BioHackathon series in 2011 and 2012

Penetration of ontology and linked data in life science domains

Toshiaki Katayama, Mark D. Wilkinson, Kiyoko F. Aoki-Kinoshita, Shuichi Kawashima, Yasunori Yamamoto, Atsuko Yamaguchi, Shinobu Okamoto, Shin Kawano, Jin Dong Kim, Yue Wang, Hongyan Wu, Yoshinobu Kano, Hiromasa Ono, Hidemasa Bono, Simon Kocbek, Jan Aerts, Yukie Akune, Erick Antezana, Kazuharu Arakawa, Bruno Aranda & 65 others Joachim Baran, Jerven Bolleman, Raoul J.P. Bonnal, Pier Luigi Buttigieg, Matthew P. Campbell, Yi An Chen, Hirokazu Chiba, Peter J.A. Cock, K. Bretonnel Cohen, Alexandru Constantin, Geraint Duck, Michel Dumontier, Takatomo Fujisawa, Toyofumi Fujiwara, Naohisa Goto, Robert Hoehndorf, Yoshinobu Igarashi, Hidetoshi Itaya, Maori Ito, Wataru Iwasaki, Matúš Kalaš, Takeo Katoda, Taehong Kim, Anna Kokubu, Yusuke Komiyama, Masaaki Kotera, Camille Laibe, Hilmar Lapp, Thomas Lütteke, M. Scott Marshall, Takaaki Mori, Hiroshi Mori, Mizuki Morita, Katsuhiko Murakami, Mitsuteru Nakao, Hisashi Narimatsu, Hiroyo Nishide, Yosuke Nishimura, Johan Nystrom-Persson, Soichi Ogishima, Yasunobu Okamura, Shujiro Okuda, Kazuki Oshita, Nicki H. Packer, Pjotr Prins, Rene Ranzinger, Philippe Rocca-Serra, Susanna Sansone, Hiromichi Sawaki, Sung Ho Shin, Andrea Splendiani, Francesco Strozzi, Shu Tadaka, Philip Toukach, Ikuo Uchiyama, Masahito Umezaki, Rutger Vos, Patricia L. Whetzel, Issaku Yamada, Chisato Yamasaki, Riu Yamashita, William S. York, Christian M. Zmasek, Shoko Kawamoto, Toshihisa Takagi

Research output: Contribution to journalReview article

21 Citations (Scopus)

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.

Original languageEnglish
Article number5
JournalJournal of Biomedical Semantics
Volume5
Issue number1
DOIs
Publication statusPublished - 2014

Fingerprint

Biological Science Disciplines
Semantics
Ontology
Semantic Web
Interoperability
Bioinformatics
Metadata
Technology
Data Mining
Software engineering
Visualization
Computational Biology
Japan
Software
Databases

Keywords

  • BioHackathon
  • Bioinformatics
  • Data integration
  • Data models
  • Data sharing
  • Databases
  • Knowledge representation
  • Ontology
  • Semantic interoperability
  • Semantic Web
  • Visualization
  • Web services

ASJC Scopus subject areas

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

Cite this

Katayama, T., Wilkinson, M. D., Aoki-Kinoshita, K. F., Kawashima, S., Yamamoto, Y., Yamaguchi, A., ... Takagi, T. (2014). BioHackathon series in 2011 and 2012: Penetration of ontology and linked data in life science domains. Journal of Biomedical Semantics, 5(1), [5]. https://doi.org/10.1186/2041-1480-5-5

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; 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.

In: Journal of Biomedical Semantics, Vol. 5, No. 1, 5, 2014.

Research output: Contribution to journalReview article

Katayama, T, Wilkinson, MD, Aoki-Kinoshita, KF, Kawashima, S, Yamamoto, Y, Yamaguchi, A, Okamoto, S, Kawano, S, Kim, JD, Wang, Y, Wu, H, Kano, Y, Ono, H, Bono, H, Kocbek, S, Aerts, J, Akune, Y, Antezana, E, Arakawa, K, Aranda, B, Baran, J, Bolleman, J, Bonnal, RJP, Buttigieg, PL, Campbell, MP, Chen, YA, Chiba, H, Cock, PJA, Cohen, KB, Constantin, A, Duck, G, Dumontier, M, Fujisawa, T, Fujiwara, T, Goto, N, Hoehndorf, R, Igarashi, Y, Itaya, H, Ito, M, Iwasaki, W, Kalaš, M, Katoda, T, Kim, T, Kokubu, A, Komiyama, Y, Kotera, M, Laibe, C, Lapp, H, Lütteke, T, Marshall, MS, Mori, T, Mori, H, Morita, M, Murakami, K, Nakao, M, Narimatsu, H, Nishide, H, Nishimura, Y, Nystrom-Persson, J, Ogishima, S, Okamura, Y, Okuda, S, Oshita, K, Packer, NH, Prins, P, Ranzinger, R, Rocca-Serra, P, Sansone, S, Sawaki, H, Shin, SH, Splendiani, A, Strozzi, F, Tadaka, S, Toukach, P, Uchiyama, I, Umezaki, M, Vos, R, Whetzel, PL, Yamada, I, Yamasaki, C, Yamashita, R, York, WS, Zmasek, CM, Kawamoto, S & Takagi, T 2014, 'BioHackathon series in 2011 and 2012: Penetration of ontology and linked data in life science domains', Journal of Biomedical Semantics, vol. 5, no. 1, 5. https://doi.org/10.1186/2041-1480-5-5
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 ; 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. / BioHackathon series in 2011 and 2012 : Penetration of ontology and linked data in life science domains. In: Journal of Biomedical Semantics. 2014 ; Vol. 5, No. 1.
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TY - JOUR

