Ensembl, programmatically

Ensembl provides a genome browser that acts as a single point of access for annotated genomes. Genes, genetic variants and regulatory features are all annotated onto genomes, with comparative genomics analyses carried out on genes and genomes. The Ensembl REST API provides a number of endpoints for flexible programmatic access to all these data.

For a practical introduction to the Ensembl API you can take the Ensembl REST API course. You can learn more about Ensembl in our Ensembl: Quick tour.

This webinar took place on 6th June 2017 and was hosted by Matthew Laird. The webinar includes:

  • What is Ensembl? (0:28)
  • Methods to access Ensembl data (2:00)
  • The Ensembl REST server documentation. (2:19)
  • How to query the REST server. (3:32)
  • Ensembl REST API endpoints (4:47)
    • What does a HTTP response look like? (7:52)
    • Content types (9:37)
    • Chaining requests and decoding the response (10:10)
  • Live example – fetch a gene based on symbol (11:36)
  • HTTP methods – POST requests (13:03)
  • Where to go for help and documentation (16:47)

Please note that at the time of the recording, the rest.ensemblgenomes.org server was used, however rest.ensembl.org is now used for all species (vertebrates and non-vertebrates).

You can find out more about Ensembl REST API endpoints and other Ensembl APIs on the Ensembl help pages. You can also find a user guide and sample clients on GitHub.

For help and support with Ensembl get in touch with the Ensembl help desk.

You can download the slides and the scripts used for the gene symbol and loop examples using these links: