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

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 program...

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Autores principales: 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
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753204/
https://www.ncbi.nlm.nih.gov/pubmed/29092050
http://dx.doi.org/10.1093/nar/gkx1011
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author 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
author_facet 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
author_sort Kersey, Paul Julian
collection PubMed
description 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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spelling pubmed-57532042018-01-05 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 Nucleic Acids Res Database Issue 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. Oxford University Press 2018-01-04 2017-10-30 /pmc/articles/PMC5753204/ /pubmed/29092050 http://dx.doi.org/10.1093/nar/gkx1011 Text en © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Database Issue
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
Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species
title Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species
title_full Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species
title_fullStr Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species
title_full_unstemmed Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species
title_short Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species
title_sort ensembl genomes 2018: an integrated omics infrastructure for non-vertebrate species
topic Database Issue
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753204/
https://www.ncbi.nlm.nih.gov/pubmed/29092050
http://dx.doi.org/10.1093/nar/gkx1011
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