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PMID: 25897122 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

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

Nucleic acids research ·Vol. 43 ·No. W1 ·2015-07-01 ·Pages W589-98

Smedley D, Haider S, Durinck S, Pandini L, Provero P, Allen J, Arnaiz O, Awedh MH, Baldock R, Barbiera G, Bardou P, Beck T, Blake A, Bonierbale M, Brookes AJ, Bucci G, Buetti I, Burge S, Cabau C, Carlson JW, Chelala C, Chrysostomou C, Cittaro D, Collin O, Cordova R, Cutts RJ, Dassi E, Di Genova A, Djari A, Esposito A, Estrella H, Eyras E, Fernandez-Banet J, Forbes S, Free RC, Fujisawa T, Gadaleta E, Garcia-Manteiga JM, Goodstein D, Gray K, Guerra-Assunção JA, Haggarty B, Han DJ, Han BW, Harris T, Harshbarger J, Hastings RK, Hayes RD, Hoede C, Hu S, Hu ZL, Hutchins L, Kan Z, Kawaji H, Keliet A, Kerhornou A, Kim S, Kinsella R, Klopp C, Kong L, Lawson D, Lazarevic D, Lee JH, Letellier T, Li CY, Lio P, Liu CJ, Luo J, Maass A, Mariette J, Maurel T, Merella S, Mohamed AM, Moreews F, Nabihoudine I, Ndegwa N, Noirot C, Perez-Llamas C, Primig M, Quattrone A, Quesneville H, Rambaldi D, Reecy J, Riba M, Rosanoff S, Saddiq AA, Salas E, Sallou O, Shepherd R, Simon R, Sperling L, Spooner W, Staines DM, Steinbach D, Stone K, Stupka E, Teague JW, Dayem Ullah AZ, Wang J, Ware D, Wong-Erasmus M, Youens-Clark K, Zadissa A, Zhang SJ, Kasprzyk A

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.

