skills.rest
LeonChaoX
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ensembl-database

Query Ensembl REST API for genes, sequences, variants, and orthologs.

783|65|Updated Feb 27, 2026
Search Tags:#rest api#comparative genomics#sequence retrieval#variant analysis#ensembl#gene lookup#vep prediction
One-click install
npx skills add https://github.com/LeonChaoX/qinyan-academic-skills --skill ensembl-database-leonchaox
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: ensembl-database
Source: https://github.com/LeonChaoX/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/LeonChaoX/qinyan-academic-skills --skill ensembl-database-leonchaox

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires requests, argparse, time, json, typing, and includes scripts (resource) and references (resource) components.

What problem does it solve?

Ensembl data retrieval is fragmented across many endpoints, so researchers waste time manually searching gene, sequence, and variant information instead of quickly getting the exact results they need for genomic analysis.

Core Features & Use Cases

  • Gene & cross-reference lookup: Resolve genes by symbol or Ensembl ID and pull detailed annotations and external database links.
  • Sequence retrieval: Download genomic, transcript, and protein sequences (including region-based sequence extraction).
  • Variant consequence analysis (VEP): Predict functional effects from rsIDs or HGVS notations and analyze variants in context.
  • Comparative genomics: Find orthologs/paralogs and retrieve gene trees across species.
  • Genomic region discovery & assembly mapping: Collect overlapping features within a region and map coordinates between assemblies (e.g., GRCh37 to GRCh38) using the correct base URLs.

Quick Start

Use this skill to fetch BRCA2 gene details and related sequences from Ensembl by querying the gene symbol in a specified species.

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?▼

Use the Ensembl REST API to fetch gene sequences and annotations by querying a gene symbol or Ensembl ID. This retrieves detailed genomic, transcript, or protein sequences and external database cross-references in JSON or FASTA format.

Can I predict variant functional effects using HGVS notations and rsIDs with VEP?▼

Yes, you can predict variant functional effects by submitting rsIDs or HGVS notations to the VEP prediction endpoint. This analyzes variant consequences and retrieves functional impact predictions directly from the Ensembl REST API.

What's the best way to find orthologs and gene trees for comparative genomics across species?▼

Query the Ensembl REST API to find orthologs, paralogs, and gene trees across species and assemblies. This comparative genomics approach retrieves cross-species genomic relationships to integrate into evolutionary research pipelines.

Does the Ensembl REST API support mapping genomic coordinates between GRCh37 and GRCh38 assemblies?▼

Yes, the Ensembl REST API supports assembly mapping between GRCh37 and GRCh38. It translates genomic coordinates across assemblies by using assembly-aware mapping with the correct base URLs to ensure accurate coordinate conversion.

How do I handle rate limits when querying the Ensembl REST API for variant analysis?▼

Handle Ensembl REST API rate limits by implementing request pacing using the requests library during variant analysis. This manages query throughput to prevent exceeding API thresholds while retrieving genomic features and annotations.

When do I need assembly-aware mapping for genomic region discovery in Ensembl?▼

You need assembly-aware mapping for genomic region discovery when collecting overlapping features across different genome builds. Using the correct base URLs ensures accurate coordinate translation between assemblies like GRCh37 and GRCh38.

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