. 2015 Jul 1;43(W1):W589-98.

doi: 10.1093/nar/gkv350. Epub 2015 Apr 20.

The BioMart community portal: an innovative alternative to large, centralized data repositories

Damian Smedley¹, Syed Haider², Steffen Durinck³, Luca Pandini⁴, Paolo Provero⁵, James Allen⁶, Olivier Arnaiz⁷, Mohammad Hamza Awedh⁸, Richard Baldock⁹, Giulia Barbiera⁴, Philippe Bardou¹⁰, Tim Beck¹¹, Andrew Blake¹², Merideth Bonierbale¹³, Anthony J Brookes¹¹, Gabriele Bucci⁴, Iwan Buetti⁴, Sarah Burge⁶, Cédric Cabau¹⁰, Joseph W Carlson¹⁴, Claude Chelala¹⁵, Charalambos Chrysostomou¹¹, Davide Cittaro⁴, Olivier Collin¹⁶, Raul Cordova¹³, Rosalind J Cutts¹⁵, Erik Dassi¹⁷, Alex Di Genova¹⁸, Anis Djari¹⁹, Anthony Esposito²⁰, Heather Estrella²⁰, Eduardo Eyras²¹, Julio Fernandez-Banet²⁰, Simon Forbes¹, Robert C Free¹¹, Takatomo Fujisawa²², Emanuela Gadaleta¹⁵, Jose M Garcia-Manteiga⁴, David Goodstein¹⁴, Kristian Gray²³, José Afonso Guerra-Assunção¹⁵, Bernard Haggarty⁹, Dong-Jin Han²⁴, Byung Woo Han²⁵, Todd Harris²⁶, Jayson Harshbarger²⁷, Robert K Hastings¹¹, Richard D Hayes¹⁴, Claire Hoede¹⁹, Shen Hu²⁸, Zhi-Liang Hu²⁹, Lucie Hutchins³⁰, Zhengyan Kan²⁰, Hideya Kawaji³¹, Aminah Keliet³², Arnaud Kerhornou⁶, Sunghoon Kim²⁴, Rhoda Kinsella⁶, Christophe Klopp¹⁹, Lei Kong³³, Daniel Lawson³⁴, Dejan Lazarevic⁴, Ji-Hyun Lee³⁵, Thomas Letellier³², Chuan-Yun Li³⁶, Pietro Lio³⁷, Chu-Jun Liu³⁶, Jie Luo⁶, Alejandro Maass³⁸, Jerome Mariette¹⁹, Thomas Maurel⁶, Stefania Merella⁴, Azza Mostafa Mohamed³⁹, Francois Moreews¹⁰, Ibounyamine Nabihoudine¹⁹, Nelson Ndegwa⁴⁰, Céline Noirot¹⁹, Cristian Perez-Llamas⁴¹, Michael Primig⁴², Alessandro Quattrone¹⁷, Hadi Quesneville³², Davide Rambaldi⁴, James Reecy²⁹, Michela Riba⁴, Steven Rosanoff⁶, Amna Ali Saddiq⁴³, Elisa Salas¹³, Olivier Sallou¹⁶, Rebecca Shepherd¹, Reinhard Simon¹³, Linda Sperling⁷, William Spooner⁴⁴, Daniel M Staines⁶, Delphine Steinbach³², Kevin Stone³⁰, Elia Stupka⁴, Jon W Teague¹, Abu Z Dayem Ullah¹⁵, Jun Wang³³, Doreen Ware⁴⁵, Marie Wong-Erasmus⁴⁶, Ken Youens-Clark⁴⁵, Amonida Zadissa⁶, Shi-Jian Zhang³⁶, Arek Kasprzyk⁴⁷

Affiliations

¹ Wellcome Trust Sanger Institute, Welcome Trust Genome Campus, Hinxton, CB10 1SD, UK.
² The Weatherall Institute Of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK.
³ Genentech, Inc. 1 DNA Way South San Francisco, CA 94080, USA.
⁴ Center for Translational Genomics and Bioinformatics San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy.
⁵ Center for Translational Genomics and Bioinformatics San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy Dept of Molecular Biotechnology and Health Sciences University of Turin, Italy.
⁶ European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
⁷ Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris Sud, 1 avenue de la terrasse, 91198 Gif sur Yvette, France.
⁸ Department of Electrical and Computer Engineering, Faculty of Engineering, King Abdulaziz University, Jeddah, Saudi Arabia.
⁹ MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK.
¹⁰ Sigenae, INRA, Castanet-Tolosan, France.
¹¹ Department of Genetics, University of Leicester, University Road, Leicester, LE1 7RH, UK.
¹² MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK.
¹³ International Potato Center (CIP), Lima, 1558, Peru.
¹⁴ Department of Energy, Joint Genome Institute, Walnut Creek, USA.
¹⁵ Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK.
¹⁶ IRISA-INRIA, Campus de Beaulieu 35042 Rennes, France.
¹⁷ Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, Trento, Italy.
¹⁸ Center for Mathematical Modeling and Center for Genome Regulation, University of Chile, Beauchef 851, 7th floor, Chile.
¹⁹ Plate-forme bio-informatique Genotoul, Mathématiques et Informatique Appliquées de Toulouse, INRA, Castanet-Tolosan, France.
²⁰ Oncology Computational Biology, Pfizer, La Jolla, USA.
²¹ Catalan Institute for Research and Advanced Studies (ICREA), Passeig Lluis Companys 23, E-08010 Barcelona, Spain Universitat Pompeu Fabra, Dr Aiguader 88 E-08003 Barcelona, Spain.
²² Kasuza DNA Research Institute, Chiba, 292-0818, Japan.
²³ HUGO Gene Nomenclature Committee (HGNC), European Bioinformatics Institute (EMBL-EBI) Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK.
²⁴ Medicinal Bioconvergence Research Center, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea Department of Molecular Medicine and Biopharmaceutical Sciences, Seoul National University, Seoul 151-742, Republic of Korea.
²⁵ Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea Information Center for Bio-pharmacological Network, Seoul National University, Suwon 443-270, Republic of Korea.
²⁶ Ontario Institute for Cancer Research, Toronto, M5G 0A3, Canada.
²⁷ RIKEN Center for Life Science Technologies (CLST), Division of Genomic Technologies (DGT), Kanagawa, 230-0045, Japan.
²⁸ School of Dentistry and Dental Research Institute, University of California Los Angeles (UCLA), Los Angeles, CA 90095-1668, USA.
²⁹ Iowa State Univeristy, USA.
³⁰ Mouse Genomic Informatics Group, The Jackson Laboratory, Bar Harbor, ME 04609, USA.
³¹ RIKEN Center for Life Science Technologies (CLST), Division of Genomic Technologies (DGT), Kanagawa, 230-0045, Japan RIKEN Preventive Medicine and Diagnosis Innovation Program, Saitama 351-0198, Japan.
³² INRA URGI Centre de Versailles, bâtiment 18 Route de Saint Cyr 78026 Versailles, France.
³³ Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, 100871, P.R. China.
³⁴ VectorBase, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK.
³⁵ Medicinal Bioconvergence Research Center, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea Information Center for Bio-pharmacological Network, Seoul National University, Suwon 443-270, Republic of Korea.
³⁶ Institute of Molecular Medicine, Peking University, Beijing, China.
³⁷ Computer Laboratory, University of Cambridge, Cambridge, CB3 0FD, UK.
³⁸ Center for Mathematical Modeling and Center for Genome Regulation, University of Chile, Beauchef 851, 7th floor, Chile Department of Mathematical Engineering, University of Chile, Av. Beauchef 851, 5th floor, Santiago, Chile.
³⁹ Departament of Biochemistry, Faculty of Science for Girls, King Abdulaziz University, Jeddah, Saudi Arabia.
⁴⁰ Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, PO Box 281, 17177 Stockholm, Sweden.
⁴¹ Universitat Pompeu Fabra, Dr Aiguader 88 E-08003 Barcelona, Spain.
⁴² Inserm U1085 IRSET, University of Rennes 1, 35042 Rennes, France.
⁴³ Department of Biological Sciences, Faculty of Science for Girls, King Abdulaziz University, Jeddah, Saudi Arabia.
⁴⁴ Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA Eagle Genomics Ltd., Babraham Research Campus, Cambridge, CB22 3AT, UK.
⁴⁵ Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
⁴⁶ Human Longevity, Inc. 10835 Road to the Cure 140 San Diego, CA 92121, USA.
⁴⁷ Center for Translational Genomics and Bioinformatics San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia Arek.Kasprzyk@gmail.com.

