ensembl-database

Query Ensembl genome database REST API for 250+ species. Gene lookups, sequence retrieval, variant analysis, comparative genomics, orthologs, VEP predictions, for genomic research.

Quality

83%

Does it follow best practices?

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Securityby

Passed

No findings from the security scan

Quality

Content

85%

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

A highly actionable, well-structured skill body with executable examples, clear workflows, and properly signaled one-level references. The only real weakness is mild verbosity from explaining domain concepts Claude already knows.

Suggestions

Trim definitional prose Claude already knows (e.g., the ortholog/paralog definitions and the Overview restatement) to improve token efficiency.

Add a brief validation step to each workflow (e.g., confirm HTTP 200 / check returned keys) so the query pipelines have explicit checkpoints.

Dimension	Reasoning	Score
Conciseness	Mostly efficient with executable code examples, but includes concepts Claude already knows (e.g., defining orthologs/paralogs and restating the database overview), so it is not fully lean.	2 / 3
Actionability	Provides fully executable, copy-paste-ready code with concrete endpoints, species identifiers, and parameters rather than pseudocode or abstract descriptions.	3 / 3
Workflow Clarity	Workflows are clearly sequenced numbered steps for read-only query operations, and the API error-handling section provides a concrete retry feedback loop for the fragile rate-limited call.	3 / 3
Progressive Disclosure	The body is an overview that signals one-level-deep references to real bundle files (references/api_endpoints.md and scripts/ensembl_query.py), both of which exist, with clear navigation.	3 / 3
	Total	11 / 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.

A specific, well-targeted description with strong natural trigger terms and clear distinctiveness. Its main weakness is the missing explicit 'Use when...' clause, which leaves the trigger guidance only implied and caps completeness.

Suggestions

Add an explicit trigger clause such as 'Use when querying the Ensembl REST API for genes, sequences, variants, orthologs, or VEP predictions.'

Confirm the release/version note ('250+ species', 'release 115') belongs in the description rather than the body, to avoid time-sensitive clutter in the trigger string.

Dimension	Reasoning	Score
Specificity	Lists multiple specific concrete actions ('Gene lookups, sequence retrieval, variant analysis, comparative genomics, orthologs, VEP predictions'), matching the score-3 anchor rather than the partial-action score-2 anchor.	3 / 3
Completeness	Clearly answers 'what' but only implies 'when' via 'for genomic research'; there is no explicit 'Use when...' trigger clause, which caps completeness at 2 per the judging guidelines.	2 / 3
Trigger Term Quality	Uses natural terms a user would actually say (gene lookups, sequence retrieval, variant analysis, orthologs, VEP predictions, genomic research) with good coverage and not just technical jargon.	3 / 3
Distinctiveness Conflict Risk	The Ensembl genome database / VEP niche is distinct with specific 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
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/ensembl-database/SKILL.md
Commit: 52845c3

Reviewed: about 9 hours ago

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