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Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species.
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.
Affiliation
  • Kersey PJ; The European Molecular Biology Laboratory, The European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.
  • Allen JE; The European Molecular Biology Laboratory, The European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.
  • Allot A; The European Molecular Biology Laboratory, The European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.
  • Barba M; The European Molecular Biology Laboratory, The European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.
  • Boddu S; The European Molecular Biology Laboratory, The European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.
  • Bolt BJ; The European Molecular Biology Laboratory, The European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.
  • Carvalho-Silva D; The European Molecular Biology Laboratory, The European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.
  • Christensen M; The European Molecular Biology Laboratory, The European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.
  • Davis P; The European Molecular Biology Laboratory, The European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.
  • Grabmueller C; The European Molecular Biology Laboratory, The European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.
  • Kumar N; The European Molecular Biology Laboratory, The European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.
  • Liu Z; The European Molecular Biology Laboratory, The European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.
  • Maurel T; The European Molecular Biology Laboratory, The European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.
  • Moore B; The European Molecular Biology Laboratory, The European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.
  • McDowall MD; The European Molecular Biology Laboratory, The European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.
  • Maheswari U; The European Molecular Biology Laboratory, The European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.
  • Naamati G; The European Molecular Biology Laboratory, The European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.
  • Newman V; The European Molecular Biology Laboratory, The European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.
  • Ong CK; The European Molecular Biology Laboratory, The European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.
  • Paulini M; The European Molecular Biology Laboratory, The European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.
  • Pedro H; The European Molecular Biology Laboratory, The European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.
  • Perry E; The European Molecular Biology Laboratory, The European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.
  • Russell M; The European Molecular Biology Laboratory, The European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.
  • Sparrow H; The European Molecular Biology Laboratory, The European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.
  • Tapanari E; The European Molecular Biology Laboratory, The European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.
  • Taylor K; The European Molecular Biology Laboratory, The European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.
  • Vullo A; The European Molecular Biology Laboratory, The European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.
  • Williams G; The European Molecular Biology Laboratory, The European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.
  • Zadissia A; The European Molecular Biology Laboratory, The European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.
  • Olson A; Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA.
  • Stein J; Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA.
  • Wei S; Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA.
  • Tello-Ruiz M; Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA.
  • Ware D; Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA.
  • Luciani A; USDA-ARS NAA Plant, Soil and Nutrition Laboratory Research Unit, Cornell University, Ithaca, NY 14853, USA.
  • Potter S; The European Molecular Biology Laboratory, The European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.
  • Finn RD; The European Molecular Biology Laboratory, The European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.
  • Urban M; The European Molecular Biology Laboratory, The European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.
  • Hammond-Kosack KE; Rothamsted Research, Department of Biointeractions and Crop Protection, Harpenden, Hertfordshire, AL5 2JQ, UK.
  • Bolser DM; Rothamsted Research, Department of Biointeractions and Crop Protection, Harpenden, Hertfordshire, AL5 2JQ, UK.
  • De Silva N; The European Molecular Biology Laboratory, The European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.
  • Howe KL; The European Molecular Biology Laboratory, The European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.
  • Langridge N; The European Molecular Biology Laboratory, The European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.
  • Maslen G; The European Molecular Biology Laboratory, The European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.
  • Staines DM; The European Molecular Biology Laboratory, The European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.
  • Yates A; The European Molecular Biology Laboratory, The European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.
Nucleic Acids Res ; 46(D1): D802-D808, 2018 01 04.
Article in En | MEDLINE | ID: mdl-29092050
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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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Bacteria / Archaea / Genomics / Databases, Genetic / Databases, Protein / Eukaryota Type of study: Prognostic_studies Limits: Animals Language: En Journal: Nucleic Acids Res Year: 2018 Document type: Article Affiliation country:
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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Bacteria / Archaea / Genomics / Databases, Genetic / Databases, Protein / Eukaryota Type of study: Prognostic_studies Limits: Animals Language: En Journal: Nucleic Acids Res Year: 2018 Document type: Article Affiliation country: