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

Damian Smedley; Syed Haider; Steffen Durinck; Luca Pandini; Paolo Provero; James Allen; Olivier Arnaiz; Mohammad Hamza Awedh; Richard Baldock; Giulia Barbiera; Philippe Bardou; Tim Beck; Andrew Blake; Merideth Bonierbale; Anthony J. Brookes; Gabriele Bucci; Iwan Buetti; Sarah Burge; Cedric Cabau; Joseph W. Carlson; Claude Chelala; Charalambos Chrysostomou; Davide Cittaro; Olivier Collin; Raul Cordova; Rosalind J. Cutts; Erik Dassi; Alex Di Genova; Anis Djari; Anthony Esposito; Heather Estrella; Eduardo Eyras; Julio Fernandez-Banet; Simon Forbes; Robert C. Free; Takatomo Fujisawa; Emanuela Gadaleta; Jose M. Garcia-Manteiga; David Goodstein; Kristian Gray; JoseE Afonso Guerra-Assuncao; Bernard Haggarty; Dong-Jin Han; Byung Woo Han; Todd Harris; Jayson Harshbarger; Robert K. Hastings; Richard D. Hayes; Claire Hoede; Shen Hu; Zhi-Liang Hu; Lucie Hutchins; Zhengyan Kan; Hideya Kawaji; Aminah Keliet; Arnaud Kerhornou; Sunghoon Kim; Rhoda Kinsella; Christophe Klopp; Lei Kong; Daniel Lawson; Dejan Lazarevic; Ji-Hyun Lee; Thomas Letellier; Chuan-Yun Li; Pietro Lio; Chu-Jun Liu; Jie Luo; Alejandro Maass; Jerome Mariette; Thomas Maurel; Stefania Merella; Azza Mostafa Mohamed; Francois Moreews; Ibounyamine Nabihoudine; Nelson Ndegwa; Celine Noirot; Cristian Perez-Llamas; Michael Primig; Alessandro Quattrone; Hadi Quesneville; Davide Rambaldi; James Reecy; Michela Riba; Steven Rosanoff; Amna Ali Saddiq; Elisa Salas; Olivier Sallou; Rebecca Shepherd; Reinhard Simon; Linda Sperling; William Spooner; Daniel M. Staines; Delphine Steinbach; Kevin Stone; Elia Stupka; Jon W. Teague; Abu Z. Dayem Ullah; Jun Wang; Doreen Ware; Marie Wong-Erasmus; Ken Youens-Clark; Amonida Zadissa; Shi-Jian Zhang; Arek Kasprzyk; USDOE Joint Genome Institute (JGI), Berkeley, CA (United States)

doi:10.1093/nar/gkv350

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

Journal article

Open access

Peer reviewed

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

Damian Smedley, Syed Haider, Steffen Durinck, Luca Pandini, Paolo Provero, James Allen, Olivier Arnaiz, Mohammad Hamza Awedh, Richard Baldock, Giulia Barbiera, …

