alterlab-ensembl

Ensembl Database

Overview

Access and query the Ensembl genome database, a comprehensive resource for vertebrate genomic data maintained by EMBL-EBI. The database provides gene annotations, sequences, variants, regulatory information, and comparative genomics data for over 250 species. Current release is 116 (April 2026).

Heads-up (verified June 2026): Release 116 is the final release served by the classic REST API at https://rest.ensembl.org. The endpoint stays online with no announced sunset date but receives no further data updates; Ensembl's new platform replaces it with GraphQL and GA4GH refget for sequence access. For current research the REST API documented here still works; plan migration for long-lived pipelines.

When to Use This Skill

This skill should be used when:

• Querying gene information by symbol or Ensembl ID
• Retrieving DNA, transcript, or protein sequences
• Analyzing genetic variants using the Variant Effect Predictor (VEP)
• Finding orthologs and paralogs across species
• Accessing regulatory features and genomic annotations
• Converting coordinates between genome assemblies (e.g., GRCh37 to GRCh38)
• Performing comparative genomics analyses
• Integrating Ensembl data into genomic research pipelines

Core Capabilities

1. Gene Information Retrieval

Query gene data by symbol, Ensembl ID, or external database identifiers.

Common operations:

• Look up gene information by symbol (e.g., "BRCA2", "TP53")
• Retrieve transcript and protein information
• Get gene coordinates and chromosomal locations
• Access cross-references to external databases (UniProt, RefSeq, etc.)

Using the ensembl_rest package:

from ensembl_rest import EnsemblClient

client = EnsemblClient()

# Look up gene by symbol
gene_data = client.symbol_lookup(
    species='human',
    symbol='BRCA2'
)

# Get detailed gene information (method is lookup, NOT lookup_id)
gene_info = client.lookup(
    'ENSG00000139618',  # BRCA2 Ensembl ID
    expand=True
)