MeSH Terms
Database Management Systems Genomics Humans Internet Neoplasms/genetics Proteomics
Authors & Affiliations
105 authors, click to expand affiliations / ORCID
Smedley Damian
Wellcome Trust Sanger Institute, Welcome Trust Genome Campus, Hinxton, CB10 1SD, UK.
Haider Syed
The Weatherall Institute Of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK.
Durinck Steffen
Genentech, Inc. 1 DNA Way South San Francisco, CA 94080, USA.
Pandini Luca
Center for Translational Genomics and Bioinformatics San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy.
Provero Paolo
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.
Allen James
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
Arnaiz Olivier
Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris Sud, 1 avenue de la terrasse, 91198 Gif sur Yvette, France.
Awedh Mohammad Hamza
Department of Electrical and Computer Engineering, Faculty of Engineering, King Abdulaziz University, Jeddah, Saudi Arabia.
Baldock Richard
MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK.
Barbiera Giulia
Center for Translational Genomics and Bioinformatics San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy.
Bardou Philippe
Sigenae, INRA, Castanet-Tolosan, France.
Beck Tim
Department of Genetics, University of Leicester, University Road, Leicester, LE1 7RH, UK.
Blake Andrew
MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK.
Bonierbale Merideth
International Potato Center (CIP), Lima, 1558, Peru.
Brookes Anthony J
Department of Genetics, University of Leicester, University Road, Leicester, LE1 7RH, UK.
Bucci Gabriele
Center for Translational Genomics and Bioinformatics San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy.
Buetti Iwan
Center for Translational Genomics and Bioinformatics San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy.
Burge Sarah
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
Cabau Cédric
Sigenae, INRA, Castanet-Tolosan, France.
Carlson Joseph W
Department of Energy, Joint Genome Institute, Walnut Creek, USA.
Chelala Claude
Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK.
Chrysostomou Charalambos
Department of Genetics, University of Leicester, University Road, Leicester, LE1 7RH, UK.
Cittaro Davide
Center for Translational Genomics and Bioinformatics San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy.
Collin Olivier
IRISA-INRIA, Campus de Beaulieu 35042 Rennes, France.
Cordova Raul
International Potato Center (CIP), Lima, 1558, Peru.
Cutts Rosalind J
Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK.
Dassi Erik
Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, Trento, Italy.
Di Genova Alex
Center for Mathematical Modeling and Center for Genome Regulation, University of Chile, Beauchef 851, 7th floor, Chile.
Djari Anis
Plate-forme bio-informatique Genotoul, Mathématiques et Informatique Appliquées de Toulouse, INRA, Castanet-Tolosan, France.
Esposito Anthony
Oncology Computational Biology, Pfizer, La Jolla, USA.
Estrella Heather
Oncology Computational Biology, Pfizer, La Jolla, USA.
Eyras Eduardo
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.
Fernandez-Banet Julio
Oncology Computational Biology, Pfizer, La Jolla, USA.
Forbes Simon
Wellcome Trust Sanger Institute, Welcome Trust Genome Campus, Hinxton, CB10 1SD, UK.
Free Robert C
Department of Genetics, University of Leicester, University Road, Leicester, LE1 7RH, UK.
Fujisawa Takatomo
Kasuza DNA Research Institute, Chiba, 292-0818, Japan.
Gadaleta Emanuela
Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK.
Garcia-Manteiga Jose M
Center for Translational Genomics and Bioinformatics San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy.
Goodstein David
Department of Energy, Joint Genome Institute, Walnut Creek, USA.
Gray Kristian
HUGO Gene Nomenclature Committee (HGNC), European Bioinformatics Institute (EMBL-EBI) Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK.
Guerra-Assunção José Afonso
Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK.
Haggarty Bernard
MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK.
Han Dong-Jin
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.
Han Byung Woo
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.
Harris Todd
Ontario Institute for Cancer Research, Toronto, M5G 0A3, Canada.
Harshbarger Jayson
RIKEN Center for Life Science Technologies (CLST), Division of Genomic Technologies (DGT), Kanagawa, 230-0045, Japan.
Hastings Robert K
Department of Genetics, University of Leicester, University Road, Leicester, LE1 7RH, UK.
Hayes Richard D
Department of Energy, Joint Genome Institute, Walnut Creek, USA.
Hoede Claire
Plate-forme bio-informatique Genotoul, Mathématiques et Informatique Appliquées de Toulouse, INRA, Castanet-Tolosan, France.
Hu Shen
School of Dentistry and Dental Research Institute, University of California Los Angeles (UCLA), Los Angeles, CA 90095-1668, USA.
Hu Zhi-Liang
Iowa State Univeristy, USA.
Hutchins Lucie
Mouse Genomic Informatics Group, The Jackson Laboratory, Bar Harbor, ME 04609, USA.
Kan Zhengyan
Oncology Computational Biology, Pfizer, La Jolla, USA.
Kawaji Hideya
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.
Keliet Aminah
INRA URGI Centre de Versailles, bâtiment 18 Route de Saint Cyr 78026 Versailles, France.
Kerhornou Arnaud
