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

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      1 , 2 , 3 , 4 , 4 , 5 , 6 , 7 , 8 , 9 , 4 , 10 , 11 , 12 , 13 , 11 , 4 , 4 , 6 , 10 , 14 , 15 , 11 , 4 , 16 , 13 , 15 , 17 ,   18 , 19 , 20 , 20 , 21 , 22 , 20 , 1 , 11 , 23 , 15 , 4 , 14 , 24 , 15 , 9 , 25 , 26 , 27 , 28 , 29 , 30 , 11 , 14 , 19 , 31 , 32 , 33 , 20 , 30 , 34 , 35 , 6 , 25 , 26 , 6 , 19 , 36 , 37 , 4 , 25 , 27 , 28 , 35 , 38 , 39 , 38 , 6 , 18 , 40 , 19 , 6 , 4 , 41 , 10 , 19 , 42 , 19 , 22 , 43 , 17 , 35 , 4 , 32 , 4 , 6 , 44 , 13 , 16 , 1 , 13 , 7 , 45 , 46 , 6 , 35 , 33 , 4 , 1 , 15 , 36 , 45 , 47 , 45 , 6 , 38 , 4 , 48 , *
      Nucleic Acids Research
      Oxford University Press

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          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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          Most cited references39

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          Integration of biological networks and gene expression data using Cytoscape.

          Cytoscape is a free software package for visualizing, modeling and analyzing molecular and genetic interaction networks. This protocol explains how to use Cytoscape to analyze the results of mRNA expression profiling, and other functional genomics and proteomics experiments, in the context of an interaction network obtained for genes of interest. Five major steps are described: (i) obtaining a gene or protein network, (ii) displaying the network using layout algorithms, (iii) integrating with gene expression and other functional attributes, (iv) identifying putative complexes and functional modules and (v) identifying enriched Gene Ontology annotations in the network. These steps provide a broad sample of the types of analyses performed by Cytoscape.
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            Ensembl BioMarts: a hub for data retrieval across taxonomic space

            For a number of years the BioMart data warehousing system has proven to be a valuable resource for scientists seeking a fast and versatile means of accessing the growing volume of genomic data provided by the Ensembl project. The launch of the Ensembl Genomes project in 2009 complemented the Ensembl project by utilizing the same visualization, interactive and programming tools to provide users with a means for accessing genome data from a further five domains: protists, bacteria, metazoa, plants and fungi. The Ensembl and Ensembl Genomes BioMarts provide a point of access to the high-quality gene annotation, variation data, functional and regulatory annotation and evolutionary relationships from genomes spanning the taxonomic space. This article aims to give a comprehensive overview of the Ensembl and Ensembl Genomes BioMarts as well as some useful examples and a description of current data content and future objectives. Database URLs: http://www.ensembl.org/biomart/martview/; http://metazoa.ensembl.org/biomart/martview/; http://plants.ensembl.org/biomart/martview/; http://protists.ensembl.org/biomart/martview/; http://fungi.ensembl.org/biomart/martview/; http://bacteria.ensembl.org/biomart/martview/
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              Activities at the Universal Protein Resource (UniProt)

              The mission of the Universal Protein Resource (UniProt) (http://www.uniprot.org) is to provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequences and functional annotation. It integrates, interprets and standardizes data from literature and numerous resources to achieve the most comprehensive catalog possible of protein information. The central activities are the biocuration of the UniProt Knowledgebase and the dissemination of these data through our Web site and web services. UniProt is produced by the UniProt Consortium, which consists of groups from the European Bioinformatics Institute (EBI), the SIB Swiss Institute of Bioinformatics (SIB) and the Protein Information Resource (PIR). UniProt is updated and distributed every 4 weeks and can be accessed online for searches or downloads.
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                Author and article information

                Journal
                Nucleic Acids Res
                Nucleic Acids Res
                nar
                nar
                Nucleic Acids Research
                Oxford University Press
                0305-1048
                1362-4962
                01 July 2015
                20 April 2015
                20 April 2015
                : 43
                : Web Server issue
                : W589-W598
                Affiliations
                [1 ]Wellcome Trust Sanger Institute, Welcome Trust Genome Campus, Hinxton, CB10 1SD, UK
                [2 ]The Weatherall Institute Of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
                [3 ]Genentech, Inc. 1 DNA Way South San Francisco, CA 94080, USA
                [4 ]Center for Translational Genomics and Bioinformatics San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
                [5 ]Dept of Molecular Biotechnology and Health Sciences University of Turin, Italy
                [6 ]European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
                [7 ]Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris Sud, 1 avenue de la terrasse, 91198 Gif sur Yvette, France
                [8 ]Department of Electrical and Computer Engineering, Faculty of Engineering, King Abdulaziz University, Jeddah, Saudi Arabia
                [9 ]MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK
                [10 ]Sigenae, INRA, Castanet-Tolosan, France
                [11 ]Department of Genetics, University of Leicester, University Road, Leicester, LE1 7RH, UK
                [12 ]MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK
                [13 ]International Potato Center (CIP), Lima, 1558, Peru
                [14 ]Department of Energy, Joint Genome Institute, Walnut Creek, USA
                [15 ]Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
                [16 ]IRISA-INRIA, Campus de Beaulieu 35042 Rennes, France
                [17 ]Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, Trento, Italy
                [18 ]Center for Mathematical Modeling and Center for Genome Regulation, University of Chile, Beauchef 851, 7th floor, Chile
                [19 ]Plate-forme bio-informatique Genotoul, Mathématiques et Informatique Appliquées de Toulouse, INRA, Castanet-Tolosan, France
                [20 ]Oncology Computational Biology, Pfizer, La Jolla, USA
                [21 ]Catalan Institute for Research and Advanced Studies (ICREA), Passeig Lluis Companys 23, E-08010 Barcelona, Spain
                [22 ]Universitat Pompeu Fabra, Dr Aiguader 88 E-08003 Barcelona, Spain
                [23 ]Kasuza DNA Research Institute, Chiba, 292–0818, Japan
                [24 ]HUGO Gene Nomenclature Committee (HGNC), European Bioinformatics Institute (EMBL-EBI) Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
                [25 ]Medicinal Bioconvergence Research Center, College of Pharmacy, Seoul National University, Seoul 151–742, Republic of Korea
                [26 ]Department of Molecular Medicine and Biopharmaceutical Sciences, Seoul National University, Seoul 151–742, Republic of Korea
                [27 ]Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151–742, Republic of Korea
                [28 ]Information Center for Bio-pharmacological Network, Seoul National University, Suwon 443–270, Republic of Korea
                [29 ]Ontario Institute for Cancer Research, Toronto, M5G 0A3, Canada
                [30 ]RIKEN Center for Life Science Technologies (CLST), Division of Genomic Technologies (DGT), Kanagawa, 230–0045, Japan
                [31 ]School of Dentistry and Dental Research Institute, University of California Los Angeles (UCLA), Los Angeles, CA 90095–1668, USA
                [32 ]Iowa State Univeristy, USA
                [33 ]Mouse Genomic Informatics Group, The Jackson Laboratory, Bar Harbor, ME 04609, USA
                [34 ]RIKEN Preventive Medicine and Diagnosis Innovation Program, Saitama 351–0198, Japan
                [35 ]INRA URGI Centre de Versailles, bâtiment 18 Route de Saint Cyr 78026 Versailles, France
                [36 ]Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, 100871, P.R. China
                [37 ]VectorBase, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
                [38 ]Institute of Molecular Medicine, Peking University, Beijing, China
                [39 ]Computer Laboratory, University of Cambridge, Cambridge, CB3 0FD, UK
                [40 ]Department of Mathematical Engineering, University of Chile, Av. Beauchef 851, 5th floor, Santiago, Chile
                [41 ]Departament of Biochemistry, Faculty of Science for Girls, King Abdulaziz University, Jeddah, Saudi Arabia
                [42 ]Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, PO Box 281, 17177 Stockholm, Sweden
                [43 ]Inserm U1085 IRSET, University of Rennes 1, 35042 Rennes, France
                [44 ]Department of Biological Sciences, Faculty of Science for Girls, King Abdulaziz University, Jeddah, Saudi Arabia
                [45 ]Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
                [46 ]Eagle Genomics Ltd., Babraham Research Campus, Cambridge, CB22 3AT, UK
                [47 ]Human Longevity, Inc. 10835 Road to the Cure 140 San Diego, CA 92121, USA
                [48 ]Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
                Author notes
                [* ]To whom correspondence should be addressed. Tel: +39 02 26439139; Fax: +39 02 2643 4153; Email: Arek.Kasprzyk@ 123456gmail.com
                Article
                10.1093/nar/gkv350
                4489294
                25897122
                3d1e1f0b-6afe-4df9-8f91-7efe95d4fa05
                © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 02 April 2015
                : 21 March 2015
                : 09 February 2015
                Page count
                Pages: 10
                Categories
                Web Server issue
                Custom metadata
                1 July 2015

                Genetics
                Genetics

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