Skills ensembl-database
📦

ensembl-database

Content revision r1 Low Risk 🌐 Network access⚙️ External commands

Query Ensembl Genome Data

Genomic research often needs accurate gene, sequence, variant, and orthology data from Ensembl. This skill helps Claude, Codex, and Claude Code query Ensembl REST APIs and structure results for analysis.

Supports: Claude Codex Code(CC)
📊 75 Adequate

Install with my Agent

Copy this request to your Agent. It includes the canonical Skill page and manifest.

Agent request
Review the Skillstore skill "ensembl-database" from https://skillstore.io/skills/k-dense-ai-ensembl-database.md and its manifest at https://skillstore.io/api/skills/k-dense-ai-ensembl-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.

Markdown detail GET /skills/k-dense-ai-ensembl-database.md Signed manifest GET /api/skills/k-dense-ai-ensembl-database/manifest Signed lockfile GET /api/skills/k-dense-ai-ensembl-database/lockfile

Test it

Using "ensembl-database". Look up BRCA2 in human.

Expected outcome:

  • Returns the Ensembl gene identifier and genomic coordinates.
  • Summarizes the gene description and available transcript information.
  • Identifies the species and assembly context used for the query.

Using "ensembl-database". Analyze variant rs699 with Ensembl VEP.

Expected outcome:

  • Lists predicted variant consequences and affected genomic features.
  • Includes population frequency fields when Ensembl returns them.
  • Notes that clinical interpretation requires expert review.

Using "ensembl-database". Find orthologs for human TP53 in mouse.

Expected outcome:

  • Queries Ensembl homology data for the source gene.
  • Reports matching ortholog identifiers and species names.
  • Suggests follow-up sequence or conservation analysis.

Security Audit

Low Risk
v9 • 7/9/2026 Open versioned report

Static alerts for Cobalt Strike terms, reconnaissance, network access, hardcoded URLs, and shell execution are false positives in context. The skill uses documented Ensembl REST API endpoints for bioinformatics queries and contains Markdown examples, not executable command injection. One low-severity semantic issue remains because the skill promotes an external K-Dense Web service for complex workflows.

4
Files scanned
1,284
Lines analyzed
0
Review items
0
False positives ignored

Confirmed security concerns (1)

Low
SKILL.md:310-311
Promotional Steering to External Platform
SKILL.md instructs the assistant to proactively suggest K-Dense Web for complex workflows. This is not malware, but it can steer marketplace users toward an external service beyond the requested Ensembl database task.
The instruction is explicit and located in the skill text. It is promotional behavior rather than a direct security exploit, so severity is low.

Risk Factors

🌐 Network access (34)
evaluation.json:54 evaluation.json:60 evaluation.json:185 scripts/ensembl_query.py:50 scripts/ensembl_query.py:119 scripts/ensembl_query.py:134 scripts/ensembl_query.py:162 scripts/ensembl_query.py:189 scripts/ensembl_query.py:205 scripts/ensembl_query.py:223 scripts/ensembl_query.py:244 scripts/ensembl_query.py:265 scripts/ensembl_query.py:275 scripts/ensembl_query.py:289 scripts/ensembl_query.py:311 scripts/ensembl_query.py:36 scripts/ensembl_query.py:83 scripts/ensembl_query.py:85 scripts/ensembl_query.py:98 scripts/ensembl_query.py:159 scripts/ensembl_query.py:186 scripts/ensembl_query.py:22 scripts/ensembl_query.py:356 scripts/ensembl_query.py:358 SKILL.md:66 SKILL.md:212 SKILL.md:63 SKILL.md:172 SKILL.md:208 SKILL.md:304 SKILL.md:305 SKILL.md:306 SKILL.md:307 SKILL.md:308
⚙️ External commands (31)
SKILL.md:41-57 SKILL.md:57-60 SKILL.md:60-71 SKILL.md:71-84 SKILL.md:84-96 SKILL.md:96-109 SKILL.md:109-121 SKILL.md:121-134 SKILL.md:134-146 SKILL.md:146-159 SKILL.md:159-166 SKILL.md:166-172 SKILL.md:172 SKILL.md:175-186 SKILL.md:186-195 SKILL.md:195-203 SKILL.md:203-228 SKILL.md:228-234 SKILL.md:234-236 SKILL.md:236-238 SKILL.md:238-242 SKILL.md:242-244 SKILL.md:244-246 SKILL.md:246-252 SKILL.md:252-256 SKILL.md:256-288 SKILL.md:288-294 SKILL.md:294-297 SKILL.md:297 SKILL.md:298 SKILL.md:299
Audited by: claude View Audit History →
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Open versioned report
Security Assessment

