Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species

Paul Kersey(European Bioinformatics Institute), James E. Allen(European Bioinformatics Institute), Alexis Allot(European Bioinformatics Institute), Matthieu Barba(European Bioinformatics Institute), Sanjay Boddu(European Bioinformatics Institute), Bruce J. Bolt(European Bioinformatics Institute), Denise Carvalho‐Silva(European Bioinformatics Institute), Mikkel Christensen(European Bioinformatics Institute), Paul A. Davis(European Bioinformatics Institute), Christoph Grabmueller(European Bioinformatics Institute), Navin Kumar(European Bioinformatics Institute), Zicheng Liu(European Bioinformatics Institute), Thomas Maurel(European Bioinformatics Institute), Benjamin Moore(European Bioinformatics Institute), Mark D. McDowall(European Bioinformatics Institute), Uma Maheswari(European Bioinformatics Institute), Guy Naamati(European Bioinformatics Institute), Victoria Newman(European Bioinformatics Institute), Chuang Kee Ong(European Bioinformatics Institute), Michael Paulini(European Bioinformatics Institute), Helder Pedro(European Bioinformatics Institute), Emily Perry(European Bioinformatics Institute), Matthew Russell(European Bioinformatics Institute), Helen Sparrow(European Bioinformatics Institute), Electra Tapanari(European Bioinformatics Institute), Kieron Taylor(European Bioinformatics Institute), Alessandro Vullo(European Bioinformatics Institute), Gareth Williams(European Bioinformatics Institute), Amonida Zadissia(European Bioinformatics Institute), Andrew Olson(Cold Spring Harbor Laboratory), Joshua C. Stein(Cold Spring Harbor Laboratory), Sharon Wei(Cold Spring Harbor Laboratory), Marcela K Tello-Ruiz(Cold Spring Harbor Laboratory), Doreen Ware(Cornell University), Aurélien Luciani(European Bioinformatics Institute), Simon Potter(European Bioinformatics Institute), ROBERT FINN(European Bioinformatics Institute), Martin Urban(Rothamsted Research), K. E. Hammond‐Kosack(Rothamsted Research), Dan Bolser(European Bioinformatics Institute), Nishadi De Silva(European Bioinformatics Institute), Kevin Howe(European Bioinformatics Institute), Nicholas Langridge(European Bioinformatics Institute), G. Maslen(European Bioinformatics Institute), D. Staines(European Bioinformatics Institute), Andrew Yates(European Bioinformatics Institute)
Nucleic Acids Research
October 24, 2017
10.1093/nar/gkx1011
Cited by 484Open Access
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Abstract

Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of programmatic and interactive interfaces to a rich range of data including genome sequence, gene models, transcript sequence, genetic variation, and comparative analysis. This paper provides an update to the previous publications about the resource, with a focus on recent developments and expansions. These include the incorporation of almost 20 000 additional genome sequences and over 35 000 tracks of RNA-Seq data, which have been aligned to genomic sequence and made available for visualization. Other advances since 2015 include the release of the database in Resource Description Framework (RDF) format, a large increase in community-derived curation, a new high-performance protein sequence search, additional cross-references, improved annotation of non-protein-coding genes, and the launch of pre-release and archival sites. Collectively, these changes are part of a continuing response to the increasing quantity of publicly-available genome-scale data, and the consequent need to archive, integrate, annotate and disseminate these using automated, scalable methods.

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