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

68%

Does it follow best practices?

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Securityby

Passed

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

Quality

Content

61%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 and actionable with concrete code and properly signaled bundle references, but it is somewhat verbose and its workflows lack validation checkpoints. Tightening the Overview, relocating release/version info, and adding verification steps to workflows would raise the lowest dimensions.

Suggestions

Trim the Overview's background on what Ensembl is and move the 'Current release is 115 (September 2025)' note to a dedicated versioning section to avoid time-sensitive decay in the main flow.

Add validation checkpoints to each workflow (e.g., verify the gene ID was found before retrieving transcripts; confirm VEP returned results before reporting).

Reduce duplication between 'When to Use This Skill' and 'Core Capabilities' to tighten token use.

Dimension	Reasoning	Score
Conciseness	Mostly efficient with concrete code per capability, but it explains context Claude already knows in the Overview and embeds time-sensitive info ('Current release is 115 (September 2025)') outside a deprecated/old-patterns section, which the guideline says should penalize conciseness.	3 / 5
Actionability	Provides concrete, mostly executable code for each capability plus a retry/error-handling helper and install commands, with only minor gaps (some examples omit imports or rely on an assumed client instance).	4 / 5
Workflow Clarity	The three numbered workflows list steps but include no validation checkpoints or feedback loops, matching the score-3 anchor; although the operations are read queries rather than destructive ones, no verification is woven into the sequences.	3 / 5
Progressive Disclosure	Good structure with well-signaled one-level-deep references to the real bundle files (references/api_endpoints.md and scripts/ensembl_query.py), though the SKILL.md body itself runs ~310 lines with considerable inline content that keeps it just shy of a lean overview.	4 / 5
	Total	14 / 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 and distinctive with strong keyword coverage, but it lacks an explicit 'Use when...' trigger clause, leaving the 'when' only weakly implied and capping completeness. Adding a concrete trigger sentence would lift the weakest dimension.

Suggestions

Add an explicit 'Use when...' clause, e.g. 'Use when querying Ensembl for genes, sequences, variants, orthologs, or VEP predictions across species.'

Include common synonyms users say, such as 'homology', 'paralogs', and 'gene annotation', to broaden trigger coverage.

Drop the generic trailing phrase 'for genomic research' in favor of concrete trigger conditions.

Dimension	Reasoning	Score
Specificity	Lists multiple concrete actions — 'Gene lookups, sequence retrieval, variant analysis, comparative genomics, orthologs, VEP predictions' — giving comprehensive coverage of the API's capabilities, matching the score-5 anchor.	5 / 5
Completeness	The 'what' is clear ('Query Ensembl genome database REST API...'), but the 'when' is only weakly implied by the trailing phrase 'for genomic research' with no explicit 'Use when...' clause, so per the guideline completeness is capped at 3.	3 / 5
Trigger Term Quality	Includes natural domain terms a genomics user would say ('gene lookups', 'sequence retrieval', 'variant analysis', 'orthologs', 'VEP predictions'), but misses common synonyms such as 'homology', 'paralogs', and 'gene annotation', so it falls just below comprehensive (5).	4 / 5
Distinctiveness Conflict Risk	'Query Ensembl genome database REST API' names a clear niche with distinct triggers and minimal overlap with other skills, matching the score-5 anchor.	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/ensembl-database/SKILL.md
Commit: 3a6c3a9

Reviewed: about 24 hours ago

Table of Contents

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