ensembl-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 ```bash pip install requests ``` ## Quick Start ```python impor...