version' is missing

Warning

frontmatter_unknown_keys

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

Warning

Total

13

/

16

Passed

Repository

synthetic-sciences/openscience

Path

backend/cli/skills/databases/geo-database/SKILL.md

Revision

6a85742

Reviewed

Table of Contents

DiscoveryImplementationValidation

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