F1000Research (Feb 2020)
BioHackathon 2015: Semantics of data for life sciences and reproducible research [version 1; peer review: 2 approved]
- Rutger A. Vos,
- Toshiaki Katayama,
- Hiroyuki Mishima,
- Shin Kawano,
- Shuichi Kawashima,
- Jin-Dong Kim,
- Yuki Moriya,
- Toshiaki Tokimatsu,
- Atsuko Yamaguchi,
- Yasunori Yamamoto,
- Hongyan Wu,
- Peter Amstutz,
- Erick Antezana,
- Nobuyuki P. Aoki,
- Kazuharu Arakawa,
- Jerven T. Bolleman,
- Evan Bolton,
- Raoul J. P. Bonnal,
- Hidemasa Bono,
- Kees Burger,
- Hirokazu Chiba,
- Kevin B. Cohen,
- Eric W. Deutsch,
- Jesualdo T. Fernández-Breis,
- Gang Fu,
- Takatomo Fujisawa,
- Atsushi Fukushima,
- Alexander García,
- Naohisa Goto,
- Tudor Groza,
- Colin Hercus,
- Robert Hoehndorf,
- Kotone Itaya,
- Nick Juty,
- Takeshi Kawashima,
- Jee-Hyub Kim,
- Akira R. Kinjo,
- Masaaki Kotera,
- Kouji Kozaki,
- Sadahiro Kumagai,
- Tatsuya Kushida,
- Thomas Lütteke,
- Masaaki Matsubara,
- Joe Miyamoto,
- Attayeb Mohsen,
- Hiroshi Mori,
- Yuki Naito,
- Takeru Nakazato,
- Jeremy Nguyen-Xuan,
- Kozo Nishida,
- Naoki Nishida,
- Hiroyo Nishide,
- Soichi Ogishima,
- Tazro Ohta,
- Shujiro Okuda,
- Benedict Paten,
- Jean-Luc Perret,
- Philip Prathipati,
- Pjotr Prins,
- Núria Queralt-Rosinach,
- Daisuke Shinmachi,
- Shinya Suzuki,
- Tsuyosi Tabata,
- Terue Takatsuki,
- Kieron Taylor,
- Mark Thompson,
- Ikuo Uchiyama,
- Bruno Vieira,
- Chih-Hsuan Wei,
- Mark Wilkinson,
- Issaku Yamada,
- Ryota Yamanaka,
- Kazutoshi Yoshitake,
- Akiyasu C. Yoshizawa,
- Michel Dumontier,
- Kenjiro Kosaki,
- Toshihisa Takagi
Affiliations
- Rutger A. Vos
- Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
- Toshiaki Katayama
- Database Center for Life Science, Tokyo, Japan
- Hiroyuki Mishima
- Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
- Shin Kawano
- Database Center for Life Science, Tokyo, Japan
- Shuichi Kawashima
- Database Center for Life Science, Tokyo, Japan
- Jin-Dong Kim
- Database Center for Life Science, Tokyo, Japan
- Yuki Moriya
- Database Center for Life Science, Tokyo, Japan
- Toshiaki Tokimatsu
- DDBJ Center, National Institute of Genetics, Mishima, Japan
- Atsuko Yamaguchi
- Database Center for Life Science, Tokyo, Japan
- Yasunori Yamamoto
- Database Center for Life Science, Tokyo, Japan
- Hongyan Wu
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Peter Amstutz
- Curoverse, Somerville, USA
- Erick Antezana
- Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
- Nobuyuki P. Aoki
- Faculty of Science and Engineering, SOKA University, Tokyo, Japan
- Kazuharu Arakawa
- Institute for Advanced Biosciences, Keio University, Tokyo, Japan
- Jerven T. Bolleman
- SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, Lausanne, Switzerland
- Evan Bolton
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, USA
- Raoul J. P. Bonnal
- Istituto Nazionale Genetica Molecolare, Romeo ed Enrica Invernizzi, Milan, Italy
- Hidemasa Bono
- Database Center for Life Science, Tokyo, Japan
- Kees Burger
- Dutch Techcentre for Life Sciences, Utrecht, The Netherlands
- Hirokazu Chiba
- National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Japan
- Kevin B. Cohen
- Computational Bioscience Program, University of Colorado School of Medicine, Denver, USA
- Eric W. Deutsch
- Institute for Systems Biology, Seattle, USA
- Jesualdo T. Fernández-Breis
- Universidad de Murcia, IMIB-Arrixaca, Murcia, Spain
- Gang Fu
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, USA
- Takatomo Fujisawa
- National Institute of Genetics, Mishima, Japan
- Atsushi Fukushima
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Alexander García
- Polytechnic University of Madrid, Madrid, Spain
- Naohisa Goto
- Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
- Tudor Groza
