The 3rd DBCLS BioHackathon: Improving life science data integration with Semantic Web technologies

Toshiaki Katayama, Mark D. Wilkinson, Gos Micklem, Shuichi Kawashima, Atsuko Yamaguchi, Mitsuteru Nakao, Yasunori Yamamoto, Shinobu Okamoto, Kenta Oouchida, Hong Woo Chun, Jan Aerts, Hammad Afzal, Erick Antezana, Kazuharu Arakawa, Bruno Aranda, Francois Belleau, Jerven Bolleman, Raoul J.P. Bonnal, Brad Chapman, Peter J.A. CockTore Eriksson, Paul M.K. Gordon, Naohisa Goto, Kazuhiro Hayashi, Heiko Horn, Ryosuke Ishiwata, Eli Kaminuma, Arek Kasprzyk, Hideya Kawaji, Nobuhiro Kido, Young Joo Kim, Akira R. Kinjo, Fumikazu Konishi, Kyung Hoon Kwon, Alberto Labarga, Anna Lena Lamprecht, Yu Lin, Pierre Lindenbaum, Luke McCarthy, Hideyuki Morita, Katsuhiko Murakami, Koji Nagao, Kozo Nishida, Kunihiro Nishimura, Tatsuya Nishizawa, Soichi Ogishima, Keiichiro Ono, Kazuki Oshita, Keun Joon Park, Pjotr Prins, Taro L. Saito, Matthias Samwald, Venkata P. Satagopam, Yasumasa Shigemoto, Richard Smith, Andrea Splendiani, Hideaki Sugawara, James Taylor, Rutger A. Vos, David Withers, Chisato Yamasaki, Christian M. Zmasek, Shoko Kawamoto, Kosaku Okubo, Kiyoshi Asai, Toshihisa Takagi

Research output: Contribution to journalReview article

14 Citations (Scopus)

Abstract

Background: BioHackathon 2010 was the third in a series of meetings hosted by the Database Center for Life Sciences (DBCLS) in Tokyo, Japan. The overall goal of the BioHackathon series is to improve the quality and accessibility of life science research data on the Web by bringing together representatives from public databases, analytical tool providers, and cyber-infrastructure researchers to jointly tackle important challenges in the area of in silico biological research. Results: The theme of BioHackathon 2010 was the 'Semantic Web', and all attendees gathered with the shared goal of producing Semantic Web data from their respective resources, and/or consuming or interacting those data using their tools and interfaces. We discussed on topics including guidelines for designing semantic data and interoperability of resources. We consequently developed tools and clients for analysis and visualization. Conclusion: We provide a meeting report from BioHackathon 2010, in which we describe the discussions, decisions, and breakthroughs made as we moved towards compliance with Semantic Web technologies - from source provider, through middleware, to the end-consumer.

Original languageEnglish
Article number6
JournalJournal of Biomedical Semantics
Volume4
Issue number1
DOIs
Publication statusPublished - 2013 Feb 11
Externally publishedYes

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Keywords

  • BioHackathon
  • Data integration
  • Data visualization
  • Databases
  • Interfaces
  • Open source
  • Semantic Web
  • Software
  • Web services

ASJC Scopus subject areas

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

Cite this

Katayama, T., Wilkinson, M. D., Micklem, G., Kawashima, S., Yamaguchi, A., Nakao, M., Yamamoto, Y., Okamoto, S., Oouchida, K., Chun, H. W., Aerts, J., Afzal, H., Antezana, E., Arakawa, K., Aranda, B., Belleau, F., Bolleman, J., Bonnal, R. J. P., Chapman, B., ... Takagi, T. (2013). The 3rd DBCLS BioHackathon: Improving life science data integration with Semantic Web technologies. Journal of Biomedical Semantics, 4(1), [6]. https://doi.org/10.1186/2041-1480-4-6