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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.
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:
- GET info/divisions - Get list of all Ensembl divisions for which information is available
- GET info/genomes/division/:division - Find information about all genomes in a given division. May be large for Ensembl Bacteria.
- GET info/genomes/taxonomy:taxon - Find information about all genomes beneath a given node of the taxonomy (includes Ensembl and Ensembl Genomes)
- GET info/genomes/:name - Find information about a given genome
- GET info/genomes - Find information about all genomes. Response may be very large.
- GET info/genomes/accession - Find information about genomes containing a specified INSDC accession
- GET info/genomes/assembly - Find information about a genome with a specified assembly
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: