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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. The BioMart community portal: an innovative alternative to large, centralized data repositories. Nucleic Acids Res 2015; 43:W589-98. [PMID: 25897122 PMCID: PMC4489294 DOI: 10.1093/nar/gkv350] [Citation(s) in RCA: 491] [Impact Index Per Article: 54.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 04/02/2015] [Indexed: 01/17/2023] Open
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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Affiliation(s)
- Damian Smedley
- Wellcome Trust Sanger Institute, Welcome Trust Genome Campus, Hinxton, CB10 1SD, UK
| | - Syed Haider
- The Weatherall Institute Of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Steffen Durinck
- Genentech, Inc. 1 DNA Way South San Francisco, CA 94080, USA
| | - Luca Pandini
- Center for Translational Genomics and Bioinformatics San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
| | - Paolo Provero
- 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
| | - James Allen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Olivier Arnaiz
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris Sud, 1 avenue de la terrasse, 91198 Gif sur Yvette, France
| | - Mohammad Hamza Awedh
- Department of Electrical and Computer Engineering, Faculty of Engineering, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Richard Baldock
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK
| | - Giulia Barbiera
- Center for Translational Genomics and Bioinformatics San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
| | | | - Tim Beck
- Department of Genetics, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Andrew Blake
- MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK
| | | | - Anthony J Brookes
- Department of Genetics, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Gabriele Bucci
- Center for Translational Genomics and Bioinformatics San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
| | - Iwan Buetti
- Center for Translational Genomics and Bioinformatics San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
| | - Sarah Burge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | | | | | - Claude Chelala
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | | | - Davide Cittaro
- Center for Translational Genomics and Bioinformatics San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
| | | | - Raul Cordova
- International Potato Center (CIP), Lima, 1558, Peru
| | - Rosalind J Cutts
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Erik Dassi
- Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, Trento, Italy
| | - Alex Di Genova
- Center for Mathematical Modeling and Center for Genome Regulation, University of Chile, Beauchef 851, 7th floor, Chile
| | - Anis Djari
- Plate-forme bio-informatique Genotoul, Mathématiques et Informatique Appliquées de Toulouse, INRA, Castanet-Tolosan, France
| | | | | | - Eduardo Eyras
- 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
| | | | - Simon Forbes
- Wellcome Trust Sanger Institute, Welcome Trust Genome Campus, Hinxton, CB10 1SD, UK
| | - Robert C Free
- Department of Genetics, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | | | - Emanuela Gadaleta
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Jose M Garcia-Manteiga
- Center for Translational Genomics and Bioinformatics San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
| | - David Goodstein
- Department of Energy, Joint Genome Institute, Walnut Creek, USA
| | - Kristian Gray
- HUGO Gene Nomenclature Committee (HGNC), European Bioinformatics Institute (EMBL-EBI) Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
| | - José Afonso Guerra-Assunção
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Bernard Haggarty
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK
| | - Dong-Jin Han
- 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
| | - Byung Woo Han
- 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
| | - Todd Harris
- Ontario Institute for Cancer Research, Toronto, M5G 0A3, Canada
| | - Jayson Harshbarger
- RIKEN Center for Life Science Technologies (CLST), Division of Genomic Technologies (DGT), Kanagawa, 230-0045, Japan
| | - Robert K Hastings
- Department of Genetics, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Richard D Hayes
- Department of Energy, Joint Genome Institute, Walnut Creek, USA
| | - Claire Hoede
- Plate-forme bio-informatique Genotoul, Mathématiques et Informatique Appliquées de Toulouse, INRA, Castanet-Tolosan, France
| | - Shen Hu
- School of Dentistry and Dental Research Institute, University of California Los Angeles (UCLA), Los Angeles, CA 90095-1668, USA
| | | | - Lucie Hutchins
- Mouse Genomic Informatics Group, The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - Zhengyan Kan
