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ensembl-database

Query the Ensembl REST API for gene, sequence, variant, and regulatory data.

1|Updated Mar 11, 2026
Search Tags:#bioinformatics#genomics#orthologs#sequence#rest-api#ensembl#variant-analysis
One-click install
npx skills add https://github.com/SciMate-AI/scicli --skill ensembl-database-scimate-ai
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: ensembl-database
Source: https://github.com/SciMate-AI/scicli/tree/main/internal/skills/bundled/claude-scientific-skills/skills/ensembl-database
Command: npx skills add https://github.com/SciMate-AI/scicli --skill ensembl-database-scimate-ai

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires requests, and includes scripts (resource) and references (resource) components.

What problem does it solve?

Query Ensembl data programmatically to support genomics research workflows, enabling retrieval of gene annotations, sequences, variants, and regulatory information without manual browsing.

Core Features & Use Cases

  • Gene information retrieval by symbol or Ensembl ID (lookup)
  • Sequence, variant, and regulatory feature extraction
  • Orthologs/paralogs discovery and cross-species comparison
  • Coordinate conversion and assembly mapping between assemblies (e.g., GRCh37 to GRCh38)

Quick Start

Query the Ensembl REST API for a gene (e.g., BRCA2) in human to retrieve basic gene information and coordinates.

Frequently Asked Questions about ensembl-database

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I query Ensembl REST API for human gene information by symbol or Ensembl ID?▼

Query the Ensembl REST API by providing a gene symbol like BRCA2 or an Ensembl ID to retrieve gene annotations, genomic coordinates, and regulatory features without manual browsing.

Can I convert genomic coordinates between GRCh37 and GRCh38 assemblies using Ensembl data?▼

Coordinate conversion and assembly mapping between GRCh37 and GRCh38 is supported, enabling accurate genomic coordinate translation for cross-assembly variant analysis and sequence alignment workflows.

How do I fetch DNA sequences and variants from the Ensembl database for bioinformatics pipelines?▼

Fetch sequences and variants directly from the Ensembl REST API, extracting regulatory features and genomic data with built-in rate limiting and error handling for reliable research pipeline integration.

What's the best way to find orthologs across species using Ensembl gene annotations?▼

Discover orthologs and paralogs through Ensembl REST API queries, performing cross-species comparisons by retrieving homologous gene annotations and sequence data for evolutionary genomics analysis.

Do I need Python requests library to access Ensembl REST API programmatically?▼

The Python requests library is required as the sole dependency to access the Ensembl REST API, handling HTTP requests for gene lookups, sequence retrieval, and variant extraction.

Why does my Ensembl REST API query fail with rate limiting in automated pipelines?▼

Ensembl REST API queries implement rate limiting and robust error handling to prevent failures, ensuring reliable access when retrieving genomic data within automated bioinformatics research pipelines.

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