This document provides a comprehensive technical guide for accessing and querying the Ensembl genome database via REST API. It covers gene information retrieval, sequence fetching, variant analysis using VEP, comparative genomics for ortholog identification, assembly mapping between genome versions, and best practices for API usage including rate limiting and error handling. The guide includes practical Python code examples using the ensembl_rest package and direct HTTP requests, targeting genomic researchers working with over 250 vertebrate species.
Key findings
The Ensembl REST API supports querying gene data by symbol or ID for 250+ species
Variant Effect Predictor (VEP) enables functional consequence prediction for genetic variants
AssemblyMapper facilitates coordinate conversion between genome assemblies such as GRCh37 to GRCh38
Batch endpoints and caching strategies are essential for managing API rate limits of 15 requests per second
Comparative genomics endpoints provide access to orthologs, paralogs, and gene trees across species
Limitations & open questions
Documentation focuses on vertebrate genomes with limited coverage of non-vertebrate species
Rate limiting constraints may restrict high-throughput analyses without local data caching
Examples assume Python programming knowledge and do not cover R or other language implementations