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.

 

2 thoughts on “Ensembl REST API – Ensembl Data from Any Language

  1. Hi,
    I tested the API of getting consequences to a specific variant in a region.
    It did not work for human species do you support it?
    what is the best practice to use the API in mass ( thousands of records)?
    should we download code and data to a local machine?
    Regards
    Yuval

    • Hi Yuval. All Ensembl species are supported by the consequences API. Please email helpdesk with the query which is failing, your expected consequences and we will be happy to look into the issue. As for bulk querying we ask people respect the rate limit of 3 queries per second whilst we are in beta. If you wish to query the service faster than this please download the server and databases to a local machine. We are working on increasing the throughput of this service and will release it in the near future.