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      BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains

      review-article
      1 , , 2 , 3 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 4 , 1 , 1 , 1 , 5 , 6 , 3 , 7 , 8 , 9 , 10 , 11 , 12 , 13 , 14 , 15 , 16 , 17 , 18 , 19 , 19 , 20 , 21 , 22 , 23 , 24 , 15 , 8 , 15 , 25 , 26 , 3 , 27 , 3 , 28 , 29 , 30 , 31 , 32 , 33 , 3 , 34 , 35 , 36 , 37 , 38 , 16 , 29 , 15 , 39 , 40 , 41 , 8 , 42 , 43 , 44 , 45 , 45 , 38 , 27 , 46 , 47 , 48 , 40 ,   49 , 16 , 50 , 51 , 52 , 53 , 15 , 36 , 54 , 44 , 55 , 1 , 56
      Journal of Biomedical Semantics
      BioMed Central
      BioHackathon, Bioinformatics, Semantic Web, Web services, Ontology, Visualization, Knowledge representation, Databases, Semantic interoperability, Data models, Data sharing, Data integration

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          Abstract

          The application of semantic technologies to the integration of biological data and the interoperability of bioinformatics analysis and visualization tools has been the common theme of a series of annual BioHackathons hosted in Japan for the past five years. Here we provide a review of the activities and outcomes from the BioHackathons held in 2011 in Kyoto and 2012 in Toyama. In order to efficiently implement semantic technologies in the life sciences, participants formed various sub-groups and worked on the following topics: Resource Description Framework (RDF) models for specific domains, text mining of the literature, ontology development, essential metadata for biological databases, platforms to enable efficient Semantic Web technology development and interoperability, and the development of applications for Semantic Web data. In this review, we briefly introduce the themes covered by these sub-groups. The observations made, conclusions drawn, and software development projects that emerged from these activities are discussed.

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          Most cited references37

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          Reorganizing the protein space at the Universal Protein Resource (UniProt)

          The mission of UniProt is to support biological research by providing a freely accessible, stable, comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with extensive cross-references and querying interfaces. UniProt is comprised of four major components, each optimized for different uses: the UniProt Archive, the UniProt Knowledgebase, the UniProt Reference Clusters and the UniProt Metagenomic and Environmental Sequence Database. A key development at UniProt is the provision of complete, reference and representative proteomes. UniProt is updated and distributed every 4 weeks and can be accessed online for searches or download at http://www.uniprot.org.
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            BioPAX – A community standard for pathway data sharing

            BioPAX (Biological Pathway Exchange) is a standard language to represent biological pathways at the molecular and cellular level. Its major use is to facilitate the exchange of pathway data (http://www.biopax.org). Pathway data captures our understanding of biological processes, but its rapid growth necessitates development of databases and computational tools to aid interpretation. However, the current fragmentation of pathway information across many databases with incompatible formats presents barriers to its effective use. BioPAX solves this problem by making pathway data substantially easier to collect, index, interpret and share. BioPAX can represent metabolic and signaling pathways, molecular and genetic interactions and gene regulation networks. BioPAX was created through a community process. Through BioPAX, millions of interactions organized into thousands of pathways across many organisms, from a growing number of sources, are available. Thus, large amounts of pathway data are available in a computable form to support visualization, analysis and biological discovery.
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                Author and article information

