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gene-database

Query NCBI Gene via E-utilities/Datasets API. Search by symbol/ID, retrieve gene info (RefSeqs, GO, locations, phenotypes), batch lookups, for gene annotation and functional analysis.

59

Quality

74%

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SecuritybySnyk

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tessl review fix ./backend/cli/skills/databases/gene-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.

A well-structured, largely actionable body with excellent progressive disclosure — verified one-level-deep references and executable commands for every script. Weaknesses are moderate padding (redundant sections and format-choice explanations Claude already knows) and the batch workflow's missing validation steps, which the rubric caps at 3.

Suggestions

Add explicit validation steps to the batch workflow: specify the gene_list.txt input format, check the output for unmatched or invalid gene symbols, and show how to inspect and retry failures before using results.

Trim redundant or background sections — the Resources listing duplicates earlier script/reference descriptions, and the Data Formats guidance (choose JSON vs XML vs FASTA) explains concepts Claude already knows; keep only NCBI-specific format options.

Collapse or cut the Overview and When to Use sections, which largely restate the frontmatter description and general NCBI background.

DimensionReasoningScore

Conciseness

Mostly efficient (commands, query patterns, error codes), but several padded sections: the Overview paragraph describing NCBI Gene, a Data Formats section explaining JSON/XML/FASTA tradeoffs Claude already knows, a "When to Use" section restating the description, and a Resources section duplicating the script/reference listings already given. Fits anchor 3 ("some unnecessary explanation or could be tightened"), not 4 whose over-explanation would be only minor.

3 / 5

Actionability

Copy-paste-ready bash commands for each script with realistic examples ("--search \"BRCA1\" --organism \"human\""), concrete error codes and rate limits. Not 5: the batch workflow never specifies the gene_list.txt input format and no expected output is shown — minor gaps matching anchor 4.

4 / 5

Workflow Clarity

Sequences are clearly listed per workflow, but the batch lookup workflow — explicitly a batch operation — has no validation or verification step (no check for unmatched symbols, no inspect-and-retry loop); "Retry failed requests with exponential backoff" is generic API guidance, not an embedded checkpoint. Per the rubric's cap for batch operations without validation, workflow clarity is capped at 3.

3 / 5

Progressive Disclosure

Clear overview with real, one-level-deep references (references/api_reference.md, references/common_workflows.md), each described with its purpose plus explicit navigation guidance ("Search these references when needing specific API endpoint details..."), and all referenced scripts exist in the bundle. Matches anchor 5: content appropriately split and easy to navigate.

5 / 5

Total

15

/

20

Passed

Description

75%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, specific description that clearly states what the skill does with concrete NCBI-specific terminology and low conflict risk. Its main weakness is the absence of an explicit "Use when..." trigger clause, leaving activation guidance only weakly implied and capping completeness.

Suggestions

Add an explicit trigger clause, e.g. "Use when working with gene symbols, NCBI Gene IDs, gene annotations, or batch gene lookups."

Include a few more natural user phrasings such as "gene data", "look up a gene", or "gene sequence retrieval" to broaden trigger coverage.

DimensionReasoningScore

Specificity

Lists multiple specific concrete actions — "Search by symbol/ID", "retrieve gene info (RefSeqs, GO, locations, phenotypes)", "batch lookups" — with comprehensive coverage across search, retrieval detail, and batching, matching the score-5 anchor rather than the 'minor gaps' of score 4.

5 / 5

Completeness

The "what" is clear and specific, but there is no "Use when..." clause; the trailing "for gene annotation and functional analysis" states purpose rather than explicit trigger guidance, so per the rubric guideline completeness is capped at 3 ('when' only weakly implied).

3 / 5

Trigger Term Quality

Good keyword coverage with natural terms like "gene", "symbol", "phenotypes", "batch", and "gene annotation", but common user phrasings such as "gene data", "look up a gene", "sequence retrieval", or organism names are missing — between anchors 3 and 5, so 4.

4 / 5

Distinctiveness Conflict Risk

Naming "NCBI Gene", "E-utilities", and "Datasets API" carves out a clear niche with distinct triggers and minimal conflict risk with other skills — a clean match for the score-5 anchor.

5 / 5

Total

17

/

20

Passed

Validation

87%

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

CriteriaDescriptionResult

metadata_version

'metadata.version' is missing

Warning

frontmatter_unknown_keys

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

Warning

Total

14

/

16

Passed

Repository

synthetic-sciences/openscience

Path

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

Reviewed

Table of Contents

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