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Nucleic Acids Res. 2018 Jan 4;46(D1):D802-D808. doi: 10.1093/nar/gkx1011.

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

Author information

1
The European Molecular Biology Laboratory, The European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.
2
Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA.
3
USDA-ARS NAA Plant, Soil and Nutrition Laboratory Research Unit, Cornell University, Ithaca, NY 14853, USA.
4
Rothamsted Research, Department of Biointeractions and Crop Protection, Harpenden, Hertfordshire, AL5 2JQ, UK.

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.

PMID:
29092050
PMCID:
PMC5753204
DOI:
10.1093/nar/gkx1011
[Indexed for MEDLINE]
Free PMC Article

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