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:** ```python 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.l...