Ensembl REST API – Ensembl Data from Any Language

An example of output and documentation from the Ensembl REST ServiceWe are pleased to announce the beta release of our programming language agnostic REST API, for Release 68 data, at beta.rest.ensembl.org. Our initial release provides access to:

  • Sequences (genomic, cDNA, CDS and protein)
  • VEP (Variant Effect Predictor)
  • Homologies
  • Gene Trees
  • Assembly and coordinate mapping

Data can be retrieved in JSON, XML and a variety of bioinformatical formats such as FASTA. Each endpoint is fully documented with live service responses and example clients in Perl, Python, Ruby and the Unix command line.

Since 2006, Perl has been the only language to have a supported API. Third party alternatives are available but can lag in their support of new data. The REST service has been developed using Catalyst and the Perl API providing a stable base for development and provides access to all of Ensembl’s functionality. Using the Perl API also means that any Ensembl compatible resource can provide data using the same REST server. Our sister project, Ensembl Genomes, has already taken advantage of this feature and are hosting release 15 data at test.rest.ensemblgenomes.org.

Development is on-going so please let us know about any features you would like to see in a future release. Please send any feedback to helpdesk.