skills.rest
qinyan-ai
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ensembl-database

Query Ensembl REST API for gene, sequence, and variant data across species.

48|6|Updated Mar 9, 2026
Search Tags:#rest#genomics#sequence#ensembl#assembly-mapping#gene-lookup#vep
One-click install
npx skills add https://github.com/qinyan-ai/qinyan-academic-skills --skill ensembl-database-qinyan-ai
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: ensembl-database
Source: https://github.com/qinyan-ai/qinyan-academic-skills/tree/main/skills/12-%E7%A7%91%E5%AD%A6%E6%95%B0%E6%8D%AE%E5%BA%93/ensembl-database
Command: npx skills add https://github.com/qinyan-ai/qinyan-academic-skills --skill ensembl-database-qinyan-ai

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This Skill provides a unified interface to query Ensembl's REST API for gene data, sequences, variants, and cross-species comparisons, streamlining genomic research workflows.

Core Features & Use Cases

  • Gene lookup by symbol or Ensembl ID to fetch annotations and coordinates.
  • Retrieve DNA, transcript, and protein sequences, as well as region-based sequences.
  • Analyze variants with VEP predictions and access comparative genomics data across species.
  • Map coordinates between assemblies (GRCh37, GRCh38) and find orthologs/paralogs for cross-species studies.

Quick Start

Run the Ensembl REST client to fetch BRCA2 gene data for human and retrieve its sequence.

Frequently Asked Questions about ensembl-database

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

FAQPage Schema
How do I retrieve gene sequences and annotations from the Ensembl REST API?▼

To retrieve Ensembl REST API sequences and annotations, query gene symbols or Ensembl IDs to fetch coordinates and DNA, transcript, or protein sequences across 250+ vertebrate species.

Can I map genomic coordinates between GRCh37 and GRCh38 assemblies?▼

Yes, you can map genomic coordinates between GRCh37 and GRCh38 assemblies using the assembly mapping feature, which translates region positions across different reference genome builds.

Does the Ensembl REST API support VEP variant analysis and orthology lookups?▼

The Ensembl REST API supports VEP variant analysis to predict variant effects and comparative genomics lookups to find orthologs and paralogs for cross-species studies.

What is the best way to handle rate limiting when querying Ensembl genomic data?▼

The best way to handle Ensembl rate limiting is to use a client with built-in retry handling and rate-limiting logic, ensuring continuous REST API data retrieval without connection interruptions.

What species are supported for gene lookup and variant retrieval via Ensembl?▼

Ensembl supports gene lookup, sequence retrieval, and variant analysis across 250+ vertebrate genomes, allowing comprehensive cross-species comparative genomics research workflows.

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