BioHackathon series in 2011 and 2012: Penetration of ontology and linked data in life science domains
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Wilkinson, Mark D.
Aoki-Kinoshita, Kiyoko F.
Kawashima, Shuichi
Yamamoto, Yasunori
Yamaguchi, Atsuko
Okamoto, Shinobu
Kawano, Shin
Kim, Jin-Dong
Wang, Yue
Wu, Hongyan
Kano, Yoshinobu
Ono, Hiromasa
Bono, Hidemasa
Kocbek, Simon
Aerts, Jan
Akune, Yukie
Antezana, Erick
Arakawa, Kazuharu
Aranda, Bruno
Baran, Joachim
Bolleman, Jerven
Bonnal, Raoul J. P.
Buttigieg, Pier Luigi
Campbell, Matthew P.
Chen, Yi-an
Chiba, Hirokazu
Cock, Peter J. A.
Packer, Nicolle H.
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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.
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Journal of Biomedical Semantics
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5
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1
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© Katayama et al.; licensee BioMed Central Ltd. 2014. This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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Other biological sciences
Other biological sciences not elsewhere classified
Information systems