ensembl-database

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 115 (September 2025).

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
gene_info = client.lookup_id(
    id='ENSG00000139618',  # BRCA2 Ensembl ID
    expand=True
)

Direct REST API (no package):

import requests

server = "https://rest.ensembl.org"

# Symbol lookup
response = requests.get(
    f"{server}/lookup/symbol/homo_sapiens/BRCA2",
    headers={"Content-Type": "application/json"}
)
gene_data = response.json()

2. Sequence Retrieval

Fetch genomic, transcript, or protein sequences in various formats (JSON, FASTA, plain text).

Operations:

• Get DNA sequences for genes or genomic regions
• Retrieve transcript sequences (cDNA)
• Access protein sequences
• Extract sequences with flanking regions or modifications