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Dan Bolser edited this page Mar 8, 2016 · 5 revisions
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Overview

Ensembl Genomes provides a fully featured REST server based on the codebase provided by our sister project Ensembl.

Since Ensembl Genomes has different content and use-cases to Ensembl, particularly when dealing with over 15,000 bacterial genomes, the Ensembl Genomes REST server provides some additional endpoints, which are available as plugins in this repository and described below.

Endpoints

Ensembl Genomes version

To find the current Ensembl Genomes version, you can use info/eg_version

Genome information discovery

To make life easier when dealing with thousands of genomes from across the taxonomy, Ensembl Genomes provides ensemblgenomes-api, an auxillary Perl API for genome discovery (described here). The following REST endpoints are provided that expose the functionality of this API:

Bacterial genome retrieval

To support the retrieval of complete gene model and annotation sets for small genomes such as bacteria, an additional endpoint has been added which can be configured to retrieve gene models to different depths, with and without cross-references. For more information, visit GET lookup/genome/:name.

Bacterial family data

The majority of bacterial genomes are not used for building Ensembl Compara gene trees, but instead are grouped into families based on HAMAP or Panther annotation. To retrieve these families, the following endpoints are provided: