Biohackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains
Katayama, Toshiaki Wilkinson, Mark D Aoki-Kinoshita, Kiyoko F Kawashima, Shuichi Yamamoto, Yasunori Yamaguchi, Atsuko Okamoto, Shinobu Kawano, Shin Kim, Jin-Dong Wang, Yue
Katayama, Toshiaki
Wilkinson, Mark D
Aoki-Kinoshita, Kiyoko F
Kawashima, Shuichi
Yamamoto, Yasunori
Yamaguchi, Atsuko
Okamoto, Shinobu
Kawano, Shin
Kim, Jin-Dong
Wang, Yue
Publication Date
2014-01-01
Keywords
biohackathon, bioinformatics, semantic web, web services, ontology, visualization, knowledge representation, databases, semantic interoperability, data models, data sharing, data integration, bioinformatics web services, genome analysis environment, metabolic pathways, semantic web, gene, integration, glycomics, sequences, software, biology
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Article
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Katayama, Toshiaki; 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 JP; Buttigieg, Pier; Campbell, Matthew P; Chen, Yi-an; Chiba, Hirokazu; Cock, Peter JA; Cohen, K; Constantin, Alexandru; Duck, Geraint; Dumontier, Michel; Fujisawa, Takatomo; Fujiwara, Toyofumi; Goto, Naohisa; Hoehndorf, Robert; Igarashi, Yoshinobu; Itaya, Hidetoshi; Ito, Maori; Iwasaki, Wataru; Kalaš, Matúš; Katoda, Takeo; Kim, Taehong; Kokubu, Anna; Komiyama, Yusuke; Kotera, Masaaki; Laibe, Camille; Lapp, Hilmar; Lütteke, Thomas; Marshall, M; Mori, Takaaki; Mori, Hiroshi; Morita, Mizuki; Murakami, Katsuhiko; Nakao, Mitsuteru; Narimatsu, Hisashi; Nishide, Hiroyo; Nishimura, Yosuke; Nystrom-Persson, Johan; Ogishima, Soichi; Okamura, Yasunobu; Okuda, Shujiro; Oshita, Kazuki; Packer, Nicki H; Prins, Pjotr; Ranzinger, Rene; Rocca-Serra, Philippe; Sansone, Susanna; Sawaki, Hiromichi; Shin, Sung-Ho; Splendiani, Andrea; Strozzi, Francesco; Tadaka, Shu; Toukach, Philip; Uchiyama, Ikuo; Umezaki, Masahito; Vos, Rutger; Whetzel, Patricia L; Yamada, Issaku; Yamasaki, Chisato; Yamashita, Riu; York, William S; Zmasek, Christian M; Kawamoto, Shoko; Takagi, Toshihisa (2014). Biohackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains. Journal of Biomedical Semantics 5 ,
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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Publisher
Springer Nature
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Attribution-NonCommercial-NoDerivs 3.0 Ireland