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; 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.; Cohen, K. Bretonnel; 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. Scott; Mori, Takaaki; Mori, Hiroshi; Morita, Mizuki; Murakami, Katsuhiko; Nakao, Mitsuteru; Narimatsu, Hisashi; Nishide, Hiroyo; Nishimura, Yosuke; Nyström-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
Peer reviewed, Journal article
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URI
https://hdl.handle.net/1956/8517
Date
2014-02-05
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Original version
https://doi.org/10.1186/2041-1480-5-5
Abstract
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.
Publisher
BioMed Central
Journal
Journal of Biomedical Semantics
Copyright
Toshiaki Katayama et al.; licensee BioMed Central Ltd.
Copyright 2014 Katayama et al.; licensee BioMed Central Ltd.
Attribution CC BY
Except where otherwise noted, this item's license is described as Attribution CC BY