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

Toshiaki Katayama, Mark D. Wilkinson, Kiyoko F. Aoki-Kinoshita, Shuichi Kawashima, Yasunori Yamamoto, Atsuko Yamaguchi, Shinobu Okamoto, Shin Kawano, Jin Dong Kim, Yue Wang, Hongyan Wu, Yoshinobu Kano, Hiromasa Ono, Hidemasa Bono, Simon Kocbek, Jan Aerts, Yukie Akune, Erick Antezana, Kazuharu Arakawa, Bruno ArandaJoachim Baran, Jerven Bolleman, Raoul J.P. Bonnal, Pier Luigi Buttigieg, Matthew P. Campbell, Yi An Chen, Hirokazu Chiba, Peter J.A. Cock, K. Bretonnel Cohen, Alexandru Constantin, Geraint Duck, Michel Dumontier, Takatomo Fujisawa, Toyofumi Fujiwara, Naohisa Goto, Robert Hoehndorf, Yoshinobu Igarashi, Hidetoshi Itaya, Maori Ito, Wataru Iwasaki, Matúš Kalaš, Takeo Katoda, Taehong Kim, Anna Kokubu, Yusuke Komiyama, Masaaki Kotera, Camille Laibe, Hilmar Lapp, Thomas Lütteke, M. Scott Marshall, Takaaki Mori, Hiroshi Mori, Mizuki Morita, Katsuhiko Murakami, Mitsuteru Nakao, Hisashi Narimatsu, Hiroyo Nishide, Yosuke Nishimura, Johan Nystrom-Persson, Soichi Ogishima, Yasunobu Okamura, Shujiro Okuda, Kazuki Oshita, Nicki H. Packer, Pjotr Prins, Rene Ranzinger, Philippe Rocca-Serra, Susanna Sansone, Hiromichi Sawaki, Sung Ho Shin, Andrea Splendiani, Francesco Strozzi, Shu Tadaka, Philip Toukach, Ikuo Uchiyama, Masahito Umezaki, Rutger Vos, Patricia L. Whetzel, Issaku Yamada, Chisato Yamasaki, Riu Yamashita, William S. York, Christian M. Zmasek, Shoko Kawamoto, Toshihisa Takagi

Research output: Contribution to journalReview article

23 Citations (Scopus)

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.

Original languageEnglish
Article number5
JournalJournal of Biomedical Semantics
Volume5
Issue number1
DOIs
Publication statusPublished - Jan 1 2014

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Keywords

  • BioHackathon
  • Bioinformatics
  • Data integration
  • Data models
  • Data sharing
  • Databases
  • Knowledge representation
  • Ontology
  • Semantic Web
  • Semantic interoperability
  • Visualization
  • Web services

ASJC Scopus subject areas

  • Information Systems
  • Computer Science Applications
  • Health Informatics
  • Computer Networks and Communications

Cite this

Katayama, T., Wilkinson, M. D., Aoki-Kinoshita, K. F., Kawashima, S., Yamamoto, Y., Yamaguchi, A., Okamoto, S., Kawano, S., Kim, J. D., Wang, Y., Wu, H., Kano, Y., Ono, H., Bono, H., Kocbek, S., Aerts, J., Akune, Y., Antezana, E., Arakawa, K., ... Takagi, T. (2014). BioHackathon series in 2011 and 2012: Penetration of ontology and linked data in life science domains. Journal of Biomedical Semantics, 5(1), [5]. https://doi.org/10.1186/2041-1480-5-5