PMID: 25897122
PMCID: PMC4489294
DOI: 10.1093/nar/gkv350

The BioMart community portal: an innovative alternative to large, centralized data repositories

Damian Smedley et al. Nucleic Acids Res. 2015.

. 2015 Jul 1;43(W1):W589-98.

doi: 10.1093/nar/gkv350. Epub 2015 Apr 20.

Authors

Affiliations

¹ Wellcome Trust Sanger Institute, Welcome Trust Genome Campus, Hinxton, CB10 1SD, UK.
² The Weatherall Institute Of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK.
³ Genentech, Inc. 1 DNA Way South San Francisco, CA 94080, USA.
⁴ Center for Translational Genomics and Bioinformatics San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy.
⁵ Center for Translational Genomics and Bioinformatics San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy Dept of Molecular Biotechnology and Health Sciences University of Turin, Italy.
⁶ European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
⁷ Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris Sud, 1 avenue de la terrasse, 91198 Gif sur Yvette, France.
⁸ Department of Electrical and Computer Engineering, Faculty of Engineering, King Abdulaziz University, Jeddah, Saudi Arabia.
⁹ MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK.
¹⁰ Sigenae, INRA, Castanet-Tolosan, France.
¹¹ Department of Genetics, University of Leicester, University Road, Leicester, LE1 7RH, UK.
¹² MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK.
¹³ International Potato Center (CIP), Lima, 1558, Peru.
¹⁴ Department of Energy, Joint Genome Institute, Walnut Creek, USA.
¹⁵ Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK.
¹⁶ IRISA-INRIA, Campus de Beaulieu 35042 Rennes, France.
¹⁷ Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, Trento, Italy.
¹⁸ Center for Mathematical Modeling and Center for Genome Regulation, University of Chile, Beauchef 851, 7th floor, Chile.
¹⁹ Plate-forme bio-informatique Genotoul, Mathématiques et Informatique Appliquées de Toulouse, INRA, Castanet-Tolosan, France.
²⁰ Oncology Computational Biology, Pfizer, La Jolla, USA.
²¹ Catalan Institute for Research and Advanced Studies (ICREA), Passeig Lluis Companys 23, E-08010 Barcelona, Spain Universitat Pompeu Fabra, Dr Aiguader 88 E-08003 Barcelona, Spain.
²² Kasuza DNA Research Institute, Chiba, 292-0818, Japan.
²³ HUGO Gene Nomenclature Committee (HGNC), European Bioinformatics Institute (EMBL-EBI) Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK.
²⁴ Medicinal Bioconvergence Research Center, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea Department of Molecular Medicine and Biopharmaceutical Sciences, Seoul National University, Seoul 151-742, Republic of Korea.
²⁵ Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea Information Center for Bio-pharmacological Network, Seoul National University, Suwon 443-270, Republic of Korea.
²⁶ Ontario Institute for Cancer Research, Toronto, M5G 0A3, Canada.
²⁷ RIKEN Center for Life Science Technologies (CLST), Division of Genomic Technologies (DGT), Kanagawa, 230-0045, Japan.
²⁸ School of Dentistry and Dental Research Institute, University of California Los Angeles (UCLA), Los Angeles, CA 90095-1668, USA.
²⁹ Iowa State Univeristy, USA.
³⁰ Mouse Genomic Informatics Group, The Jackson Laboratory, Bar Harbor, ME 04609, USA.
³¹ RIKEN Center for Life Science Technologies (CLST), Division of Genomic Technologies (DGT), Kanagawa, 230-0045, Japan RIKEN Preventive Medicine and Diagnosis Innovation Program, Saitama 351-0198, Japan.
³² INRA URGI Centre de Versailles, bâtiment 18 Route de Saint Cyr 78026 Versailles, France.
³³ Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, 100871, P.R. China.
³⁴ VectorBase, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK.
³⁵ Medicinal Bioconvergence Research Center, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea Information Center for Bio-pharmacological Network, Seoul National University, Suwon 443-270, Republic of Korea.
³⁶ Institute of Molecular Medicine, Peking University, Beijing, China.
³⁷ Computer Laboratory, University of Cambridge, Cambridge, CB3 0FD, UK.
³⁸ Center for Mathematical Modeling and Center for Genome Regulation, University of Chile, Beauchef 851, 7th floor, Chile Department of Mathematical Engineering, University of Chile, Av. Beauchef 851, 5th floor, Santiago, Chile.
³⁹ Departament of Biochemistry, Faculty of Science for Girls, King Abdulaziz University, Jeddah, Saudi Arabia.
⁴⁰ Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, PO Box 281, 17177 Stockholm, Sweden.
⁴¹ Universitat Pompeu Fabra, Dr Aiguader 88 E-08003 Barcelona, Spain.
⁴² Inserm U1085 IRSET, University of Rennes 1, 35042 Rennes, France.
⁴³ Department of Biological Sciences, Faculty of Science for Girls, King Abdulaziz University, Jeddah, Saudi Arabia.
⁴⁴ Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA Eagle Genomics Ltd., Babraham Research Campus, Cambridge, CB22 3AT, UK.
⁴⁵ Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
⁴⁶ Human Longevity, Inc. 10835 Road to the Cure 140 San Diego, CA 92121, USA.
⁴⁷ Center for Translational Genomics and Bioinformatics San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia Arek.Kasprzyk@gmail.com.

