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ensembl-database

Query Ensembl genomic data via REST API for genes, sequences, variants, and coordinates.

1|Updated Jan 26, 2026
Search Tags:#genomics#rest-api#ensembl#variant-analysis#gene-lookup#sequence-retrieval
One-click install
npx skills add https://github.com/Victory-Hugo/S2-Agent-Skill --skill ensembl-database-victory-hugo
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: ensembl-database
Source: https://github.com/Victory-Hugo/S2-Agent-Skill/tree/main/skills/databases/ensembl-database
Command: npx skills add https://github.com/Victory-Hugo/S2-Agent-Skill --skill ensembl-database-victory-hugo

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This Skill provides programmatic access to Ensembl genomic data via REST API, consolidating information across 250+ species to support genomic research workflows.

Core Features & Use Cases

  • Gene lookup by symbol or Ensembl ID with optional transcript data.
  • Retrieve DNA, transcript, and protein sequences; access variant data and VEP predictions.
  • Cross-species comparative genomics and assembly coordinate mapping to enable cross-reference analyses.
  • Use case: A researcher wants to fetch BRCA2 gene coordinates in human, retrieve its transcripts and VEP consequences, and map coordinates to GRCh38.

Quick Start

Run a simple query to look up a human BRCA2 gene symbol and fetch its Ensembl entry, then retrieve its sequence if needed.

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 genomic data via REST API across multiple species?▼

Query Ensembl genomic data via REST API by making standard HTTP requests to endpoints for gene lookup, sequence retrieval, variant analysis, orthology, and coordinate mapping across 250+ species.

Can I retrieve DNA and protein sequences using the Ensembl REST API?▼

Yes, you can retrieve sequences using the Ensembl REST API. It supports fetching DNA, transcript, and protein sequences, along with variant data and VEP predictions for genomic research pipelines.

How does Ensembl coordinate mapping work for cross-reference analyses?▼

Ensembl coordinate mapping works by converting assembly coordinates across species via REST API endpoints. This enables cross-species comparative genomics and cross-reference analyses between different genome assemblies like GRCh38.

Do I need the requests library to access Ensembl REST endpoints?▼

Yes, you need the Python requests library to make standard REST calls to access Ensembl endpoints. The Skill provides guidance on rate limits and error handling for these queries.

What's the best way to look up a gene by symbol and fetch its Ensembl entry?▼

The best way to look up a gene by symbol is via Ensembl REST API gene lookup endpoints. You can fetch Ensembl entries with optional transcript data and retrieve sequences if needed for your research workflow.

Are there rate limits I should consider when running Ensembl variant analysis queries?▼

Yes, Ensembl variant analysis queries via REST API have rate limits. The Skill provides guidance on rate limits and error handling to ensure your genomic research pipelines run without interruption.

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