BioMart Publications
When citing BioMart, refer to this paper:
BioMart: driving a paradigm change in biological data management.

Kasprzyk A.

Database (Oxford). 2011 Nov 13;2011:bar049. Print 2011. PubMed PMID: 22083790;

Nature Methods' Technology Feature
Quantitative data: learning to share.

Monya Baker

Nature Methods 9, 39–41 (2012) doi:10.1038/nmeth.1815

DATABASE Special Issue Dedicated to BioMart

BioMart is a unique open source data federation technology that provides unified access to distributed databases storing a wide range of data. This DATABASE issue recognizes BioMart's outstanding contributions to bioinformatics and documents the achievements of the BioMart community, which has grown impressively over the last ten years to become what it is today, a collaboration between numerous database projects on five continents: Asia, Australia, Europe, North America and South America.

Publications by the BioMart Team
BioMart: driving a paradigm change in biological data management

Kasprzyk A

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

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

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

BioMart Central Portal - unified access to biological data

Haider S, Ballester B, Smedley, D, Zhang J, Rice P, Kasprzyk A

BioMart - biological queries made easy

Smedley D, Haider S, Ballester B, Holland R, London D, Thorisson G, Kasprzyk A

BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis

Durinck S, Moreau Y, Kasprzyk A, Davis S, De Moor B, Brazma A, Huber W

EnsMart: A Generic System for Fast and Flexible Access to Biological Data

Kasprzyk A, Keefe D, Smedley D, London D, Spooner W, Melsopp C, Hammond M, Rocca-Serra P, Cox T, Birney E

Publications by the BioMart Community
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

Integrative Cancer Genomics (IntOGen) in BioMart

Christian Perez-Llamas, Gunes Gundem and Nuria Lopez-Bigas

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

The Reactome BioMart

Robin Haw, David Croft, Christina K Yung, Nelson Ndegwa, Peter D’Eustachio, Henning Hermajakob and Lincoln Stein

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

The BioMart interface to the EMAGE gene expression database

Peter Stevenson, Lorna Richardson, Shanmugasundaram Venkataraman, Yiya Yang, Richard Baldock

BioMart as an integration solution for the International Knockout Mouse Consortium

Darren J. Oakley, Vivek Iyer, William C. Skarnes, and Damian Smedley

SigReannot-mart: A query environment for expression microarray probe re-annotations

François Moreews, Gaelle Rauffet, Patrice Dehais, and Christophe Klopp

Using BioMart as a framework to manage and query pancreatic cancer data

Rosalind J. Cutts, Emanuela Gadaleta, Nicholas R. Lemoine, and Claude Chelala

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

Shopping in the genome market with EnsMart

Gilbert D