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ensembl-database

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

16|7|Updated Nov 20, 2025
Search Tags:#rest#genomics#orthologs#ensembl#VEP#assembly-mapping
One-click install
npx skills add https://github.com/jackspace/ClaudeSkillz --skill ensembl-database-jackspace
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: ensembl-database
Source: https://github.com/jackspace/ClaudeSkillz/tree/main/skills/scientific-db-ensembl-database
Command: npx skills add https://github.com/jackspace/ClaudeSkillz --skill ensembl-database-jackspace

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This Skill provides programmatic access to the Ensembl REST API for gene lookup, sequence retrieval, variant analysis, and comparative genomics across 250+ species.

Core Features & Use Cases

  • Gene information retrieval by symbol or Ensembl ID
  • Sequence retrieval (DNA, cDNA, protein)
  • Variant analysis (VEP) and orthology across species
  • Assembly coordinate mapping between GRCh37 and GRCh38

Quick Start

Install ensembl_rest (or use direct REST calls) and perform symbol lookups and sequence fetches.

Frequently Asked Questions about ensembl-database

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

FAQPage Schema
How do I query gene information from the Ensembl REST API?▼

Query gene information from the Ensembl REST API by symbol or Ensembl ID using the ensembl_rest Python client or direct HTTP calls. The Skill handles rate limiting, error recovery, and returns structured gene metadata across 250+ species.

Can I retrieve DNA, cDNA, and protein sequences across multiple species?▼

Yes, sequence retrieval works across 250+ species in DNA, cDNA, and protein formats. The Skill manages batch requests and caching to optimize performance for large-scale lookups.

How do I map genomic coordinates between GRCh37 and GRCh38 assemblies?▼

Assembly coordinate mapping converts positions between GRCh37 and GRCh38 via the Ensembl REST API. The Skill abstracts the API calls and handles coordinate transformation across genome versions.

What variant analysis and orthology features does the Ensembl REST API support?▼

Variant effect prediction (VEP) and ortholog detection work via the Ensembl REST API for comparative genomics across species. The Skill manages batch queries and robust error handling for large variant datasets.

Do I need to handle rate limiting and errors when querying Ensembl directly?▼

Yes, direct Ensembl REST API access requires rate limiting and error handling. This Skill provides built-in mechanisms for robust queries, retries, and data caching to simplify integration.

Can I perform batch queries and cache results to improve performance?▼

Batch querying and data caching are built into this Skill to reduce redundant API calls and improve throughput. The Skill handles multi-species and multi-gene lookups efficiently with configurable caching.

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