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 Keliet 29 Arnaud Kerhornou 1 Sunghoon Kim 23 Rhoda Kinsella 1 Christophe 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 Mariette 36 Thomas Maurel 1 Stefania Merella 4 Azza Mostafa Mohamed 7 Francois Moreews 37 Ibounyamine Nabihoudine 38 Nelson Ndegwa 1 Celine Noirot 39 Cristian Perez-Llamas 40 Alessandro Quattrone 16 Michael Primig 41 Davide Rambaldi 4 Olivier Sallou 15 James Reecy 42 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, 43 Daniel M. Staines 1 Delphine Steinbach 29 Kevin Stone 28 Elia Stupka 4 Jon W. Teague 21 Abu Z. Dayem Ullah 14 Jun Wang 44, 45 Doreen Ware 24 Marie Wong-Erasmus 46 Ken Youens-Clark 24 Amonida Zadissa 1 Shi-Jian Zhang 32 Arek Kasprzyk 46
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 International Potato Center
13 DOE - Department of Energy / Joint Genome Institute
14 Centre for Molecular Oncology and Imaging
15 Plateforme bioinformatique GenOuest [Rennes]
IRISA - Institut de Recherche en Informatique et Systèmes Aléatoires, UR1 - Université de Rennes 1, Plateforme Génomique Santé Biogenouest®, Inria Rennes – Bretagne Atlantique
16 University of Trento [Trento]
17 University of Chile [Santiago]
18 UBIA - Unité de Biométrie et Intelligence Artificielle
19 Pfizer Oncology
20 ICREA - Institució Catalana de Recerca i Estudis Avançats [Barcelona]
21 Cancer Genome Project
22 Kasuza DNA Research Institute
23 Seoul National University [Seoul]
24 CSHL - Cold Spring Harbor Laboratory
25 RIKEN
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 [Pekin]
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
36 MIAT - Unité Mathématiques et Informatique Appliquées de Toulouse
37 PEGASE - Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes]
38 MIAT INRA - Unité de Mathématiques et Informatique Appliquées de Toulouse
39 Mathématiques et Informatique Appliquées Toulouse
40 Universitat Pompeu Fabra [Barcelona]
41 Irset - Institut de recherche, santé, environnement et travail
42 Department of Animal Science
43 Eagle Genomics Ltd
44 State Key Laboratory of Lithospheric Evolution
45 University of the Chinese Academy of Sciences
46 OICR - Ontario Institute for Cancer Research [Canada]
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.
Type de document :
Article dans une revue
Nucleic Acids Research, Oxford University Press, 2015, 43, pp.W589-W598. 〈10.1093/nar/gkv350〉
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https://hal-univ-rennes1.archives-ouvertes.fr/hal-01146849
Contributeur : Laurent Jonchère <>
Soumis le : mercredi 29 avril 2015 - 11:26:24
Dernière modification le : mercredi 20 février 2019 - 15:54:09

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UNIV-RENNES1 | IRSET | UPMC | INRA | UNAM | INRIA | IRISA-D7 | BIOSIT | INSTITUT-TELECOM | IRISA | UR1-UFR-SVE | CENTRALESUPELEC | UR1-UFR-ISTIC | I2BC | UNIV-ANGERS | UNIV-PARIS-SACLAY | IRSET-7 | UNIV-AG | UNIV-RENNES | SORBONNE-UNIVERSITE

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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, Oxford University Press, 2015, 43, pp.W589-W598. 〈10.1093/nar/gkv350〉. 〈hal-01146849〉

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