ensembl-database

Access Ensembl REST API for genomic data retrieval across 250+ species.

1|Updated Mar 12, 2026

Search Tags:#bioinformatics #genomics #sequence retrieval #variant analysis #ensembl #gene lookup

Ready to run

npx skills add https://github.com/yf8578/clawomics --skill ensembl-database-yf8578

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: ensembl-database
Source: https://github.com/yf8578/clawomics/tree/main/skills/ensembl-database
Command: npx skills add https://github.com/yf8578/clawomics --skill ensembl-database-yf8578

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 genome database, enabling researchers to retrieve comprehensive genomic information for over 250 species without manual web browsing.

Core Features & Use Cases

Gene Information: Look up genes by symbol or ID, retrieve sequences, and access cross-references.
Variant Analysis: Query genetic variations and predict their functional consequences using VEP.
Comparative Genomics: Find orthologs and paralogs across different species.
Use Case: A researcher needs to find all known human genes associated with a specific disease and retrieve their protein sequences for further analysis.

Quick Start

Use the ensembl-database skill to find all orthologs for the human gene BRCA2 in the mouse species.

Frequently Asked Questions about ensembl-database

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

FAQPage Schema

How do I retrieve genomic sequences and gene information from the Ensembl database?▼

Retrieve Ensembl genomic sequences and gene information by querying the REST API to look up genes by symbol or ID and access cross-references across 250+ species. The API returns sequence data and gene annotations directly for bioinformatics research.

How do I find orthologs for a specific gene across different species using Ensembl?▼

Find orthologs across species using Ensembl comparative genomics endpoints to identify related genes in different organisms. The system queries the REST API to return ortholog and paralog data for comparative genomic studies.

Can I predict the functional consequences of genetic variations using VEP through Ensembl?▼

Predict functional consequences of genetic variations using the Ensembl Variant Effect Predictor (VEP) via the REST API. The variant analysis feature queries genetic variations and returns predicted functional impact data for genomic research.

Does the Ensembl REST API support coordinate mapping between different genome assemblies?▼

The Ensembl REST API supports coordinate mapping between different genome assemblies to facilitate comparative genomics. This feature allows researchers to translate genomic coordinates across assembly versions for accurate sequence retrieval.

How many species are supported for genomic data retrieval in the Ensembl database?▼

Ensembl database genomic data retrieval supports comprehensive access across 250+ species via the REST API. This coverage enables researchers to perform gene lookups, sequence retrieval, and comparative genomics for diverse organisms.

What dependencies are required to access the Ensembl genome database programmatically?▼

Accessing the Ensembl genome database programmatically requires the ensembl_rest and requests dependencies. These libraries establish API connectivity to query genomic data and integrate retrieval functions into bioinformatics pipelines.