Ensembl Genome Database

Ensembl Genome Database

Overview

Ensembl is a comprehensive genome annotation database covering 300+ vertebrate and non-vertebrate species. The Ensembl REST API provides programmatic access to gene models, transcript/protein sequences, variant annotations, cross-references, regulatory features, and comparative genomics without requiring any login or API key.

When to Use

• Retrieving official gene and transcript annotations (stable IDs, biotype, genomic coordinates) for human or model organism genes
• Converting between gene identifier namespaces (HGNC symbol ↔ Ensembl ID ↔ RefSeq ↔ UniProt)
• Fetching genomic or cDNA/CDS/protein sequences for a gene or transcript
• Looking up variant consequences and functional impact (VEP) for a list of SNPs
• Querying regulatory features (promoters, enhancers, CTCF sites) in a genomic region
• Performing comparative genomics queries (orthologs, paralogs, gene trees) across species
• For local offline access to large genomic annotations, use pyensembl instead
• For pathway and metabolic annotations, use kegg-database or reactome-database instead

Prerequisites

• Python packages: requests
• Data requirements: gene symbols, Ensembl stable IDs (ENSG…/ENST…/ENSP…), or genomic coordinates
• Environment: internet connection required; no API key needed
• Rate limits: max ~15 requests/second; use expand=1 and batch endpoints to minimize calls

pip install requests

Quick Start

import requests

BASE = "https://rest.ensembl.org"
HEADERS = {"Content-Type": "application/json"}

def ensembl_get(endpoint, params=None):
    r = requests.get(f"{BASE}{endpoint}", headers=HEADERS, params=params)
    r.raise_for_status()
    return r.json()