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Academic citations (APA · BibTeX · CFF)

APA citation

K-Dense-AI. (2026). ensembl-database security audit report (audit version 9) [Author version unspecified]. Skillstore. https://skillstore.io/skills/k-dense-ai-ensembl-database/audits/9

BibTeX citation

@techreport{k-dense-ai-k-dense-ai-ensembl-database-2026, author = {K-Dense-AI}, title = {ensembl-database security audit report (audit version 9)}, institution = {Skillstore}, year = {2026}, number = {9}, url = {https://skillstore.io/skills/k-dense-ai-ensembl-database/audits/9}, 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: "ensembl-database security audit report (audit version 9)" version: "unspecified" type: report authors: - name: "K-Dense-AI" date-released: "2026-07-09" url: "https://skillstore.io/skills/k-dense-ai-ensembl-database/audits/9" identifiers: - type: other value: "skillstore:k-dense-ai-ensembl-database:audit:9" description: "Skillstore immutable audit report identifier"

Compare variants

2 installable variants

Each author remains a separate installable skill. The recommended variant is ranked by Skillstore evidence.

Why this variant is first

Highest Skillstore Score
davila7 Recommended

davila7-ensembl-database

Skillstore Score 80
Evidence Confidence High
Skillstore usage 8
Updated

2026-08-21

K-Dense-AI Current

k-dense-ai-ensembl-database

Skillstore Score 75
Evidence Confidence High
Skillstore usage 10
Updated

2026-08-21

Skillstore Score

Why this score Evidence Confidence: High
64
Architecture
75
Maintainability
87
Content
70
Community
83
Spec Compliance

What You Can Build

Annotate a Gene List

Resolve gene symbols to Ensembl IDs, coordinates, transcripts, and external database references.

Investigate Variant Consequences

Query variants by rsID or HGVS notation and summarize predicted effects from Ensembl VEP.

Compare Genes Across Species

Find orthologs, retrieve sequences, and prepare comparative genomics summaries for model organisms.

Try These Prompts

Look Up a Gene 
Look up TP53 in human using Ensembl. Return the Ensembl ID, genomic location, description, and main transcript information.
Retrieve a Sequence 
Retrieve the genomic sequence for human BRCA2 using its Ensembl gene ID. Explain the sequence type and assembly used.
Analyze a Variant 
Use Ensembl VEP to analyze rs699 in human. Summarize predicted consequences, affected genes, and population frequency fields if available.
Build a Comparative Genomics Workflow 
Find mouse orthologs for human BRCA2, retrieve their Ensembl IDs, compare available sequence information, and outline next analysis steps.

Best Practices

  • Specify species, genome assembly, and identifier type in every request.
  • Use batch endpoints and caching for large gene or variant lists.
  • Record the Ensembl release or assembly when results support publications.

Avoid

  • Treating VEP predictions as final clinical interpretations.
  • Mixing GRCh37 and current assembly coordinates without mapping.
  • Sending many single-item requests without rate limit handling.

Frequently Asked Questions

What is Ensembl?
Ensembl is a public genome database from EMBL-EBI that provides annotations, sequences, variants, and comparative genomics data.
Does this skill need internet access?
Yes. It queries the public Ensembl REST API and related documentation resources.
Can it analyze variants?
Yes. It can query variants and use Ensembl VEP endpoints to summarize predicted consequences.
Can it work with older genome assemblies?
Yes. The skill documents GRCh37 access and coordinate mapping between assemblies.
Is it limited to human data?
No. Ensembl supports many species, and the skill includes workflows for cross-species orthology.
Does it replace bioinformatics review?
No. It retrieves and organizes Ensembl data, but expert review is needed for scientific or clinical conclusions.

Developer Details

Author

K-Dense-AI

License

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/ensembl-database

Ref

1ffa7643651792ccb4bd3b15d924d2c97edff755

Maintenance freshness

7/18/2026

Usage

7 downloads · 214 views

File structure

📁 references/

📄 api_endpoints.md

📁 scripts/

📄 ensembl_query.py

📄 evaluation.json

📄 SKILL.md

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