T1 - BioHackathon series in 2011 and 2012

T2 - Penetration of ontology and linked data in life science domains

AU - Katayama, Toshiaki

AU - Wilkinson, Mark D.

AU - Aoki-Kinoshita, Kiyoko F.

AU - Kawashima, Shuichi

AU - Yamamoto, Yasunori

AU - Yamaguchi, Atsuko

AU - Okamoto, Shinobu

AU - Kawano, Shin

AU - Kim, Jin Dong

AU - Wang, Yue

AU - Wu, Hongyan

AU - Kano, Yoshinobu

AU - Ono, Hiromasa

AU - Bono, Hidemasa

AU - Kocbek, Simon

AU - Aerts, Jan

AU - Akune, Yukie

AU - Antezana, Erick

AU - Arakawa, Kazuharu

AU - Aranda, Bruno

AU - Baran, Joachim

AU - Bolleman, Jerven

AU - Bonnal, Raoul J.P.

AU - Buttigieg, Pier Luigi

AU - Campbell, Matthew P.

AU - Chen, Yi An

AU - Chiba, Hirokazu

AU - Cock, Peter J.A.

AU - Cohen, K. Bretonnel

AU - Constantin, Alexandru

AU - Duck, Geraint

AU - Dumontier, Michel

AU - Fujisawa, Takatomo

AU - Fujiwara, Toyofumi

AU - Goto, Naohisa

AU - Hoehndorf, Robert

AU - Igarashi, Yoshinobu

AU - Itaya, Hidetoshi

AU - Ito, Maori

AU - Iwasaki, Wataru

AU - Kalaš, Matúš

AU - Katoda, Takeo

AU - Kim, Taehong

AU - Kokubu, Anna

AU - Komiyama, Yusuke

AU - Kotera, Masaaki

AU - Laibe, Camille

AU - Lapp, Hilmar

AU - Lütteke, Thomas

AU - Marshall, M. Scott

AU - Mori, Takaaki

AU - Mori, Hiroshi

AU - Morita, Mizuki

AU - Murakami, Katsuhiko

AU - Nakao, Mitsuteru

AU - Narimatsu, Hisashi

AU - Nishide, Hiroyo

AU - Nishimura, Yosuke

AU - Nystrom-Persson, Johan

AU - Ogishima, Soichi

AU - Okamura, Yasunobu

AU - Okuda, Shujiro

AU - Oshita, Kazuki

AU - Packer, Nicki H.

AU - Prins, Pjotr

AU - Ranzinger, Rene

AU - Rocca-Serra, Philippe

AU - Sansone, Susanna

AU - Sawaki, Hiromichi

AU - Shin, Sung Ho

AU - Splendiani, Andrea

AU - Strozzi, Francesco

AU - Tadaka, Shu

AU - Toukach, Philip

AU - Uchiyama, Ikuo

AU - Umezaki, Masahito

AU - Vos, Rutger

AU - Whetzel, Patricia L.

AU - Yamada, Issaku

AU - Yamasaki, Chisato

AU - Yamashita, Riu

AU - York, William S.

AU - Zmasek, Christian M.

AU - Kawamoto, Shoko

AU - Takagi, Toshihisa

PY - 2014

Y1 - 2014

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AB - 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.

KW - BioHackathon

KW - Bioinformatics

KW - Data integration

KW - Data models

KW - Data sharing

KW - Databases

KW - Knowledge representation

KW - Ontology

KW - Semantic interoperability

KW - Semantic Web

KW - Visualization

KW - Web services

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DO - 10.1186/2041-1480-5-5

M3 - Review article

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JF - Journal of Biomedical Semantics

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