ena-database

Access European Nucleotide Archive via API/FTP. Retrieve DNA/RNA sequences, raw reads (FASTQ), genome assemblies by accession, for genomics and bioinformatics pipelines. Supports multiple formats.

Quality

70%

Does it follow best practices?

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Securityby

Low

Low-risk findings worth noting

Fix and improve this skill with Tessl

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

Quality

Content

57%

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 strong progressive disclosure, but it is held back by duplicated overview content, several incomplete (URL-only) code examples, and a batch workflow lacking explicit validation checkpoints. Tightening examples and adding verification steps would lift the lower dimensions.

Suggestions

Complete the use-case code snippets by actually fetching and parsing each response (e.g. `requests.get(url).json()`), not just building the URL.

Add an explicit validation checkpoint to the Bulk Download Pattern, such as verifying file checksums/counts after download before pipeline processing.

Remove the Overview/When-to-Use duplication of the description to tighten the token budget.

Dimension	Reasoning	Score
Conciseness	Mostly efficient reference-style content, but the Overview duplicates the description and the 8-item 'When to Use This Skill' list overlaps the frontmatter; it could be tightened. It is not a 3 because the duplication and padding do not make every token earn its place.	2 / 3
Actionability	The Portal API example is executable, but several 'Common Use Cases' snippets only construct a URL string without issuing or parsing the request, leaving key details missing. It falls short of fully copy-paste-ready across the board, so it is not a 3.	2 / 3
Workflow Clarity	The Bulk Download Pattern is sequenced into numbered steps, but it lacks explicit validation/verification checkpoints for a batch download operation, which caps workflow clarity at 2 per the guideline.	2 / 3
Progressive Disclosure	The body is a clear overview that signals one real, one-level-deep reference ('references/api_reference.md') with explicit 'when to load' guidance, and detailed parameter tables are appropriately split into that file.	3 / 3
	Total	9 / 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.

The description is specific and distinctive with strong natural trigger terms, but it omits an explicit 'Use when...' trigger clause, leaving the 'when to use' guidance only implied. Adding an explicit trigger sentence would raise completeness.

Suggestions

Add an explicit trigger clause, e.g. 'Use when retrieving nucleotide sequences, raw reads (FASTQ), or genome assemblies from ENA by accession or metadata.'

Drop the generic 'Supports multiple formats' filler in favor of naming the concrete formats (FASTQ, FASTA, EMBL, XML) that matter.

Dimension	Reasoning	Score
Specificity	Lists multiple concrete actions such as 'Retrieve DNA/RNA sequences, raw reads (FASTQ), genome assemblies by accession', matching the multiple-specific-actions anchor rather than naming only a domain.	3 / 3
Completeness	The 'what' is explicit, but 'when' is only implied by 'for genomics and bioinformatics pipelines' with no 'Use when...' clause or equivalent explicit trigger, which caps completeness at 2 per the guideline.	2 / 3
Trigger Term Quality	Uses natural user-facing terms ('DNA/RNA sequences', 'raw reads (FASTQ)', 'genome assemblies', 'accession', 'genomics and bioinformatics pipelines') that a user would plausibly say, rather than only technical jargon.	3 / 3
Distinctiveness Conflict Risk	The European Nucleotide Archive niche with ENA/FASTQ/accession triggers is clearly distinct and unlikely to fire for unrelated 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/ena-database/SKILL.md
Commit: 52845c3

Reviewed: about 11 hours ago

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