alterlab-ensembl

You can query the Ensembl REST API by gene symbol or Ensembl ID to retrieve core gene annotations, coordinates, transcripts, and genomic, transcript, or protein sequences across 250+ species. The Skill applies rate limiting and error handling for robust data retrieval.

Yes, you can run Variant Effect Predictor (VEP) predictions and retrieve variant-level data directly through the Ensembl REST API. The Skill manages VEP requests with built-in rate limiting and error handling to ensure robust variant annotation retrieval.

The best way to find orthologs and paralogs is querying Ensembl comparative genomics REST endpoints to discover cross-species mappings. The Skill retrieves ortholog and paralog data across 250+ species to support comparative genomics and conservation analysis.

Yes, the Ensembl REST API supports assembly mapping to convert genomic coordinates between assemblies like GRCh37 and GRCh38. The Skill includes region utilities to map coordinates and query genomic features within defined regions.

Yes, the requests library is required as a dependency to access Ensembl REST data. The Skill uses Python requests to query REST endpoints for genes, sequences, variants, and orthologs across 250+ species with built-in rate limiting and error handling.

Ensembl REST API queries may fail due to rate limiting or network errors during variant data retrieval. The Skill implements rate limiting and error handling to ensure robust data retrieval, preventing failed requests when querying VEP results and variant-level annotations.