Skills ensembl-database
🧬

ensembl-database

Safe 🌐 Network access⚙️ External commands

Query Ensembl Genome Database

Also available from: davila7

Query the Ensembl genome database REST API for vertebrate genomic data. Look up genes, retrieve sequences, analyze variants with VEP, and perform comparative genomics across 250+ species.

Supports: Claude Codex Code(CC)
🥉 76 Bronze
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Test it

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

Expected outcome:

  • Ensembl ID: ENSG00000139618
  • Location: 13q13.1 (chr13:32,315,479-32,400,586)
  • Description: BRCA2 DNA repair associated
  • Transcripts: 22 known protein-coding transcripts
  • Species: Homo sapiens (human)

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

Expected outcome:

  • Variant: rs699 (C>T)
  • Location: Chromosome 16, position 213,641
  • Gene: BLK (beta-1,3-galactosyltransferase 5)
  • Consequence: Missense variant
  • Protein change: Val281Phe

Security Audit

Safe
v4 • 1/17/2026

All 177 static findings are false positives. The skill is a legitimate bioinformatics tool querying the Ensembl genome database (maintained by EMBL-EBI). Scanner misidentified GA4GH Beacon API endpoints as Cobalt Strike keywords, HTTP status codes as cryptographic algorithms, and markdown code fences as shell command execution. Network requests target public bioinformatics APIs with proper rate limiting.

5
Files scanned
2,174
Lines analyzed
2
findings
4
Total audits

Risk Factors

🌐 Network access (3)
scripts/ensembl_query.py:22 scripts/ensembl_query.py:50-85 SKILL.md:63
⚙️ External commands (2)
SKILL.md:40-42 references/api_endpoints.md:5-7
Audited by: claude View Audit History →

Quality Score

64
Architecture
100
Maintainability
85
Content
29
Community
100
Security
83
Spec Compliance

What You Can Build

Gene Annotation Pipeline

Look up genes, retrieve transcripts, get protein sequences, find orthologs, and export results for analysis.

Variant Analysis

Query variants by rsID, predict functional consequences with VEP, check population frequencies, retrieve phenotype associations.

Comparative Genomics

Find orthologs across species, retrieve sequences, compare gene structures, analyze evolutionary conservation.

Try These Prompts

Basic Gene Lookup 
Look up the gene TP53 in human using Ensembl and return its Ensembl ID, chromosomal location, and description.
Sequence Retrieval 
Retrieve the DNA sequence for the BRCA2 gene (ENSG00000139618) in FASTA format.
Variant Analysis 
Analyze the variant rs699 using VEP and show its predicted consequences and population frequencies.
Cross-Species Comparison 
Find all mouse orthologs for human gene BRCA2 and show their Ensembl IDs and sequence similarity.

Best Practices

  • Respect the 15 requests per second rate limit for anonymous users
  • Use batch endpoints when querying multiple items to improve efficiency
  • Cache frequently accessed data to reduce API calls

Avoid

  • Making sequential single requests instead of using batch endpoints
  • Ignoring rate limit responses (429 status codes)
  • Not specifying the correct assembly (GRCh37 vs GRCh38) for coordinate queries

Frequently Asked Questions

What species are supported?
Ensembl covers 250+ vertebrate species including human, mouse, zebrafish, and fruit fly.
How do I handle rate limits?
Implement retry logic with the Retry-After header. Maximum 15 requests per second for anonymous users.
What is VEP?
Variant Effect Predictor analyzes genetic variants and predicts their functional consequences on genes and proteins.
How do I query older genome assemblies?
Use https://grch37.rest.ensembl.org for GRCh37/hg19 queries. Current assemblies use https://rest.ensembl.org.
Can I batch multiple queries?
Yes, use POST endpoints with JSON arrays to query multiple IDs in a single request.
What output formats are available?
Most endpoints support JSON, FASTA for sequences, and some support XML or plain text.

Developer Details

Author

K-Dense-AI

License

MIT

Repository

https://github.com/K-Dense-AI/claude-scientific-skills/tree/main/scientific-skills/ensembl-database

Ref

main

File structure

📁 references/

📄 api_endpoints.md

📁 scripts/

📄 ensembl_query.py

📄 evaluation.json

📄 SKILL.md