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HolobiomicsLab
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ensembl-database

Query Ensembl REST API for gene lookup, sequences, variants, and orthologs.

4|1|Updated Jun 18, 2025
Search Tags:#genomics#orthologs#rest-api#ensembl#variant-analysis#gene-lookup#sequence-retrieval
One-click install
npx skills add https://github.com/HolobiomicsLab/Toolomics --skill ensembl-database-holobiomicslab
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: ensembl-database
Source: https://github.com/HolobiomicsLab/Toolomics/tree/main/mcp_host/skills/scientific-skills/scientific-skills/ensembl-database
Command: npx skills add https://github.com/HolobiomicsLab/Toolomics --skill ensembl-database-holobiomicslab

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

Ensembl REST API access enables researchers to programmatically retrieve gene annotations, sequences, variants, and cross-species comparative genomics data across 250+ species without manual database queries.

Core Features & Use Cases

  • Gene lookup by symbol or Ensembl ID to obtain annotations and cross-references.
  • Sequence retrieval for genes, transcripts, and proteins, plus region-based sequences.
  • Variant analysis and orthology queries, including VEP predictions and cross-species comparisons.
  • Coordinate mapping between assemblies (GRCh37/GRCh38) and species references for comparative studies.

Quick Start

Run the Ensembl REST API query script to look up a gene, retrieve sequences, or query a variant and print the resulting JSON.

Frequently Asked Questions about ensembl-database

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

FAQPage Schema
How do I retrieve a gene sequence using the Ensembl REST API in Python?▼

You can retrieve a gene sequence using the Ensembl REST API by querying the Python client with an Ensembl ID or gene symbol to fetch transcript, protein, or region-based sequences directly.

Can I look up orthologs across species using Ensembl IDs?▼

Yes, you can look up orthologs across species using Ensembl IDs. The client supports comparative genomics queries to retrieve cross-species gene information and orthology data.

Does this Skill support batch variant analysis and VEP predictions?▼

Yes, this Skill supports batch variant analysis and VEP predictions. The Python client handles both single and batch queries to retrieve variant effect predictions from Ensembl.

What is the best way to map genomic coordinates between GRCh37 and GRCh38 assemblies?▼

The best way to map genomic coordinates between GRCh37 and GRCh38 assemblies is using the coordinate mapping functionality, which converts positions across assembly references for comparative studies.

How does the Ensembl client handle rate limits and API errors?▼

The Ensembl client handles rate limits and API errors through built-in rate-limited requests and robust error handling with automatic retries, ensuring stable genomic data retrieval.

Do I need the requests library to run Ensembl queries?▼

Yes, you need the requests library installed in your Python environment to run Ensembl queries, as it is the required dependency for executing the REST API calls.

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