Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species. Issue Volume 46:Issue D1(2018) (30th October 2017)

• Record Type: Journal Article
• Authors: Kersey, Paul Julian; Allen, James E; Allot, Alexis; Barba, Matthieu; Boddu, Sanjay; Bolt, Bruce J; Carvalho-Silva, Denise; Christensen, Mikkel; Davis, Paul; Grabmueller, Christoph; Kumar, Navin; Liu, Zicheng; Maurel, Thomas; Moore, Ben; McDowall, Mark D; Maheswari, Uma; Naamati, Guy; Newman, Victoria; Ong, Chuang Kee; Paulini, Michael; Pedro, Helder; Perry, Emily; Russell, Matthew; Sparrow, Helen; Tapanari, Electra; Taylor, Kieron; Vullo, Alessandro; Williams, Gareth; Zadissia, Amonida; Olson, Andrew; Stein, Joshua; Wei, Sharon; Tello-Ruiz, Marcela; Ware, Doreen; Luciani, Aurelien; Potter, Simon; Finn, Robert D; Urban, Martin; Hammond-Kosack, Kim E; Bolser, Dan M; De Silva, Nishadi; Howe, Kevin L; Langridge, Nicholas; Maslen, Gareth; Staines, Daniel Michael; Yates, Andrew;
• Is Part Of: Nucleic acids research. Volume 46:Issue D1(2018)
• Page Start: D802
• Page End: D808
• Publication Date: 2017-10-30
• Subjects: Nucleic acids -- Periodicals; Molecular biology -- Periodicals; 572.805
• DOI: 10.1093/nar/gkx1011
• Languages: English
• ISSNs: 0305-1048

Abstract

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.