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BioMart Virtual Issue


This virtual issue of DATABASE is dedicated to BioMart : an open source data federation system and its applications to different types of biological data. 2011 marks the 10 year anniversary of the BioMart project. The project originated at the European Bioinformatics Institute as an Ensembl genomic database data mining solution that was designed and implemented by a single developer. Since then, BioMart has grown to become a multi-institute collaboration involving a large number of different database projects on five continents: Asia, Australia, Europe, North America and South America. Recently, BioMart has successfully solved the unprecedented data management challenges of the International Cancer Genome Consortium, proving that BioMart's technology scales when applied to next generation sequencing data produced in a distributed environment. Building on its achievements and supported by the dedicated community of users and developers, the BioMart project will continue to deliver the most innovative data management solutions for scientific research for years to come.

BioMart: driving a paradigm change in biological data management
Arek Kasprzyk
Database Vol. 2011, doi:10.1093/database/bar049
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Data mining using the Catalogue of Somatic Mutations in Cancer BioMart
Rebecca Shepherd, Simon A. Forbes, David Beare, S. Bamford, Charlotte G. Cole, Sari Ward, Nidhi Bindal, Prasad Gunasekaran, Mingming Jia, Chai Yin Kok, Kenric Leung, Andrew Menzies, Adam P. Butler, Jon W. Teague, Peter J. Campbell, Michael R. Stratton, and P. Andrew Futreal
Database Vol. 2011, doi:10.1093/database/bar018
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Using BioMart as a framework to manage and query pancreatic cancer data
Rosalind J. Cutts, Emanuela Gadaleta, Nicholas R. Lemoine, and Claude Chelala
Database Vol. 2011, doi:10.1093/database/bar024
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SigReannot-mart: A query environment for expression microarray probe re-annotations
François Moreews, Gaelle Rauffet, Patrice Dehais, and Christophe Klopp
Database Vol. 2011, doi:10.1093/database/bar025
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International Cancer Genome Consortium Data Portal: A One Stop Shop for Cancer Genomics Data
Junjun Zhang, Joachim Baran, A. Cros, Jonathan M. Guberman, Syed Haider, Jack Hsu, Yong Liang, Elena Rivkin, Jianxin Wang, Brett Whitty, Marie Wong-Erasmus, Long Yao, and Arek Kasprzyk
Database Vol. 2011, doi:10.1093/database/bar026
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BioMart as an integration solution for the International Knockout Mouse Consortium
Darren J. Oakley, Vivek Iyer, William C. Skarnes, and Damian Smedley
Database Vol. 2011, doi:10.1093/database/bar028
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The BioMart interface to the EMAGE gene expression database
Peter Stevenson, Lorna Richardson, Shanmugasundaram Venkataraman, Yiya Yang, Richard Baldock.
Database Vol. 2011, doi:10.1093/database/bar029
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Ensembl BioMarts: a hub for data retrieval across the taxonomic space
Rhoda J. Kinsella, Andreas Kähäri, Syed Haider, Jorge Zamora, Glenn Proctor, Giulietta Spudich, Jeff Almeida-King, Daniel Staines, Paul Derwent, Arnaud Kerhornou, Paul Kersey, and Paul Flicek
Database Vol. 2011, doi:10.1093/database/bar030
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The Reactome BioMart
Robin Haw, David Croft, Christina K Yung, Nelson Ndegwa, Peter D’Eustachio, Henning Hermajakob and Lincoln Stein
Database Vol. 2011, doi:10.1093/database/bar031
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The InterPro BioMart: Powerful, federated query and web-service access to the InterPro resource
Philip Jones, David Binns, Conor McMenamin, Craig McAnulla, and Sarah Hunter
Database Vol. 2011, doi:10.1093/database/bar033
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BioMart: A data federation framework for large collaborative projects
Junjun Zhang, Syed Haider, Joachim Baran, Anthony Cros, Jonathan M. Guberman, Jack Hsu, Yong Liang, Long Yao, and Arek Kasprzyk
Database Vol. 2011, doi:10.1093/database/bar038
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Integrative Cancer Genomics (IntOGen) in BioMart
Christian Perez-Llamas, Gunes Gundem and Nuria Lopez-Bigas
Database Vol. 2011, doi:10.1093/database/bar039
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BioMart Central Portal: An Open Database Network for Biological Community
Jonathan M. Guberman, J. Ai, O. Arnaiz, Joachim Baran, Andrew Blake, Richard Baldock, Claude Chelala, David Croft, Anthony Cros, Rosalind J. Cutts, A. Di Génova, Simon Forbes, T. Fujisawa, E. Gadaleta, D. M. Goodstein, Gunes Gundem, Bernard Haggarty, Syed Haider, Matthew Hall, Todd Harris, Robin Haw, S. Hu, Simon Hubbard, Jack Hsu, Vivek Iyer, Philip Jones, Toshiaki Katayama, R. Kinsella, Lei Kong, Daniel Lawson, Yong Liang, Nuria Lopez-Bigas, J. Luo, Michael Lush, Jeremy Mason, Francois Moreews, Nelson Ndegwa, Darren Oakley, Christian Perez-Llamas, Michael Primig, Elena Rivkin, S. Rosanoff, Rebecca Shepherd, Reinhard Simon, B. Skarnes, Damian Smedley, Linda Sperling, William Spooner, Peter Stevenson, Kevin Stone, J. Teague, Jun Wang, Jianxin Wang, Brett Whitty, D. T. Wong, Marie Wong-Erasmus, L. Yao, Ken Youens-Clark, Christina Yung, Junjun Zhang, and Arek Kasprzyk
Database Vol. 2011, doi:10.1093/database/bar041
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Critical amino acid residues in proteins: a BioMart integration of Reactome protein annotations with PRIDE mass spectrometry data and COSMIC somatic mutations
Nelson Ndegwa, Richard G. Côté, David Ovelleiro, Peter D'Eustachio, Henning Hermjakob, Juan A. Vizcaíno and David Croft
Database Vol. 2011, doi:10.1093/database/bar047
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GrameneMart: the BioMart data portal for the Gramene project
William Spooner, Ken Youens-Clark, Daniel Staines, and Doreen Ware
Database Vol.2012, doi:10.1093/database/bar056
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