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

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.

SUBMITTER: Katayama T

PROVIDER: S-EPMC3978116 | biostudies-literature | 2014 Feb

REPOSITORIES: biostudies-literature

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

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

Journal of biomedical semantics 20140205 1

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 ...[more]

PMID: 24495517

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Dataset Information

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

Publications

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

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