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

Journal of Biomedical Semantics

Toshihisa Takagi⁷  Shoko Kawamoto^2,27  Christian M Zmasek^3,35  William S York^1,19  Riu Yamashita⁶  Chisato Yamasaki^3,33  Issaku Yamada^3,34  Patricia L Whetzel^4,49  Rutger Vos^1,15  Masahito Umezaki^3,31  Ikuo Uchiyama^4,48  Philip Toukach^3,32  Shu Tadaka^4,46  Francesco Strozzi^4,40  Andrea Splendiani^1,10  Sung-Ho Shin^1,18  Hiromichi Sawaki^1,14  Susanna Sansone^2,25  Philippe Rocca-Serra^2,25  Rene Ranzinger^1,19  Pjotr Prins^2,29  Nicki H Packer^3,30  Kazuki Oshita³  Shujiro Okuda^4,41  Yasunobu Okamura^4,46  Soichi Ogishima^4,45  Johan Nystrom-Persson^5,52  Yosuke Nishimura^1,11  Hiroyo Nishide^4,48  Hisashi Narimatsu^1,14  Mitsuteru Nakao^2,20  Katsuhiko Murakami^3,33  Mizuki Morita¹  Hiroshi Mori^4,43  Takaaki Mori^3,38  M Scott Marshall^3,36  Thomas Lütteke⁹  Hilmar Lapp^2,28  Camille Laibe^1,12  Masaaki Kotera^1,11  Yusuke Komiyama^4,42  Anna Kokubu^3,38  Taehong Kim^1,18  Takeo Katoda^3,38  Matúš Kalaš⁵  Wataru Iwasaki^2,21  Maori Ito^5,52  Hidetoshi Itaya³  Yoshinobu Igarashi^5,52  Robert Hoehndorf^1,17  Naohisa Goto^1,13  Toyofumi Fujiwara^2,26  Takatomo Fujisawa^4,47  Michel Dumontier^3,37  Geraint Duck^5,54  Alexandru Constantin^5,54  K Bretonnel Cohen^2,22  Peter JA Cock^5,53  Hirokazu Chiba^4,48  Yi-an Chen^5,52  Matthew P Campbell^3,39  Pier Luigi Buttigieg^4,44  Raoul JP Bonnal⁸  Jerven Bolleman^2,24  Joachim Baran²  Bruno Aranda^1,16  Kazuharu Arakawa³  Erick Antezana^5,50  Yukie Akune^3,38  Jan Aerts⁴  Simon Kocbek^2,27  Hidemasa Bono^2,27  Hiromasa Ono^2,27  Yoshinobu Kano^2,23  Hongyan Wu^2,27  Yue Wang^2,27  Jin-Dong Kim^2,27  Shin Kawano^2,27  Shinobu Okamoto^2,27  Atsuko Yamaguchi^2,27  Yasunori Yamamoto^2,27  Shuichi Kawashima^2,27  Kiyoko F Aoki-Kinoshita^3,38  Mark D Wilkinson^5,51  Toshiaki Katayama^2,27 

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

关键词: Data integration;    Data sharing;    Data models;    Semantic interoperability;    Databases;    Knowledge representation;    Visualization;    Ontology;    Web services;    Semantic Web;    Bioinformatics;    BioHackathon;   

Others  :  1217973
DOI  :  10.1186/2041-1480-5-5

 received in 2013-05-16, accepted in 2013-11-26,  发布年份 2014

【 摘 要 】

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.

【 授权许可】

   
2014 Katayama et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

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