PMID: 25897122
PMCID: PMC4489294
DOI: 10.1093/nar/gkv350

Abstract

The BioMart Community Portal (www.biomart.org) is a community-driven effort to provide a unified interface to biomedical databases that are distributed worldwide. The portal provides access to numerous database projects supported by 30 scientific organizations. It includes over 800 different biological datasets spanning genomics, proteomics, model organisms, cancer data, ontology information and more. All resources available through the portal are independently administered and funded by their host organizations. The BioMart data federation technology provides a unified interface to all the available data. The latest version of the portal comes with many new databases that have been created by our ever-growing community. It also comes with better support and extensibility for data analysis and visualization tools. A new addition to our toolbox, the enrichment analysis tool is now accessible through graphical and web service interface. The BioMart community portal averages over one million requests per day. Building on this level of service and the wealth of information that has become available, the BioMart Community Portal has introduced a new, more scalable and cheaper alternative to the large data stores maintained by specialized organizations.

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Figures

**Figure 1.**
BioMart community databases and their host countries.

**Figure 2.**
The network graphic output of the BioMart enrichment tool. The Gene Ontology (GO) enrichment analysis was performed using BED file containing human data. This tool is also accessible through web services (Java version only). The programmatic access complies with a standard BioMart interface: dataset, filter and attribute.

**Figure 3.**
The XML web service query (A) and the corresponding two types of output: tab delimited following setting a processor to ‘TSV’ (B) and JSON following setting processor to ‘JSON’.

See this image and copyright information in PMC

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The BioMart community portal: an innovative alternative to large, centralized data repositories

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The BioMart community portal: an innovative alternative to large, centralized data repositories

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