Nucleic acids research, Vol.43(W1), pp.W589-W598

2015

DOI: https://doi.org/10.1093/nar/gkv350

PMCID: PMC4489294

PMID: 25897122

Abstract

Biochemistry & Molecular Biology

Life Sciences & Biomedicine

Science & Technology

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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Title: The BioMart community portal: an innovative alternative to large, centralized data repositories
Creators - without role: Damian Smedley - Wellcome Sanger Institute
Syed Haider - MRC Weatherall Institute of Molecular Medicine
Steffen Durinck - Genentech
Luca Pandini - Ist Sci San Raffaele, Ctr Translat Genom & Bioinformat, I-20132 Milan, Italy
Paolo Provero - University of Turin
James Allen - European Bioinformatics Institute
Olivier Arnaiz - Institute of Integrative Biology of the Cell
Mohammad Hamza Awedh - King Abdulaziz University
Richard Baldock - MRC Institute of Genetics and Molecular Medicine
Giulia Barbiera - Ist Sci San Raffaele, Ctr Translat Genom & Bioinformat, I-20132 Milan, Italy
Philippe Bardou - Génétique Physiologie et Systèmes d'Elevage
Tim Beck - University of Leicester
Andrew Blake - Mary Lyon Centre at MRC Harwell
Merideth Bonierbale - International Potato Center
Anthony J. Brookes - University of Leicester
Gabriele Bucci - Ist Sci San Raffaele, Ctr Translat Genom & Bioinformat, I-20132 Milan, Italy
Iwan Buetti - Ist Sci San Raffaele, Ctr Translat Genom & Bioinformat, I-20132 Milan, Italy
Sarah Burge - European Bioinformatics Institute
Cedric Cabau - Génétique Physiologie et Systèmes d'Elevage
Joseph W. Carlson - Joint Genome Institute
Claude Chelala - Queen Mary University of London
Charalambos Chrysostomou - University of Leicester
Davide Cittaro - Ist Sci San Raffaele, Ctr Translat Genom & Bioinformat, I-20132 Milan, Italy
Olivier Collin - French Institute for Research in Computer Science and Automation
Raul Cordova - International Potato Center
Rosalind J. Cutts - Queen Mary University of London
Erik Dassi - University of Trento
Alex Di Genova - University of Chile
Anis Djari - INRA, Plate Forme Bioinformat Genotoul, Math & Informat Appl Toulouse, F-31326 Castanet Tolosan, France
Anthony Esposito - Pfizer
Heather Estrella - Pfizer
Eduardo Eyras - Institució Catalana de Recerca i Estudis Avançats
Julio Fernandez-Banet - Pfizer
Simon Forbes - Wellcome Sanger Institute
Robert C. Free - University of Leicester
Takatomo Fujisawa - Kazusa DNA Research Institute
Emanuela Gadaleta - Queen Mary University of London
Jose M. Garcia-Manteiga - Ist Sci San Raffaele, Ctr Translat Genom & Bioinformat, I-20132 Milan, Italy
David Goodstein - Joint Genome Institute
Kristian Gray - European Bioinformatics Institute
JoseE Afonso Guerra-Assuncao - Queen Mary University of London
Bernard Haggarty - MRC Institute of Genetics and Molecular Medicine
Dong-Jin Han - College Station Medical Center
Byung Woo Han - Seoul Natl Univ, Coll Pharm, Res Inst Pharmaceut Sci, Seoul 151742, South Korea
Todd Harris - Ontario Institute for Cancer Research
Jayson Harshbarger - DGT
Robert K. Hastings - University of Leicester
Richard D. Hayes - Joint Genome Institute
Claire Hoede - INRA, Plate Forme Bioinformat Genotoul, Math & Informat Appl Toulouse, F-31326 Castanet Tolosan, France
Shen Hu - University of California, Los Angeles
Zhi-Liang Hu - Iowa State University
Lucie Hutchins - Jackson Laboratory
Zhengyan Kan - Pfizer
Hideya Kawaji - RIKEN
Aminah Keliet - INRA URGI Ctr Versailles, F-78026 Versailles, France
Arnaud Kerhornou - European Bioinformatics Institute
Sunghoon Kim - Seoul National University
Rhoda Kinsella - European Bioinformatics Institute
Christophe Klopp - INRA, Plate Forme Bioinformat Genotoul, Math & Informat Appl Toulouse, F-31326 Castanet Tolosan, France
Lei Kong - Peking University
Daniel Lawson - European Bioinformatics Institute
Dejan Lazarevic - Ist Sci San Raffaele, Ctr Translat Genom & Bioinformat, I-20132 Milan, Italy
Ji-Hyun Lee - Seoul National University
Thomas Letellier - INRA URGI Ctr Versailles, F-78026 Versailles, France
Chuan-Yun Li - Peking University
Pietro Lio - University of Cambridge
Chu-Jun Liu - Peking University
