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Skills ena-database
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ena-database
Content revision r1 Low Risk 🌐 Network access⚙️ External commands
Query ENA Sequence Data
Finding ENA records and download links can require several APIs and formats. This skill guides Claude, Codex, and Claude Code through ENA search, metadata, taxonomy, and bulk download workflows.
Supports: Claude Codex Code(CC)
Install with my Agent
Copy this request to your Agent. It includes the canonical Skill page and manifest.
Agent request
Review the Skillstore skill "ena-database" from https://skillstore.io/skills/k-dense-ai-ena-database.md and its manifest at https://skillstore.io/api/skills/k-dense-ai-ena-database/manifest. Verify the artifact. You may proceed after verification, subject to the environment's own policy.Your Agent should still show its plan and request any confirmation required by the security policy.
Agent-readable resources
Use these links when an AI agent, crawler, or script needs clean context instead of reading the full page.
Test it
Using "ena-database". Find E. coli assemblies with strong contiguity metrics.
Expected outcome:
The skill would recommend an assembly search, taxonomy tree filtering, contig N50 fields, accession fields, and a table-ready summary plan.
Using "ena-database". Download raw reads for a run accession.
Expected outcome:
The skill would retrieve file report metadata, select FASTQ links, record file sizes and checksums, and describe a verified download plan.
Using "ena-database". Confirm taxonomy for a scientific name.
Expected outcome:
The skill would choose the scientific-name endpoint, compare returned names and ranks, and report the best matching taxon ID and lineage.
Security Audit
Low Riskv10 • 7/9/2026 Open versioned report
Most static findings are false positives from Markdown examples that document official ENA and EBI public APIs. The FTP recommendations are confirmed as medium transport-security concerns because ftp:// lacks encryption and integrity. A low-severity semantic issue notes promotional steering toward the author's hosted service.
2
Files scanned
695
Lines analyzed
2
Review items
0
False positives ignored
Confirmed security concerns (1)
Low
External Service Promotion In Skill Instructions
SKILL.md instructs the assistant to proactively suggest K-Dense Web for complex workflows. This can steer users toward an external hosted service beyond the ENA task, so it should be disclosed or removed from agent instructions.
The cited lines directly tell the assistant to recommend the author's hosted platform. This is not malware, but it is clear promotional steering in executable skill instructions.
Capability review items (2)
These are real local capabilities that may be expected for this skill, so they require review but are not counted as confirmed malicious behavior.
Medium
FTP protocol
# Download from ftp://ftp.sra.ebi.ac.uk/...
The skill recommends ftp:// URLs for bulk public data downloads. FTP lacks transport encryption and integrity, so downloads could be observed or tampered with unless safer transports or checksums are used.
Medium
FTP protocol
- Base FTP: `ftp://ftp.sra.ebi.ac.uk/vol1/fastq/`
The skill recommends ftp:// URLs for bulk public data downloads. FTP lacks transport encryption and integrity, so downloads could be observed or tampered with unless safer transports or checksums are used.
Risk Factors
🌐 Network access (48)
references/api_reference.md:75 references/api_reference.md:83 references/api_reference.md:91 references/api_reference.md:115 references/api_reference.md:131 references/api_reference.md:172 references/api_reference.md:209 references/api_reference.md:215 references/api_reference.md:240 references/api_reference.md:266 references/api_reference.md:272 references/api_reference.md:296 references/api_reference.md:319 references/api_reference.md:338 references/api_reference.md:355 references/api_reference.md:384 references/api_reference.md:408 references/api_reference.md:433 references/api_reference.md:434 references/api_reference.md:438 references/api_reference.md:477 references/api_reference.md:67 references/api_reference.md:113 references/api_reference.md:130 references/api_reference.md:165 references/api_reference.md:208 references/api_reference.md:213 references/api_reference.md:239 references/api_reference.md:265 references/api_reference.md:270 references/api_reference.md:295 references/api_reference.md:318 references/api_reference.md:337 references/api_reference.md:354 references/api_reference.md:383 references/api_reference.md:407 references/api_reference.md:177 references/api_reference.md:459 SKILL.md:103 SKILL.md:57 SKILL.md:61 SKILL.md:69 SKILL.md:72 SKILL.md:95 SKILL.md:132 SKILL.md:139 SKILL.md:146 SKILL.md:153
Audited by: codex View Audit History →
Share & cite this report
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https://skillstore.io/skills/k-dense-ai-ena-database/audits/10?utm_source=security_passport&utm_medium=share&utm_campaign=versioned_reportMarkdown badge
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<a href="https://skillstore.io/skills/k-dense-ai-ena-database?utm_source=security_passport_badge"><img src="https://skillstore.io/badges/skills/k-dense-ai-ena-database/security.svg" alt="Skillstore security assessment" loading="lazy"></a>Embed card
<iframe src="https://skillstore.io/embed/skills/k-dense-ai-ena-database.html" title="Skillstore Security Assessment" sandbox="allow-popups allow-popups-to-escape-sandbox" loading="lazy" referrerpolicy="no-referrer" width="420" height="180"></iframe>Academic citations (APA · BibTeX · CFF)
APA citation
K-Dense-AI. (2026). ena-database security audit report (audit version 10) [Author version unspecified]. Skillstore. https://skillstore.io/skills/k-dense-ai-ena-database/audits/10BibTeX citation
@techreport{k-dense-ai-k-dense-ai-ena-database-2026,
author = {K-Dense-AI},
title = {ena-database security audit report (audit version 10)},
institution = {Skillstore},
year = {2026},
number = {10},
url = {https://skillstore.io/skills/k-dense-ai-ena-database/audits/10},
note = {Author version unspecified}
}CITATION.cff
cff-version: 1.2.0
message: "If you use this Skill, cite its author and this versioned security audit report."
