Programmatic access

In addition to the web browser, the Ensembl platform provides a variety of different ways to work with Ensembl Genomes data programmatically.

Ensembl Perl API

The most widely-used and well-established interface to Ensembl Genomes data is the Ensembl Perl API, which provides a comprehensive set of interfaces for accessing Ensembl Genomes data from Perl scripts and applications.

REST service

A recent addition to the suite of interfaces for Ensembl Genomes data is the REST service (currently in beta) which provides language-independent access to Ensembl Genomes data.

MySQL database access

Most Ensembl Genomes data is stored in MySQL relational databases, which can be accessed directly, though the use of the Ensembl Perl API or REST service is recommended.

External APIs

APIs have also been developed by third parties to allow Ensembl Genomes data to be accessed with other languages. Please note that Ensembl Genomes do not provide support for these and the links below are provided for information only:


For more information, watch this YouTube video of a presentation on programatic access to Ensembl Genomes delivered at the Plant and Animal Genomes meeting, January 2015, as part of a workshop organised by Gramene, our U.S.-based collaborators on Ensembl Plants.