Jie Luo - European Bioinformatics Institute
Alejandro Maass - University of Chile
Jerome Mariette - INRA, Plate Forme Bioinformat Genotoul, Math & Informat Appl Toulouse, F-31326 Castanet Tolosan, France
Thomas Maurel - European Bioinformatics Institute
Stefania Merella - Ist Sci San Raffaele, Ctr Translat Genom & Bioinformat, I-20132 Milan, Italy
Azza Mostafa Mohamed - King Abdulaziz University
Francois Moreews - Génétique Physiologie et Systèmes d'Elevage
Ibounyamine Nabihoudine - INRA, Plate Forme Bioinformat Genotoul, Math & Informat Appl Toulouse, F-31326 Castanet Tolosan, France
Nelson Ndegwa - Karolinska Institutet
Celine Noirot - INRA, Plate Forme Bioinformat Genotoul, Math & Informat Appl Toulouse, F-31326 Castanet Tolosan, France
Cristian Perez-Llamas - Univ Pompeu Fabra, E-08003 Barcelona, Spain
Michael Primig - University of Rennes
Alessandro Quattrone - University of Trento
Hadi Quesneville - INRA URGI Ctr Versailles, F-78026 Versailles, France
Davide Rambaldi - Ist Sci San Raffaele, Ctr Translat Genom & Bioinformat, I-20132 Milan, Italy
James Reecy - Iowa State University
Michela Riba - Ist Sci San Raffaele, Ctr Translat Genom & Bioinformat, I-20132 Milan, Italy
Steven Rosanoff - European Bioinformatics Institute
Amna Ali Saddiq - King Abdulaziz University
Elisa Salas - International Potato Center
Olivier Sallou - French Institute for Research in Computer Science and Automation
Rebecca Shepherd - Wellcome Sanger Institute
Reinhard Simon - International Potato Center
Linda Sperling - Institute of Integrative Biology of the Cell
William Spooner - Eagle Genomics
Daniel M. Staines - European Bioinformatics Institute
Delphine Steinbach - INRA URGI Ctr Versailles, F-78026 Versailles, France
Kevin Stone - Jackson Laboratory
Elia Stupka - Ist Sci San Raffaele, Ctr Translat Genom & Bioinformat, I-20132 Milan, Italy
Jon W. Teague - Wellcome Sanger Institute
Abu Z. Dayem Ullah - Queen Mary University of London
Jun Wang - Peking University
Doreen Ware - Cold Spring Harbor Laboratory
Marie Wong-Erasmus - Human Longev Inc, San Diego, CA 92121 USA
Ken Youens-Clark - Cold Spring Harbor Lab, Cold Spring Harbor, NY 11724 USA
Amonida Zadissa - European Bioinformat Inst, European Mol Biol Lab, Cambridge CB10 1SD, England
Shi-Jian Zhang - Peking University
Arek Kasprzyk - Ist Sci San Raffaele, Ctr Translat Genom & Bioinformat, I-20132 Milan, Italy
USDOE Joint Genome Institute (JGI), Berkeley, CA (United States)
Publication Details: Nucleic acids research, Vol.43(W1), pp.W589-W598
Publisher: Oxford Univ Press
Number of pages: 10
Grant note: ICREA Japanese Ministry of Education, Culture, Sports, Science and Technology [FANTOM5 BioMart] 96-130-35-HiCi / Deanship of Scientific Research (DSR) King Abdulaziz University Fondap-1509007 / Center for Genome Regulation [SalmonDB] Basal-PFB 03 / Center for Mathematical Modelling NRF-2013M3A6A4043695 / Global Frontier Project - Ministry of Science, ICT and Future Planning through National Research Foundation of Korea; National Research Foundation of Korea ANR-10-BLAN-1122; ANR-12-BSV6-0017-03; ANR-14-CE10-0005-03 / Agence National de la Recherche; Agence Nationale de la Recherche (ANR) 1127112 / Direct For Biological Sciences; Division Of Integrative Organismal Systems; National Science Foundation (NSF); NSF - Directorate for Biological Sciences (BIO) 077012/Z/05/Z; WT095908; WT098051 / Wellcome Trust DE-AC02-05CH11231 / Office of Science of the U.S. Department of Energy; United States Department of Energy (DOE) MC_PC_U127527203 / Medical Research Council; UK Research & Innovation (UKRI); Medical Research Council UK (MRC) BIO2011-23920; CSD2009-00080 / Spanish Government King Abdulaziz University 09TBBAR / Breast Cancer Campaign Tissue Bank MC_PC_U127527203 / MRC; UK Research & Innovation (UKRI); Medical Research Council UK (MRC) FSI2013 / Sandra Ibarra Foundation for Cancer Centre National de la Recherche Scientifique; Centre National de la Recherche Scientifique (CNRS) European Molecular Biology Laboratory
Identifiers: 9933119508331
Academic Unit: University of Jeddah; King Abdulaziz University
Language: English
Resource Type: Journal article