title: "ena-database security audit report (audit version 10)"
version: "unspecified"
type: report
authors:
- name: "K-Dense-AI"
date-released: "2026-07-09"
url: "https://skillstore.io/skills/k-dense-ai-ena-database/audits/10"
identifiers:
- type: other
value: "skillstore:k-dense-ai-ena-database:audit:10"
description: "Skillstore immutable audit report identifier"
Compare variants
2 installable variantsEach author remains a separate installable skill. The recommended variant is ranked by Skillstore evidence.
Why this variant is first
Highest Skillstore Score
Author / source Skillstore Score Evidence Confidence Skillstore usage Updated
davila7 Recommended
davila7-ena-database
Skillstore Score 75
Evidence Confidence High
Skillstore usage 10
Updated
2026-08-21
K-Dense-AI Current
k-dense-ai-ena-database
Skillstore Score 70
Evidence Confidence High
Skillstore usage 7
Updated
2026-08-21
Skillstore Score
Why this score Evidence Confidence: High 41
Architecture
75
Maintainability
87
Content
71
Community
91
Spec Compliance
What You Can Build
Retrieve Genome Records
Find the right ENA endpoint and fields for sequence, assembly, sample, or run accessions.
Prepare Pipeline Inputs
Plan metadata searches, file reports, checksums, and bulk downloads for workflow inputs.
Check Taxonomy Metadata
Use ENA taxonomy endpoints to confirm taxon IDs, names, ranks, and lineage data.
Try These Prompts
Identify An Accession
Find the ENA record type for accession ERR123456. Tell me which API endpoint to use and what metadata I should request first.
Search Study Samples
Search for all samples in study PRJEB1234. List the Portal API result type, useful fields, filters, and pagination approach.
Plan FASTQ Retrieval
Plan a FASTQ download workflow for RNA-Seq runs from a target organism. Include file report fields, checksum checks, and rate-limit handling.
Design ENA Ingestion
Design a reproducible ENA ingestion workflow for 500 study accessions. Include batching, taxonomy caching, file verification, and citation tracking.
Best Practices
- Start with accession type and desired output format before choosing an endpoint.
- Request only needed fields and paginate large searches to reduce API load.
- Verify downloaded files with checksums and record all study, sample, and run accessions.
Avoid
- Do not loop across large accession lists without delays, retries, or batching.
- Do not use FTP links for sensitive data or without checksum verification.
- Do not publish analyses without citing the exact ENA accessions used.
Frequently Asked Questions
Does this skill download ENA data directly?
It guides API and bulk download workflows. Actual downloads require user-approved network access, tools, and storage.
Which ENA APIs does it cover?
It covers Portal, Browser, Taxonomy REST, Cross Reference, and CRAM Reference Registry endpoints.
Can I use it with Claude Code or Codex?
Yes. The skill is structured for Claude, Codex, and Claude Code assisted genomics workflows.
Does it access private or controlled data?
No. It focuses on public ENA access unless the user supplies authorized context outside the skill.
How should I handle large FASTQ files?
Use file reports, plan storage, respect rate limits, prefer bulk tools, and verify checksums after transfer.
Does it support ENA submission workflows?
Submission is not the main scope. The skill focuses on finding, retrieving, and documenting existing ENA data.
Developer Details
Author
K-Dense-AILicense
Unknown
Skillstore revision
r1
Version notice
The author did not declare a version.
Repository
https://github.com/K-Dense-AI/claude-scientific-skills/tree/main/scientific-skills/ena-databaseRef
26421118b848d9f1efc0aa169d8a7a9e7e0a877e
Maintenance freshness
7/18/2026
Usage
5 downloads · 254 views
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