skills.rest
LogauaEngstrom
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ensembl-database

Query Ensembl REST API for gene, sequence, variant, and comparative genomics data.

18|1|Updated Dec 27, 2025
Search Tags:#genomics#query#orthologs#rest-api#ensembl#variant-analysis
One-click install
npx skills add https://github.com/LogauaEngstrom/claude-scientific-skills --skill ensembl-database-logauaengstrom
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: ensembl-database
Source: https://github.com/LogauaEngstrom/claude-scientific-skills/tree/main/scientific-skills/ensembl-database
Command: npx skills add https://github.com/LogauaEngstrom/claude-scientific-skills --skill ensembl-database-logauaengstrom

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

Retrieve and consolidate genomic data from the Ensembl REST API across 250+ species to streamline research workflows and reduce manual data gathering.

Core Features & Use Cases

  • Gene information retrieval by symbol or Ensembl ID to support gene-centric analyses
  • Sequence retrieval for genomic, transcript, and protein data to feed downstream analyses
  • Variant analysis and VEP predictions to assess potential functional consequences
  • Comparative genomics and cross-species homology to study conservation and evolution
  • Genomic region queries and assembly coordinate mapping to support region-driven investigations

Quick Start

Query a gene by symbol using the Ensembl REST API to return basic gene information.

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 information from the Ensembl REST API using a gene symbol?▼

To retrieve gene information from the Ensembl REST API, query a gene by its symbol or Ensembl ID using the lookup endpoint. This returns basic gene data across 250+ species to support gene-centric genomic analyses.

Can I use the Ensembl REST API for VEP variant analysis and predicting functional consequences?▼

Yes, you can perform VEP variant analysis via the Ensembl REST API to assess potential functional consequences. The tool provides high-level methods for variation endpoints to integrate variant analysis into genomic research workflows.

What is the best way to find orthologs and cross-species homology data in Ensembl?▼

The best way to find orthologs is using comparative genomics endpoints in the Ensembl REST API. This facilitates cross-species homology discovery to study conservation and evolution across 250+ species.

Does the Ensembl REST API handle rate limiting and HTTP errors for genomic queries?▼

Yes, querying the Ensembl REST API handles rate limiting and common HTTP errors with automatic retries. This ensures reliable retrieval of sequence, variant, and gene data without manual request management.

How do I map genomic coordinates and retrieve sequences for transcripts and proteins?▼

You map genomic coordinates and retrieve sequences using the assembly mapping and sequence endpoints in the Ensembl REST API. This returns genomic, transcript, and protein data to feed downstream analysis pipelines.

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