                Contributors
                Journal
                J Biomed Semantics
                J Biomed Semantics
                Journal of Biomedical Semantics
                BioMed Central
                2041-1480
                2014
                5 February 2014
                : 5
                : 5
                Affiliations
                [1 ]Database Center for Life Science, Research Organization of Information and Systems, 2-11-16, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
                [2 ]Centro de Biotecnología y Genómica de Plantas UPM-INIA (CBGP), Universidad Politécnica de Madrid, Campus Montegancedo, 28223-Pozuelo de, Alarcón, Spain
                [3 ]Department of Bioinformatics, Faculty of Engineering, Soka University, 1-236 Tangi-machi, Hachioji, Tokyo 192-8577, Japan
                [4 ]National Institute of Informatics, JST PRESTO, 2-1-2 Hitotsubashi, Chiyoda-ku, Tokyo 101-8430, Japan
                [5 ]Department of Electrical Engineering (ESAT/SCD), University of Leuven, Kasteelpark Arenberg 10, Leuven 3001, Belgium
                [6 ]iMinds Future Health Department, University of Leuven, Kasteelpark Arenberg 10, Leuven 3001, Belgium
                [7 ]Department of Biology, Norwegian University of Science and Technology (NTNU), Høgskoleringen 5, Trondheim N-7491, Norway
                [8 ]Institute for Advanced Biosciences, Keio University, Endo 5322, Fujisawa, Kanagawa 252-0882, Japan
                [9 ]Silicon Cat Ltd. 5 York Road, London HA6 1JJ, UK
                [10 ]Ontario Institute for Cancer Research, 101 College Street, Suite 800, Toronto, Ontario M5G 0A3, Canada
                [11 ]SIB Swiss Institute of Bioinformatics, CMU, rue Michel Servet, Geneve 4 1211, Switzerland
                [12 ]Integrative Biology Program, Istituto Nazionale Genetica Molecolare, Milan 20122, Italy
                [13 ]The Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, Bremerhaven 27570, Germany
                [14 ]Biomolecular Frontiers Research Centre, Macquarie University, North Ryde NSW 2109, Australia
                [15 ]National Institute of Biomedical Innovation, 7-6-8 Asagi Saito, Ibaraki-City, Osaka 567-0085, Japan
                [16 ]National Institute for Basic Biology, National Institutes of Natural Sciences, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan
                [17 ]The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
                [18 ]Center for Computational Pharmacology, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA
                [19 ]School of Computer Science, The University of Manchester, Oxford Road M13 9PL, UK
                [20 ]Department of Biology, Institute of Biochemistry, School of Computer Science, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada
                [21 ]Center for Information Biology, National Institute of Genetics, Research Organization of Information and Systems, 1111 Yata, Mishima, Shizuoka 411-08540, Japan
                [22 ]INTEC Inc, 1-3-3 Shinsuna, Koto-ku, Tokyo 136-8637, Japan
                [23 ]Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan
                [24 ]Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK
                [25 ]Atmosphere and Ocean Research Institute, the University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8564, Japan
                [26 ]Computational Biology Unit, Uni Computing and Department of Informatics, University of Bergen, Thormøhlensgate 55, Bergen 5008, Norway
                [27 ]Korea Institute of Science Technology and Information, 245 Daehangno, Yuseong, Daejeon 305-806, Korea
                [28 ]Department of Biotechnology, Bioinformation Engineering Laboratory, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
                [29 ]Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
                [30 ]EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
                [31 ]National Evolutionary Synthesis Center (NESCent), 2024 W. Main St, Durham, NC, USA
                [32 ]Justus-Liebig-University Giessen, Institute of Veterinary Physiology and Biochemistry, Frankfurter Str. 100, Giessen 35392, Germany
                [33 ]MAASTRO Clinic, Maastricht, Postbus 3035, Maastricht 6202 NA, The Netherlands
                [34 ]Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 B-36, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
                [35 ]Center for Knowledge Structuring, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan
                [36 ]Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, Aomi 2-4-7, Koto-ku, Tokyo 135-0064, Japan
                [37 ]Next Generation Systems Core Function Unit, Eisai Product Creation Systems, Eisai Co., Ltd, 5-3-1 Toukoudai, Tsukuba, Ibaraki 300-2635, Japan
                [38 ]Research Center for Medical Glycoscience, National Institute of Advanced Industrial Science and Technology (AIST) 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
                [39 ]Department of Bioclinical informatics, Tohoku Medical Megabank Organization, Tohoku University, Seiryo-cho 4-1, Aoba-ku, Sendai-shi, Miyagi 980-8575, Japan
                [40 ]Graduate School of Information Sciences (GSIS), Tohoku University, 6-3-09 Aoba, Aramaki-aza, Aoba-ku, Sendai, Miyagi, 980-8575, Japan
                [41 ]Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata 951-8510, Japan
                [42 ]Biomolecular Frontiers Research Centre, Macquarie University, North Ryde, NSW 2109, Australia
                [43 ]Laboratory of Nematology, Droevendaalsesteeg 1, Wageningen University, Wageningen, Netherlands
                [44 ]Department of Biochemistry and Molecular Biology, The University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
                [45 ]Oxford e-Research Center, University of Oxford, Oxford OX1 3QG, UK
                [46 ]Digital Enterprise Research Institute, IDA Business Park, Lower Dangan, Galway, Ireland
                [47 ]intelliLeaf.com, Cambridge, UK
                [48 ]CeRSA, Parco Tecnologico Padano, Lodi 26900, Italy
                [49 ]Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky prospekt 47, Moscow 119991, Russia
                [50 ]Division of International Cooperative Research, Research Center for Ethnomedicine, Institute of Natural Medicine, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
                [51 ]Naturalis Biodiversity Center, Postbus 9517, Leiden 2300 RA, the Netherlands
                [52 ]Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA 94305-5479, USA
                [53 ]Laboratory of Glyco-organic Chemistry, The Noguchi Institute, 1-8-1 Kaga, Itabashi-ku, Tokyo 173-0003, Japan
                [54 ]Tohoku Medical Megabank Organization, Tohoku University, Research Building No.3, 6-3-09 Aoba, Aramaki-aza, Aoba-ku, Sendai, Miyagi 980-8575, Japan
                [55 ]Program on Bioinformatics and Systems Biology, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA
                [56 ]Department of Computational Biology, University of Tokyo, Kashiwa, Chiba 277-8568, Japan
                Article
                2041-1480-5-5
                10.1186/2041-1480-5-5
                3978116
                24495517
                a8aa5a32-e9e9-4a9d-a4e1-a30be8450d1a
                Copyright © 2014 Katayama et al.; licensee BioMed Central Ltd.

                This is an open access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 16 May 2013
                : 26 November 2013
                Categories
                Review

                Bioinformatics & Computational biology
                biohackathon,bioinformatics,semantic web,web services,ontology,visualization,knowledge representation,databases,semantic interoperability,data models,data sharing,data integration

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