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Ensembl BioMarts: a hub for data retrieval across taxonomic space

For a number of years the BioMart data warehousing system has proven to be a valuable resource for scientists seeking a fast and versatile means of accessing the growing volume of genomic data provided by the Ensembl project. The launch of the Ensembl Genomes project in 2009 complemented the Ensembl...

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Autores principales: Kinsella, Rhoda J., Kähäri, Andreas, Haider, Syed, Zamora, Jorge, Proctor, Glenn, Spudich, Giulietta, Almeida-King, Jeff, Staines, Daniel, Derwent, Paul, Kerhornou, Arnaud, Kersey, Paul, Flicek, Paul
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3170168/
https://www.ncbi.nlm.nih.gov/pubmed/21785142
http://dx.doi.org/10.1093/database/bar030
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author Kinsella, Rhoda J.
Kähäri, Andreas
Haider, Syed
Zamora, Jorge
Proctor, Glenn
Spudich, Giulietta
Almeida-King, Jeff
Staines, Daniel
Derwent, Paul
Kerhornou, Arnaud
Kersey, Paul
Flicek, Paul
author_facet Kinsella, Rhoda J.
Kähäri, Andreas
Haider, Syed
Zamora, Jorge
Proctor, Glenn
Spudich, Giulietta
Almeida-King, Jeff
Staines, Daniel
Derwent, Paul
Kerhornou, Arnaud
Kersey, Paul
Flicek, Paul
author_sort Kinsella, Rhoda J.
collection PubMed
description For a number of years the BioMart data warehousing system has proven to be a valuable resource for scientists seeking a fast and versatile means of accessing the growing volume of genomic data provided by the Ensembl project. The launch of the Ensembl Genomes project in 2009 complemented the Ensembl project by utilizing the same visualization, interactive and programming tools to provide users with a means for accessing genome data from a further five domains: protists, bacteria, metazoa, plants and fungi. The Ensembl and Ensembl Genomes BioMarts provide a point of access to the high-quality gene annotation, variation data, functional and regulatory annotation and evolutionary relationships from genomes spanning the taxonomic space. This article aims to give a comprehensive overview of the Ensembl and Ensembl Genomes BioMarts as well as some useful examples and a description of current data content and future objectives. Database URLs: http://www.ensembl.org/biomart/martview/; http://metazoa.ensembl.org/biomart/martview/; http://plants.ensembl.org/biomart/martview/; http://protists.ensembl.org/biomart/martview/; http://fungi.ensembl.org/biomart/martview/; http://bacteria.ensembl.org/biomart/martview/
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spelling pubmed-31701682011-09-12 Ensembl BioMarts: a hub for data retrieval across taxonomic space Kinsella, Rhoda J. Kähäri, Andreas Haider, Syed Zamora, Jorge Proctor, Glenn Spudich, Giulietta Almeida-King, Jeff Staines, Daniel Derwent, Paul Kerhornou, Arnaud Kersey, Paul Flicek, Paul Database (Oxford) Original Article For a number of years the BioMart data warehousing system has proven to be a valuable resource for scientists seeking a fast and versatile means of accessing the growing volume of genomic data provided by the Ensembl project. The launch of the Ensembl Genomes project in 2009 complemented the Ensembl project by utilizing the same visualization, interactive and programming tools to provide users with a means for accessing genome data from a further five domains: protists, bacteria, metazoa, plants and fungi. The Ensembl and Ensembl Genomes BioMarts provide a point of access to the high-quality gene annotation, variation data, functional and regulatory annotation and evolutionary relationships from genomes spanning the taxonomic space. This article aims to give a comprehensive overview of the Ensembl and Ensembl Genomes BioMarts as well as some useful examples and a description of current data content and future objectives. Database URLs: http://www.ensembl.org/biomart/martview/; http://metazoa.ensembl.org/biomart/martview/; http://plants.ensembl.org/biomart/martview/; http://protists.ensembl.org/biomart/martview/; http://fungi.ensembl.org/biomart/martview/; http://bacteria.ensembl.org/biomart/martview/ Oxford University Press 2011-07-23 /pmc/articles/PMC3170168/ /pubmed/21785142 http://dx.doi.org/10.1093/database/bar030 Text en © The Author(s) 2011. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/2.5 This is Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Original Article
Kinsella, Rhoda J.
Kähäri, Andreas
Haider, Syed
Zamora, Jorge
Proctor, Glenn
Spudich, Giulietta
Almeida-King, Jeff
Staines, Daniel
Derwent, Paul
Kerhornou, Arnaud
Kersey, Paul
Flicek, Paul
Ensembl BioMarts: a hub for data retrieval across taxonomic space
title Ensembl BioMarts: a hub for data retrieval across taxonomic space
title_full Ensembl BioMarts: a hub for data retrieval across taxonomic space
title_fullStr Ensembl BioMarts: a hub for data retrieval across taxonomic space
title_full_unstemmed Ensembl BioMarts: a hub for data retrieval across taxonomic space
title_short Ensembl BioMarts: a hub for data retrieval across taxonomic space
title_sort ensembl biomarts: a hub for data retrieval across taxonomic space
topic Original Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3170168/
https://www.ncbi.nlm.nih.gov/pubmed/21785142
http://dx.doi.org/10.1093/database/bar030
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