ena-database

Access the European Nucleotide Archive (ENA) via REST APIs and FTP/Aspera to search and retrieve sequences, raw reads (FASTQ), assemblies, and metadata when you have accession IDs or need metadata-driven discovery for genomics pipelines.

Quality

82%

Does it follow best practices?

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Adds up to 20 points to the overall score

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Securityby

Low

Low-risk findings worth noting

Quality

Content

72%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 highly actionable with a runnable end-to-end example and clean progressive disclosure to a real reference file. It loses points for some redundant explanatory sections and for missing explicit verification steps in the bulk-download workflow.

Suggestions

Collapse the overlapping "Key Features", "Implementation Details", and "API selection guidance" sections and remove the Study/Sample/Run data-model glossary to reduce redundancy and token cost.

Add an explicit verification checkpoint to the bulk-download pipeline (e.g. validate downloaded FASTQ integrity via MD5/checksum or reconcile downloaded file counts against the Portal API result set).

Move the inlined "Query parameters and outputs (practical notes)" detail fully into references/api_reference.md, keeping only the core Portal/Browser/Taxonomy selection guidance inline.

Dimension	Reasoning	Score
Conciseness	Mostly efficient but could be tightened: the "Key Features", "Implementation Details", and "API selection guidance" sections overlap, and the data-model list explains Study/Sample/Run concepts Claude already knows.	3 / 5
Actionability	A complete, copy-paste-runnable Python script with real endpoint URLs, concrete parameters, exponential backoff on 429, and a specific invocation ("python ena_example.py PRJEB1234") covers the common search→fetch→taxonomy case.	5 / 5
Workflow Clarity	The "search → resolve → download" pattern is sequenced, but this bulk/batch download workflow lacks explicit verification checkpoints (e.g. checksum/integrity validation, count reconciliation), so per the batch-operation cap it cannot exceed 3.	3 / 5
Progressive Disclosure	A clear overview body with one well-signaled, one-level-deep reference ("see `references/api_reference.md`", a real bundle file holding the full endpoint/parameter tables); content is appropriately split and easy to navigate.	5 / 5
	Total	16 / 20 Passed

Description

92%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, third-person, and clearly states both what the skill does and when to use it with concrete trigger phrases. It carves out a distinct, low-conflict niche around ENA access.

Dimension	Reasoning	Score
Specificity	"search and retrieve sequences, raw reads (FASTQ), assemblies, and metadata" lists multiple concrete actions with comprehensive coverage of ENA's retrieval surface.	5 / 5
Completeness	Explicitly answers both "what" (search/retrieve sequences, reads, assemblies, metadata) and "when" ("when you have accession IDs or need metadata-driven discovery for genomics pipelines") with concrete trigger phrases.	5 / 5
Trigger Term Quality	Strong natural keywords (ENA, FASTQ, accession IDs, assemblies, metadata, genomics pipelines, FTP/Aspera) but missing a few common synonyms users say, e.g. "SRA" or "raw sequencing data".	4 / 5
Distinctiveness Conflict Risk	Targets a clear niche (the European Nucleotide Archive) with distinct triggers (accession IDs, FASTQ, ENA), giving minimal overlap with unrelated skills.	5 / 5
	Total	19 / 20 Passed

Validation

93%

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 — 15 / 16 Passed

Validation for skill structure

Criteria	Description	Result
frontmatter_unknown_keys	Unknown frontmatter key(s) found; consider removing or moving to metadata	Warning

	Total	15 / 16 Passed

Repository: aipoch/medical-research-skills
Path: scientific-skills/Evidence Insight/ena-database/SKILL.md
Commit: 63c61d3

Reviewed: 10 hours ago

Table of Contents

Discovery Implementation Validation

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