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.

Quality

77%

Does it follow best practices?

Run evals on this skill

Adds up to 20 points to the overall score

View guide

Securityby

Passed

No findings from the security scan

Fix and improve this skill with Tessl

tessl review fix ./backend/cli/skills/databases/gene-database/SKILL.md

Quality

Content

80%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.

The body is well-structured with executable commands and excellent progressive disclosure, but its batch workflows lack explicit validation checkpoints, which caps workflow clarity. Trimming the Overview and Data Formats explanations would further tighten conciseness.

Suggestions

Add explicit validation checkpoints to the batch workflow (e.g., verify input gene symbols before processing, confirm output row count matches input count, retry/halt on 429).

Trim the Overview paragraph and the Data Formats section — remove definitions of JSON/XML/FASTA that Claude already knows, keeping only the format-selection guidance.

Show expected output or a result-checking step alongside the script commands so users can verify a command worked.

Dimension	Reasoning	Score
Conciseness	Mostly efficient workflow and quick-start content, with minor over-explanation that could be trimmed — the Overview paragraph defining NCBI Gene and the Data Formats section explaining JSON/XML/FASTA describe things Claude already knows.	4 / 5
Actionability	Provides fully executable, copy-paste-ready bash commands for each script (e.g., 'python scripts/query_gene.py --search "BRCA1" --organism "human"') covering the common search, fetch, and batch cases, and the referenced scripts all exist in the bundle.	5 / 5
Workflow Clarity	Workflows are numbered and sequenced, but the batch gene lookup workflow lacks explicit validation/verification checkpoints; per the rubric, batch operations without validation cap workflow clarity at 3.	3 / 5
Progressive Disclosure	Clear overview with well-signaled, one-level-deep references to verified bundle files (references/api_reference.md, references/common_workflows.md); detailed API docs are appropriately split into references while the body stays an overview.	5 / 5
	Total	17 / 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.

The description is specific, distinctive, and rich in domain keywords, but it omits any explicit 'Use when...' trigger guidance, which caps its completeness. Adding a trigger clause would materially raise the score.

Suggestions

Add an explicit 'Use when...' trigger clause (e.g., 'Use when searching NCBI Gene by symbol/ID, retrieving RefSeqs/GO/phenotype data, or doing batch gene annotation').

Include natural synonyms and file extensions users mention (e.g., FASTA, .fasta, gene sequence, RefSeq) to broaden trigger term coverage.

Reframe in consistent third-person imperative voice to match the good-overall examples.

Dimension	Reasoning	Score
Specificity	Lists multiple concrete actions — 'Search by symbol/ID', 'retrieve gene info (RefSeqs, GO, locations, phenotypes)', 'batch lookups' — with comprehensive coverage of the skill's capabilities.	5 / 5
Completeness	The 'what' is clearly and comprehensively stated, but there is no 'Use when...' clause or equivalent explicit trigger guidance, so completeness is capped at 3 per the rubric guideline.	3 / 5
Trigger Term Quality	Good domain keyword coverage ('NCBI Gene', 'E-utilities/Datasets API', 'gene annotation', 'functional analysis', 'batch lookups') that users would naturally say, but missing common synonyms and file extensions (e.g., FASTA, .fasta, gene sequence).	4 / 5
Distinctiveness Conflict Risk	A clear, narrow niche ('NCBI Gene via E-utilities/Datasets API') with distinct triggers and minimal conflict risk against other skills.	5 / 5
	Total	17 / 20 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
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
Commit: 3a6c3a9

Reviewed: 1 day ago

Table of Contents

Discovery Implementation Validation

Is this your skill?

If you maintain this skill, you can claim it as your own. Once claimed, you can manage eval scenarios, bundle related skills, attach documentation or rules, and ensure cross-agent compatibility.