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
Kim Sunghoon
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.
Kinsella Rhoda
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
Klopp Christophe
Plate-forme bio-informatique Genotoul, Mathématiques et Informatique Appliquées de Toulouse, INRA, Castanet-Tolosan, France.
Kong Lei
Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, 100871, P.R. China.
Lawson Daniel
VectorBase, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK.
Lazarevic Dejan
Center for Translational Genomics and Bioinformatics San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy.
Lee Ji-Hyun
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.
Letellier Thomas
INRA URGI Centre de Versailles, bâtiment 18 Route de Saint Cyr 78026 Versailles, France.
Li Chuan-Yun
Institute of Molecular Medicine, Peking University, Beijing, China.
Lio Pietro
Computer Laboratory, University of Cambridge, Cambridge, CB3 0FD, UK.
Liu Chu-Jun
Institute of Molecular Medicine, Peking University, Beijing, China.
Luo Jie
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
Maass Alejandro
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.
Mariette Jerome
Plate-forme bio-informatique Genotoul, Mathématiques et Informatique Appliquées de Toulouse, INRA, Castanet-Tolosan, France.
Maurel Thomas
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
Merella Stefania
Center for Translational Genomics and Bioinformatics San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy.
Mohamed Azza Mostafa
Departament of Biochemistry, Faculty of Science for Girls, King Abdulaziz University, Jeddah, Saudi Arabia.
Moreews Francois
Sigenae, INRA, Castanet-Tolosan, France.
Nabihoudine Ibounyamine
Plate-forme bio-informatique Genotoul, Mathématiques et Informatique Appliquées de Toulouse, INRA, Castanet-Tolosan, France.
Ndegwa Nelson
Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, PO Box 281, 17177 Stockholm, Sweden.
Noirot Céline
Plate-forme bio-informatique Genotoul, Mathématiques et Informatique Appliquées de Toulouse, INRA, Castanet-Tolosan, France.
Perez-Llamas Cristian
Universitat Pompeu Fabra, Dr Aiguader 88 E-08003 Barcelona, Spain.
Primig Michael
Inserm U1085 IRSET, University of Rennes 1, 35042 Rennes, France.
Quattrone Alessandro
Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, Trento, Italy.
Quesneville Hadi
INRA URGI Centre de Versailles, bâtiment 18 Route de Saint Cyr 78026 Versailles, France.
Rambaldi Davide
Center for Translational Genomics and Bioinformatics San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy.
Reecy James
Iowa State Univeristy, USA.
Riba Michela
Center for Translational Genomics and Bioinformatics San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy.
Rosanoff Steven
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
Saddiq Amna Ali
Department of Biological Sciences, Faculty of Science for Girls, King Abdulaziz University, Jeddah, Saudi Arabia.
Salas Elisa
International Potato Center (CIP), Lima, 1558, Peru.
Sallou Olivier
IRISA-INRIA, Campus de Beaulieu 35042 Rennes, France.
Shepherd Rebecca
Wellcome Trust Sanger Institute, Welcome Trust Genome Campus, Hinxton, CB10 1SD, UK.
Simon Reinhard
International Potato Center (CIP), Lima, 1558, Peru.
Sperling Linda
Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris Sud, 1 avenue de la terrasse, 91198 Gif sur Yvette, France.
Spooner William
Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA Eagle Genomics Ltd., Babraham Research Campus, Cambridge, CB22 3AT, UK.
Staines Daniel M
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
Steinbach Delphine
INRA URGI Centre de Versailles, bâtiment 18 Route de Saint Cyr 78026 Versailles, France.
Stone Kevin
Mouse Genomic Informatics Group, The Jackson Laboratory, Bar Harbor, ME 04609, USA.
Stupka Elia
Center for Translational Genomics and Bioinformatics San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy.
Teague Jon W
Wellcome Trust Sanger Institute, Welcome Trust Genome Campus, Hinxton, CB10 1SD, UK.
Dayem Ullah Abu Z
Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK.
Wang Jun
Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, 100871, P.R. China.
Ware Doreen
Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
Wong-Erasmus Marie
Human Longevity, Inc. 10835 Road to the Cure 140 San Diego, CA 92121, USA.
Youens-Clark Ken
Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
Zadissa Amonida
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
Zhang Shi-Jian
Institute of Molecular Medicine, Peking University, Beijing, China.
Kasprzyk Arek
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.
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Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gkv350
Email
arek.kasprzyk@gmail.com
Published
2015-07-01
Epub
2015-00-20
Pages
W589-98
Language
English
Region
England
NLM ID
0411011
PMCID
PMC4489294
Subset
IM
Grants
Wellcome Trust · 077012/Z/05/Z · United Kingdom
NHGRI NIH HHS · U41 HG003345 · United States
Medical Research Council · MC_PC_U127527203 · United Kingdom
Wellcome Trust · WT098051 · United Kingdom
Wellcome Trust · 095908 · United Kingdom
External Links
PubMed source DOI: 10.1093/nar/gkv350 PMC Full Text View journal details
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