skills.rest
JosephWoodall
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ensembl-database

Query Ensembl REST API for gene data, sequences, and variant predictions.

1|Updated Mar 19, 2026
Search Tags:#genomics#orthologs#sequence#rest-api#ensembl#variant-analysis#gene-lookup
One-click install
npx skills add https://github.com/JosephWoodall/noosphere --skill ensembl-database-josephwoodall
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: ensembl-database
Source: https://github.com/JosephWoodall/noosphere/tree/main/.agent/skills/ensembl-database
Command: npx skills add https://github.com/JosephWoodall/noosphere --skill ensembl-database-josephwoodall

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

Researchers need programmatic access to Ensembl genomic data for a wide range of species, including gene annotations, sequences, variants, and comparative analyses. This skill provides a unified REST API workflow to fetch gene info, sequences, variants, and orthologs.

Core Features & Use Cases

  • Gene Information Retrieval: lookup by symbol or Ensembl ID, fetch coordinates, transcripts, and cross-references.
  • Sequence Retrieval: obtain genomic, transcript, or protein sequences for genes or regions.
  • Variant Analysis and VEP: predict consequences and access population data for variants.
  • Comparative Genomics: find orthologs/paralogs and align across species.
  • Region & Assembly Mapping: query features in regions and map coordinates across GRCh37/GRCh38.

Quick Start

Look up BRCA2 in human and return the gene ID, transcripts, sequences, and a sample VEP prediction.

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 transcript data from the Ensembl REST API?▼

To retrieve gene sequences and transcripts from the Ensembl REST API, query the provided endpoints using gene symbols or Ensembl IDs. The skill handles API requests to fetch genomic, transcript, or protein sequences along with cross-references across 250+ species.

Can I find orthologs and map genomic coordinates across GRCh37 and GRCh38 assemblies?▼

Yes, you can find orthologs and map assembly coordinates across GRCh37 and GRCh38. The skill queries the Ensembl REST API to perform comparative genomics analysis and convert region coordinates between different genome assemblies.

How do I run VEP variant predictions and access population allele frequencies?▼

To run VEP variant predictions, submit variant queries to the Ensembl REST API endpoints. The skill retrieves variant consequence predictions and fetches associated population data for comprehensive variant analysis.

Does the Ensembl REST API skill handle rate limits and error responses automatically?▼

The Ensembl REST API skill manages rate limits and error responses during genomic data queries. It ensures stable programmatic access for gene lookups, sequence retrieval, and variant predictions without exceeding request thresholds.

What is the best way to look up a gene by symbol across multiple species?▼

The best way to look up a gene by symbol across multiple species is using the Ensembl REST API. The skill streamlines cross-species gene lookups, returning gene IDs, coordinates, and cross-references for over 250 supported species.

Do I need Python requests installed to query Ensembl genomic data?▼

Yes, you need the Python requests library installed to query Ensembl genomic data. This dependency enables the skill to execute REST API calls for fetching gene annotations, sequences, and variant information.

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