- Oncology Computational Biology, Pfizer, La Jolla, USA
| | - Hideya Kawaji
- 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
| | - Aminah Keliet
- INRA URGI Centre de Versailles, bâtiment 18 Route de Saint Cyr 78026 Versailles, France
| | - Arnaud Kerhornou
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Sunghoon Kim
- 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
| | - Rhoda Kinsella
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Christophe Klopp
- Plate-forme bio-informatique Genotoul, Mathématiques et Informatique Appliquées de Toulouse, INRA, Castanet-Tolosan, France
| | - Lei Kong
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, 100871, P.R. China
| | - Daniel Lawson
- VectorBase, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
| | - Dejan Lazarevic
- Center for Translational Genomics and Bioinformatics San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
| | - Ji-Hyun Lee
- 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
| | - Thomas Letellier
- INRA URGI Centre de Versailles, bâtiment 18 Route de Saint Cyr 78026 Versailles, France
| | - Chuan-Yun Li
- Institute of Molecular Medicine, Peking University, Beijing, China
| | - Pietro Lio
- Computer Laboratory, University of Cambridge, Cambridge, CB3 0FD, UK
| | - Chu-Jun Liu
- Institute of Molecular Medicine, Peking University, Beijing, China
| | - Jie Luo
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Alejandro Maass
- 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
| | - Jerome Mariette
- Plate-forme bio-informatique Genotoul, Mathématiques et Informatique Appliquées de Toulouse, INRA, Castanet-Tolosan, France
| | - Thomas Maurel
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Stefania Merella
- Center for Translational Genomics and Bioinformatics San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
| | - Azza Mostafa Mohamed
- Departament of Biochemistry, Faculty of Science for Girls, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Ibounyamine Nabihoudine
- Plate-forme bio-informatique Genotoul, Mathématiques et Informatique Appliquées de Toulouse, INRA, Castanet-Tolosan, France
| | - Nelson Ndegwa
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, PO Box 281, 17177 Stockholm, Sweden
| | - Céline Noirot
- Plate-forme bio-informatique Genotoul, Mathématiques et Informatique Appliquées de Toulouse, INRA, Castanet-Tolosan, France
| | | | - Michael Primig
- Inserm U1085 IRSET, University of Rennes 1, 35042 Rennes, France
| | - Alessandro Quattrone
- Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, Trento, Italy
| | - Hadi Quesneville
- INRA URGI Centre de Versailles, bâtiment 18 Route de Saint Cyr 78026 Versailles, France
| | - Davide Rambaldi
- Center for Translational Genomics and Bioinformatics San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
| | | | - Michela Riba
- Center for Translational Genomics and Bioinformatics San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
| | - Steven Rosanoff
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Amna Ali Saddiq
- Department of Biological Sciences, Faculty of Science for Girls, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Elisa Salas
- International Potato Center (CIP), Lima, 1558, Peru
| | | | - Rebecca Shepherd
- Wellcome Trust Sanger Institute, Welcome Trust Genome Campus, Hinxton, CB10 1SD, UK
| | | | - Linda Sperling
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris Sud, 1 avenue de la terrasse, 91198 Gif sur Yvette, France
| | - William Spooner
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA Eagle Genomics Ltd., Babraham Research Campus, Cambridge, CB22 3AT, UK
| | - Daniel M Staines
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Delphine Steinbach
- INRA URGI Centre de Versailles, bâtiment 18 Route de Saint Cyr 78026 Versailles, France
| | - Kevin Stone
- Mouse Genomic Informatics Group, The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - Elia Stupka
- Center for Translational Genomics and Bioinformatics San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
| | - Jon W Teague
- Wellcome Trust Sanger Institute, Welcome Trust Genome Campus, Hinxton, CB10 1SD, UK
| | - Abu Z Dayem Ullah
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Jun Wang
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, 100871, P.R. China
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Marie Wong-Erasmus
- Human Longevity, Inc. 10835 Road to the Cure 140 San Diego, CA 92121, USA
| | - Ken Youens-Clark
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Amonida Zadissa
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Shi-Jian Zhang
- Institute of Molecular Medicine, Peking University, Beijing, China
| | - Arek Kasprzyk
- 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
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