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scientific-ensembl-genomics

Fetch genomic coordinates, transcripts, and metadata via the Ensembl REST API.

3|1|Updated Feb 11, 2026
Search Tags:#genomics#orthologs#cross-references#ensembl#gene-lookup#vep#regulatory-features
One-click install
npx skills add https://github.com/nahisaho/satori --skill scientific-ensembl-genomics
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: scientific-ensembl-genomics
Source: https://github.com/nahisaho/satori/tree/main/src/.github/skills/scientific-ensembl-genomics
Command: npx skills add https://github.com/nahisaho/satori --skill scientific-ensembl-genomics

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Ensembl genomics access provides a unified way to fetch gene coordinates, transcripts, cross-references, orthology data, and regulatory features using the Ensembl REST API, enabling researchers to integrate genomic data into analysis pipelines with consistent formatting.

Core Features & Use Cases

  • Gene lookup by Ensembl ID to retrieve coordinates, biotype, and basic annotations.
  • Orthology and paralogy searches across species to support comparative genomics.
  • Cross-reference retrieval to map Ensembl IDs to UniProt, RefSeq, HGNC, and other databases.
  • Regulatory feature discovery (promoters/enhancers) and gene-centric region queries.
  • Variant annotation scaffolding (VEP-like) for functional impact context.

Quick Start

Perform a gene lookup by Ensembl ID and fetch coordinates, transcripts, and cross-references using the Ensembl REST API.

Frequently Asked Questions about scientific-ensembl-genomics

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

FAQPage Schema
How do I retrieve genomic coordinates and transcript information using an Ensembl gene ID?▼

To retrieve genomic coordinates and transcript information, perform a gene lookup by Ensembl ID. The tool fetches basic metadata, biotype, and transcript details using the Ensembl REST API, returning structured data for downstream analysis.

Can I map Ensembl gene IDs to UniProt or RefSeq cross-references?▼

Yes, you can map Ensembl gene IDs to UniProt, RefSeq, and HGNC databases. Cross-reference retrieval queries the Ensembl REST API to translate identifiers across databases, yielding structured mappings for integration into genomics pipelines.

How do I find orthologs and paralogs across species for comparative genomics?▼

Finding orthologs and paralogs across species uses orthology search functions via the Ensembl REST API. It retrieves homologous gene relationships, returning structured comparative genomics data suitable for cross-species analysis workflows.

What's the best way to fetch regulatory features like promoters and enhancers for a gene region?▼

Fetching regulatory features like promoters and enhancers uses gene-centric region queries via the Ensembl REST API. It retrieves regulatory feature annotations, returning structured genomic region data for regulatory analysis workflows.

Does this approach support variant annotation and functional impact context similar to VEP?▼

Yes, variant annotation scaffolding provides VEP-like functional impact context. It uses the Ensembl REST API to fetch variant annotation data, returning structured functional impact information for genetic variant analysis workflows.

What species are supported for gene lookup and orthology searches?▼

Gene lookup, orthology searches, and cross-references work across species supported by the Ensembl REST API. The tool applies robust error handling to return structured genomic data regardless of the queried organism.

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