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Journal Articles Nucleic Acids Research Year : 2015

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

Damian Smedley (1) , Syed Haider (2) , Steffen Durinck (3) , Luca Pandini (4) , Paolo Provero (5) , James Allen (1) , Olivier Arnaiz (6) , Mohammad Hamza Awedh (7) , Richard Baldock (8) , Giulia Barbiera (4) , Philippe Bardou (9) , Tim Beck (10) , Andrew Blake (11) , Merideth Bonierbale (12) , Anthony J. Brookes (10) , Gabriele Bucci (4) , Iwan Buetti (4) , Sarah Burge (1) , Cédric Cabau (9) , Joseph W. Carlson (13) , Claude Chelala (14) , Charalambos Chrysostomou (10) , Davide Cittaro (4) , Olivier Collin (15) , Raul Cordova (12) , Rosalind J. Cutts (14) , Erik Dassi (16) , Alex Di Genova (17) , Anis Djari (18) , Anthony Esposito (19) , Heather Estrella (19) , Eduardo Eyras (20) , Julio Fernandez-Banet (19) , Simon Forbes (21) , Robert C. Free (10) , Takatomo Fujisawa (22) , Emanuela Gadaleta (14) , Jose M. Garcia-Manteiga (4) , David Goodstein (13) , Kristian Gray (1) , José Afonso Guerra-Assunção (14) , Bernard Haggarty (8) , Dong-Jin Han (23) , Byung Woo Han (23) , Todd Harris (24) , Jayson Harshbarger (25) , Robert K. Hastings (10) , Richard D. Hayes (13) , Claire Hoede (18) , Shen Hu (26) , Zhi-Liang Hu (27) , Lucie Hutchins (28) , Zhengyan Kan (19) , Hideya Kawaji (25) , Aminah A. Keliet (29) , Arnaud Kerhornou (1) , Sunghoon Kim (23) , Rhoda Kinsella (1) , Christophe C. Klopp (18) , Lei Kong (30) , Daniel Lawson (1) , Dejan Lazarevic (31) , Ji-Hyun Lee (23) , Thomas Letellier (29) , Chuan-Yun Li (32) , Pietro Lió (2) , Chu-Jun Liu (32) , Jie Luo (1) , Alejandro Maass (33, 34, 35) , Jérôme J. Mariette (36) , Thomas Maurel (1) , Stefania Merella (4) , Azza Mostafa Mohamed (7) , François Moreews (37) , Ibounyamine Nabihoudine (36) , Nelson Ndegwa (1) , Celine Noirot (36) , Cristian Perez-Llamas (38) , Alessandro Quattrone (16) , Michael Primig (39) , Davide Rambaldi (4) , Olivier Sallou (15) , James Reecy (40) , Michela Riba (4) , Steven Rosanoff (1) , Amna Ali Saddiq (7) , Elisa Salas (12) , Hadi Quesneville (29) , Rebecca Shepherd (21) , Reinhard Simon (12) , Linda Sperling (6) , William Spooner (24, 41) , Daniel M. Staines (1) , Delphine Steinbach (29) , Kevin Stone (28) , Elia Stupka (4) , Jon W. Teague (21) , Abu Z. Dayem Ullah (14) , Jun Wang (42, 43) , Doreen Ware (24) , Marie Wong-Erasmus (44) , Ken Youens-Clark (24) , Amonida Zadissa (1) , Shi-Jian Zhang (32) , Arek Kasprzyk (44)
1 EMBL-EBI - European Bioinformatics Institute [Hinxton]
2 Computer Laboratory [Cambridge]
3 Genentech, Inc.
4 San Raffaele Scientific Institute
5 Genetics, Biology and Biochemistry, Molecular Biotechnology Centre
6 CGM - Centre de génétique moléculaire
7 King Abdulaziz University
8 MRC Human Genetics Unit
9 LGC - Laboratoire de Génétique Cellulaire
10 Department of Genetics [Leicester]
11 Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre)
12 CIP - International Potato Center [Lima]
13 DOE - Department of Energy / Joint Genome Institute
14 Centre for Molecular Oncology and Imaging
15 Plateforme bioinformatique GenOuest [Rennes]
16 UNITN - Università degli Studi di Trento = University of Trento
17 UCHILE - Universidad de Chile = University of Chile [Santiago]
18 UBIA - Unité de Biométrie et Intelligence Artificielle (ancêtre de MIAT)
19 Pfizer Oncology
20 ICREA - Institució Catalana de Recerca i Estudis Avançats = Catalan Institution for Research and Advanced Studies
21 Cancer Genome Project
22 Kasuza DNA Research Institute
23 SNU - Seoul National University [Seoul]
24 CSHL - Cold Spring Harbor Laboratory
25 RIKEN - RIKEN - Institute of Physical and Chemical Research [Japon]
26 School of Dentistry and Dental Research Institute [UCLA]
27 Department of Animal Science and Center for Integrated Animal Genomics
28 MGI - Mouse Genomic Informatics Group
29 URGI - Unité de Recherche Génomique Info
30 Center for Bioinformatics [Peking]
31 KTH - Division of Industrial Ecology
32 Institute of Molecular Medicine
33 USACH - Universidad de Santiago de Chile [Santiago]
34 CRG - Centro de Regulación Génica
35 CMM - Centre de modélisation mathématique / Centro de Modelamiento Matemático [Santiago]
36 MIAT INRA - Unité de Mathématiques et Informatique Appliquées de Toulouse
37 PEGASE - Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes]
38 UPF - Universitat Pompeu Fabra [Barcelona]
39 Irset - Institut de recherche en santé, environnement et travail
40 Department of Animal Science
41 Eagle Genomics Ltd
42 SKL - State Key Laboratory of Lithospheric Evolution
43 UCAS - University of Chinese Academy of Sciences [Beijing]
44 OICR - Ontario Institute for Cancer Research [Canada]
Steffen Durinck
  • Function : Author
Olivier Arnaiz
Cédric Cabau
Anthony Esposito
  • Function : Author
Heather Estrella
  • Function : Author
Zhengyan Kan
  • Function : Author
Aminah A. Keliet
Dejan Lazarevic
Olivier Sallou
Hadi Quesneville

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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Dates and versions

hal-01146849 , version 1 (28-05-2020)

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Damian Smedley, Syed Haider, Steffen Durinck, Luca Pandini, Paolo Provero, et al.. The BioMart community portal: an innovative alternative to large, centralized data repositories. Nucleic Acids Research, 2015, 43 (W1), pp.W589-W598. ⟨10.1093/nar/gkv350⟩. ⟨hal-01146849⟩
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