Peer Review Report For: BioHackathon 2015: Semantics of data for life sciences and reproducible research [version 1; peer review: 2 approved]
Abstract
We report on the activities of the 2015 edition of the BioHackathon, an annual event that brings together researchers and developers from around the world to develop tools and technologies that promote the reusability of biological data. We discuss issues surrounding the representation, publication, integration, mining and reuse of biological data and metadata across a wide range of biomedical data types of relevance for the life sciences, including chemistry, genotypes and phenotypes, orthology and phylogeny, proteomics, genomics, glycomics, and metabolomics. We describe our progress to address ongoing challenges to the reusability and reproducibility of research results, and identify outstanding issues that continue to impede the progress of bioinformatics research. We share our perspective on the state of the art, continued challenges, and goals for future research and development for the life sciences Semantic Web.
Authors 74
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Leiden University · Naturalis Biodiversity Center
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Institute of Biology Leiden, Leiden University, Leiden
Naturalis Biodiversity Center, Leiden
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Toshiaki Katayama corresponding
Database Center for Life Science
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Database Center for Life Science, Tokyo
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Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki
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Database Center for Life Science
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Database Center for Life Science, Tokyo
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Database Center for Life Science
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Database Center for Life Science, Tokyo
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European Bioinformatics Institute · Database Center for Life Science
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Database Center for Life Science, Tokyo
European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton
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Database Center for Life Science
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Database Center for Life Science, Tokyo
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National Institute of Genetics
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DDBJ Center, National Institute of Genetics, Mishima
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Database Center for Life Science
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Database Center for Life Science, Tokyo
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Database Center for Life Science
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Database Center for Life Science, Tokyo
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Chinese Academy of Sciences · Shenzhen Institutes of Advanced Technology
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Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen
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Curoverse, Somerville
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Norwegian University of Science and Technology
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Department of Biology, Norwegian University of Science and Technology, Trondheim
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Faculty of Science and Engineering, SOKA University, Tokyo
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Institute for Advanced Biosciences, Keio University, Tokyo
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SIB Swiss Institute of Bioinformatics
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SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, Lausanne
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National Institutes of Health · National Center for Biotechnology Information
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National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda
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Istituto Nazionale Genetica Molecolare
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Istituto Nazionale Genetica Molecolare, Romeo ed Enrica Invernizzi, Milan
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Database Center for Life Science
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Database Center for Life Science, Tokyo
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National Institute for Basic Biology · National Institutes of Natural Sciences
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National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki
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Centre National de la Recherche Scientifique · Université Paris-Saclay · Laboratoire d'Informatique pour la Mécanique et les Sciences de l'Ingénieur · University of Colorado Anschutz · University of Colorado Denver
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Computational Bioscience Program, University of Colorado School of Medicine, Denver
Université Paris-Saclay, LIMSI, CNRS, Paris
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Institute for Systems Biology, Seattle
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Instituto Murciano de Investigación Biosanitaria · Universidad de Murcia
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Universidad de Murcia, IMIB-Arrixaca, Murcia
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National Institutes of Health · National Center for Biotechnology Information
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National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda
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National Institute of Genetics
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National Institute of Genetics, Mishima
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RIKEN Center for Sustainable Resource Science
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RIKEN Center for Sustainable Resource Science, Yokohama
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Universidad Politécnica de Madrid
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Polytechnic University of Madrid, Madrid
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Garvan Institute of Medical Research · UNSW Sydney
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Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst
St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Darlinghurst
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Malaysia Genome Institute · ST Engineering (Singapore)
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Novocraft Technologies Sdn. Bhd., Selangor
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King Abdullah University of Science and Technology
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Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal
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Institute for Advanced Biosciences, Keio University, Tokyo
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European Bioinformatics Institute
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European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton
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National Institute of Genetics
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National Institute of Genetics, Mishima
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European Bioinformatics Institute · Database Center for Life Science
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Database Center for Life Science, Tokyo
European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton
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Institute for Protein Research, Osaka University, Osaka
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School of Life Science and Technology, Tokyo Institute of Technology, Tokyo
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The Institute of Scientific and Industrial Research, Osaka University, Osaka
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Hitachi Ltd., Tokyo
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Japan Science and Technology Agency
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National Bioscience Database Center, Japan Science and Technology Agency, Tokyo
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Justus-Liebig-Universität Gießen
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Gesellschaft für innovative Personalwirtschaftssysteme mbH (GIP GmbH), Offenbach
Institute of Veterinary Physiology and Biochemistry, Justus-Liebig University Giessen, Giessen
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The Noguchi Institute, Tokyo
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National Cancer Center Japan, Tokyo
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National Institute of Biomedical Innovation, Health and Nutrition
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National Institutes of Biomedical Innovation, Health and Nutrition, Osaka
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National Institute of Genetics
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Center for Information Biology, National Institute of Genetics, Mishima
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Database Center for Life Science
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Database Center for Life Science, Tokyo
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Database Center for Life Science
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Database Center for Life Science, Tokyo
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Lawrence Berkeley National Laboratory
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Lawrence Berkeley National Laboratory, Berkeley
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RIKEN Quantitative Biology Center, Osaka
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National Institute for Basic Biology · National Institutes of Natural Sciences
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National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki
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Tohoku University · Tohoku Medical Megabank Organization
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Tohoku Medical Megabank Organization, Tohoku University, Sendai
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Database Center for Life Science
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Database Center for Life Science, Tokyo
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Niigata University Graduate School of Medical and Dental Sciences, Niigata
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University of California, Santa Cruz
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UC Santa Cruz Genomics Institute, University of California, Santa Cruz
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INVENesis, Neuchâtel
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National Institute of Biomedical Innovation, Health and Nutrition
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National Institutes of Biomedical Innovation, Health and Nutrition, Osaka
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University of Tennessee Health Science Center · University Medical Center Utrecht
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University Medical Center Utrecht, Utrecht
University of Tennessee Health Science Center, Memphis
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Department of Biomedical Informatics, Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Boston, Massachusetts
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Faculty of Science and Engineering, SOKA University, Tokyo
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School of Life Science and Technology, Tokyo Institute of Technology, Tokyo
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Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto
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RIKEN BioResource Research Center
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RIKEN BioResource Center, Ibaraki
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European Bioinformatics Institute
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European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton
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Mark Thompson Aachen
Leiden University Medical Center
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Leiden University Medical Center, Leiden
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National Institute for Basic Biology · National Institutes of Natural Sciences
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National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki
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Queen Mary University of London
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WurmLab, School of Biological & Chemical Sciences, Queen Mary University of London, London
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National Institutes of Health · National Center for Biotechnology Information
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National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda
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Universidad Politécnica de Madrid
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Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid
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The Noguchi Institute, Tokyo
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Oracle Corporation, Tokyo
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Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo
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Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto
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Institute of Data Science, Maastricht University, Maastricht
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Center for Medical Genetics, Keio University School of Medicine, Tokyo
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Japan Science and Technology Agency · The University of Tokyo
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Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo
National Bioscience Database Center, Japan Science and Technology Agency, Tokyo
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