Joint REST server for Ensembl and Ensembl Genomes in Ensembl 96

As of Ensembl release 96/Ensembl Genomes release 43, we will retire rest.ensemblgenomes.org and invite you to use rest.ensembl.org instead.

Any queries to rest.ensemblgenomes.org will return a 404 error, inviting you to replace this URL with rest.ensembl.org.

While we appreciate that this change will require you to update existing scripts and pipelines, we believe this is a positive move as all species available across all taxonomic divisions in Ensembl and Ensembl Genomes are now available through a single interface. Endpoints which only existed for vertebrates (rest.ensembl.org) are now available for invertebrate species where the data exists. Equally, endpoints which were only provided for invertebrates (rest.ensemblgenomes.org) can now be queried for vertebrates too.

We aim to make this change with as little disruption as possible, meaning that in most cases, simply replacing rest.ensemblgenomes.org with rest.ensembl.org in your REST call should work the same way as before.

Please find below the detailed list of all changes, to help you plan any required modifications ahead of Ensembl release 96/Ensembl Genomes release 43, which are scheduled for April 2019.

Comparative genomics endpoints

These endpoints provide access to gene tree and genomic alignment information. The data is split up in separate databases which are loosely based on taxonomic divisions or sub-groups. This means you need to specify which database (compara in the Ensembl jargon) to use depending on your species of interest.

You can find which databases are provided, as well as their exact names, from the info/comparas endpoint: http://rest.ensembl.org/info/comparas?content-type=application/json.

If no compara argument is specified, the endpoints default to vertebrates. If you have been using rest.ensemblgenomes.org until now without specifying a compara argument, defaulting to the plants database, you will now need to set it explicitly, otherwise you will be using the vertebrate data instead. If you have been using rest.ensembl.org until now without specifying a compara argument, you can keep doing so and still access vertebrate data. You might want to explore what other data is available across the taxonomic tree though!

Genomes endpoints

While these endpoints have been available for invertebrates for several years, they can now be used for vertebrates as well.

These endpoints allow you to find information about your favourite genome, searching by assembly accession (http://rest.ensembl.org/documentation/info/info_genomes_accession) or species name (http://rest.ensembl.org/documentation/info/info_genome), or simply explore all available species for a given division (http://rest.ensembl.org/documentation/info/info_genomes_division).

You can find out which divisions exist using the info/divisions endpoint: http://rest.ensembl.org/documentation/info/info_divisions.

The output formats of these endpoints have been partly modified from the output that used to be provided on the rest.ensemblgenomes.org server. The full list of fields in the old and new format is described here (empty fields represent field names that were not used in release 95, or will not be used in release 96, respectively):

Field name in release 95 Field name in release 96 Description
name display_name Human friendly name, e.g. “Chondrus crispus”
species name Snake_case version* of display_name, e.g. “chondrus_crispus”
url_name URL friendly version of display_name, e.g. “Chondrus_crispus”
assembly_id assembly_accession Official GCA accession
assembly_default
assembly_id Unique internal assembly ID
organism_id Unique internal organism ID
assembly_level assembly_level
assembly_name assembly_name
assembly_ucsc
base_count base_count
data_release_id
dbname
division division
genebuild genebuild
has_genome_alignments has_genome_alignments
has_other_alignments has_other_alignments
has_pan_compara has_pan_compara
has_peptide_compara has_peptide_compara
has_synteny
has_variations has_variations
is_reference is_reference
serotype serotype
species_id
species_taxonomy_id species_taxonomy_id
strain strain
taxonomy_id taxonomy_id

https://en.wikipedia.org/wiki/Snake_case

Info/species endpoint

This endpoint has been removed as its functionality is superseded by the info/genomes /division endpoint.

The full list of fields of the old info/species and the new info/genomes/division endpoint is described here:

Field name in /info/species Field name in /info/genomes/division Description
name name Species name
accession assembly_accession Official GCA accession
assembly assembly_name
assembly_id Unique internal assembly ID
assembly_level
assembly_default
assembly_ucsc
common_name
display_name display_name
url_name
division division
release
strain strain
strain_collection
taxon_id taxonomy_id
species_taxonomy_id
aliases
groups Available databases, supersed by ‘has_*’ fields
base_count
data_release_id
genebuild
has_genome_alignments
has_other_alignments
has_pan_compara
has_peptide_compara
has_synteny
has_variations
is_reference
organism_id
scientific_name
serotype

Other updates

Other updates include bug fixes and added functionality to existing endpoints, as detailed in our change log.

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