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Darlinghurst, Australia
- Colin Hercus
- Novocraft Technologies Sdn. Bhd., Selangor, Malaysia
- Robert Hoehndorf
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Kotone Itaya
- Institute for Advanced Biosciences, Keio University, Tokyo, Japan
- Nick Juty
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
- Takeshi Kawashima
- National Institute of Genetics, Mishima, Japan
- Jee-Hyub Kim
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
- Akira R. Kinjo
- Institute for Protein Research, Osaka University, Osaka, Japan
- Masaaki Kotera
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
- Kouji Kozaki
- The Institute of Scientific and Industrial Research, Osaka University, Osaka, Japan
- Sadahiro Kumagai
- Hitachi Ltd., Tokyo, Japan
- Tatsuya Kushida
- National Bioscience Database Center, Japan Science and Technology Agency, Tokyo, Japan
- Thomas Lütteke
- Institute of Veterinary Physiology and Biochemistry, Justus-Liebig University Giessen, Giessen, Germany
- Masaaki Matsubara
- The Noguchi Institute, Tokyo, Japan
- Joe Miyamoto
- National Cancer Center Japan, Tokyo, Japan
- Attayeb Mohsen
- National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
- Hiroshi Mori
- Center for Information Biology, National Institute of Genetics, Mishima, Japan
- Yuki Naito
- Database Center for Life Science, Tokyo, Japan
- Takeru Nakazato
- Database Center for Life Science, Tokyo, Japan
- Jeremy Nguyen-Xuan
- Lawrence Berkeley National Laboratory, Berkeley, USA
- Kozo Nishida
- RIKEN Quantitative Biology Center, Osaka, Japan
- Naoki Nishida
- Department of Systems Science, Osaka University, Osaka, Japan
- Hiroyo Nishide
- National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Japan
- Soichi Ogishima
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Tazro Ohta
- Database Center for Life Science, Tokyo, Japan
- Shujiro Okuda
- Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
- Benedict Paten
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, USA
- Jean-Luc Perret
- INVENesis, Neuchâtel, Switzerland
- Philip Prathipati
- National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
- Pjotr Prins
- University Medical Center Utrecht, Utrecht, The Netherlands
- Núria Queralt-Rosinach
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
- Daisuke Shinmachi
- Faculty of Science and Engineering, SOKA University, Tokyo, Japan
- Shinya Suzuki
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
- Tsuyosi Tabata
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
- Terue Takatsuki
- RIKEN BioResource Center, Ibaraki, Japan
- Kieron Taylor
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
- Mark Thompson
- Leiden University Medical Center, Leiden, The Netherlands
- Ikuo Uchiyama
- National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Japan
- Bruno Vieira
- WurmLab, School of Biological & Chemical Sciences, Queen Mary University of London, London, UK
- Chih-Hsuan Wei
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, USA
- Mark Wilkinson
- Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
- Issaku Yamada
- The Noguchi Institute, Tokyo, Japan
- Ryota Yamanaka
- Oracle Corporation, Tokyo, Japan
- Kazutoshi Yoshitake
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
- Akiyasu C. Yoshizawa
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
- Michel Dumontier
- Institute of Data Science, Maastricht University, Maastricht, The Netherlands
- Kenjiro Kosaki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
- Toshihisa Takagi
- National Bioscience Database Center, Japan Science and Technology Agency, Tokyo, Japan
- DOI
- https://doi.org/10.12688/f1000research.18236.1
- Journal volume & issue
-
Vol. 9
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.
