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BioHackathon 2015: Semantics of data for life sciences and reproducible research

Vos RA 1 , Katayama T 2 , Mishima H 3 , Kawano S 2 , Kawashima S 2 , Kim JD 2 Show all authors , Moriya Y 2 , Tokimatsu T 4 , Yamaguchi A 2 , Yamamoto Y 2 , Wu H 5 , Amstutz P 6 , Antezana E 7 , Aoki NP 8 , Arakawa K 9 , Bolleman JT 10 , Bolton E 11 , Bonnal RJP 12 , Bono H 2 , Burger K 13 , Chiba H 14 , Cohen KB 15 , Deutsch EW 16 , Fernández-Breis JT 17 , Fu G 11 , Fujisawa T 18 , Fukushima A 19 , García A 20 , Goto N 21 , Groza T 22 , Hercus C 23 , Hoehndorf R 24 , Itaya K 9 , Juty N 25 , Kawashima T 18 , Kim JH 25 , Kinjo AR 26 , Kotera M 27 , Kozaki K 28 , Kumagai S 29 , Kushida T 30 , Lütteke T 31 , Matsubara M 32 , Miyamoto J 33 , Mohsen A 34 , Mori H 35 , Naito Y 2 , Nakazato T 2 , Nguyen-Xuan J 36 , Nishida K 37 , Nishida N 38 , Nishide H 14 , Ogishima S 39 , Ohta T 2 , Okuda S 40 , Paten B 41 , Perret JL 42 , Prathipati P 34 , Prins P 43 , Queralt-Rosinach N 44 , Shinmachi D 8 , Suzuki S 27 , Tabata T 45 , Takatsuki T 46 , Taylor K 25 , Thompson M 47 , Uchiyama I 14 , Vieira B 48 , Wei CH 11 , Wilkinson M 49 , Yamada I 32 , Yamanaka R 50 , Yoshitake K 51 , Yoshizawa AC 45 , Dumontier M 52 , Kosaki K 53 , Takagi T 30

Affiliations 

  • 1 Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
  • 2 Database Center for Life Science, Tokyo, Japan
  • 3 Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
  • 4 DDBJ Center, National Institute of Genetics, Mishima, Japan
  • 5 Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
  • 6 Curoverse, Somerville, USA
  • 7 Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
  • 8 Faculty of Science and Engineering, SOKA University, Tokyo, Japan
  • 9 Institute for Advanced Biosciences, Keio University, Tokyo, Japan
  • 10 SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, Lausanne, Switzerland
  • 11 National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, USA
  • 12 Istituto Nazionale Genetica Molecolare, Romeo ed Enrica Invernizzi, Milan, Italy
  • 13 Dutch Techcentre for Life Sciences, Utrecht, The Netherlands
  • 14 National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Japan
  • 15 Computational Bioscience Program, University of Colorado School of Medicine, Denver, USA
  • 16 Institute for Systems Biology, Seattle, USA
  • 17 Universidad de Murcia, IMIB-Arrixaca, Murcia, Spain
  • 18 National Institute of Genetics, Mishima, Japan
  • 19 RIKEN Center for Sustainable Resource Science, Yokohama, Japan
  • 20 Polytechnic University of Madrid, Madrid, Spain
  • 21 Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
  • 22 St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Darlinghurst, Australia
  • 23 Novocraft Technologies Sdn. Bhd., Selangor, Malaysia
  • 24 Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
  • 25 European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
  • 26 Institute for Protein Research, Osaka University, Osaka, Japan
  • 27 School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
  • 28 The Institute of Scientific and Industrial Research, Osaka University, Osaka, Japan
  • 29 Hitachi Ltd., Tokyo, Japan
  • 30 National Bioscience Database Center, Japan Science and Technology Agency, Tokyo, Japan
  • 31 Institute of Veterinary Physiology and Biochemistry, Justus-Liebig University Giessen, Giessen, Germany
  • 32 The Noguchi Institute, Tokyo, Japan
  • 33 National Cancer Center Japan, Tokyo, Japan
  • 34 National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
  • 35 Center for Information Biology, National Institute of Genetics, Mishima, Japan
  • 36 Lawrence Berkeley National Laboratory, Berkeley, USA
  • 37 RIKEN Quantitative Biology Center, Osaka, Japan
  • 38 Department of Systems Science, Osaka University, Osaka, Japan
  • 39 Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
  • 40 Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
  • 41 UC Santa Cruz Genomics Institute, University of California, Santa Cruz, USA
  • 42 INVENesis, Neuchâtel, Switzerland
  • 43 University Medical Center Utrecht, Utrecht, The Netherlands
  • 44 Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
  • 45 Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
  • 46 RIKEN BioResource Center, Ibaraki, Japan
  • 47 Leiden University Medical Center, Leiden, The Netherlands
  • 48 WurmLab, School of Biological & Chemical Sciences, Queen Mary University of London, London, UK
  • 49 Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
  • 50 Oracle Corporation, Tokyo, Japan
  • 51 Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
  • 52 Institute of Data Science, Maastricht University, Maastricht, The Netherlands
  • 53 Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
F1000Res, 2020;9:136.
PMID: 32308977 DOI: 10.12688/f1000research.18236.1

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.

* Title and MeSH Headings from MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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