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; 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

doi:10.1186/2041-1480-5-5

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 ArandaJoachim 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

^*Corresponding author for this work

Research output: Contribution to journal › Review article › peer-review

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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.

Original language	English
Article number	5
Pages (from-to)	1-13
Number of pages	13
Journal	Journal of Biomedical Semantics
Volume	5
DOIs	https://doi.org/10.1186/2041-1480-5-5
Publication status	Published - 5 Feb 2014

Bibliographical note

Copyright the Author(s) 2014. Version archived for private and non-commercial use with the permission of the author/s and according to publisher conditions. For further rights please contact the publisher.

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10.1186/2041-1480-5-5

Publisher version (open access)Final published version, 1.05 MBLicence: CC BY

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Katayama, T., Wilkinson, M. D., Aoki-Kinoshita, K. F., Kawashima, S., Yamamoto, Y., Yamaguchi, A., Okamoto, S., Kawano, S., Kim, J. D., Wang, Y., Wu, H., Kano, Y., Ono, H., Bono, H., Kocbek, S., Aerts, J., Akune, Y., Antezana, E., Arakawa, K., ... Takagi, T. (2014). BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains. Journal of Biomedical Semantics, 5, 1-13. [5]. https://doi.org/10.1186/2041-1480-5-5

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title = "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.",

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

note = "Copyright the Author(s) 2014. Version archived for private and non-commercial use with the permission of the author/s and according to publisher conditions. For further rights please contact the publisher.",

year = "2014",

month = feb,

day = "5",

doi = "10.1186/2041-1480-5-5",

language = "English",

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journal = "Journal of Biomedical Semantics",

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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, 5, pp. 1-13. https://doi.org/10.1186/2041-1480-5-5

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

N1 - Copyright the Author(s) 2014. Version archived for private and non-commercial use with the permission of the author/s and according to publisher conditions. For further rights please contact the publisher.

PY - 2014/2/5

Y1 - 2014/2/5

N2 - 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.

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.

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U2 - 10.1186/2041-1480-5-5

DO - 10.1186/2041-1480-5-5

M3 - Review article

C2 - 24495517

AN - SCOPUS:84988878542

VL - 5

SP - 1

EP - 13

JO - Journal of Biomedical Semantics

JF - Journal of Biomedical Semantics

SN - 2041-1480

M1 - 5

ER -

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

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