The 3rd DBCLS BioHackathon: improving life science data integration with semantic Web technologies

Toshiaki Katayama; Mark D Wilkinson; Gos Micklem; Shuichi Kawashima; Atsuko Yamaguchi; Mitsuteru Nakao; Yasunori Yamamoto; Shinobu Okamoto; Kenta Oouchida; Hong-Woo Chun; Jan Aerts; Hammad Afzal; Erick Antezana; Kazuharu Arakawa; Bruno Aranda; Francois Belleau; Jerven Bolleman; Raoul Jean Bonnal; Brad Chapman; Peter Cock; Tore Eriksson; Paul Gordon; Naohisa Goto; Kazuhiro Hayashi; Heiko Horn; Ryosuke Ishiwata; Eli Kaminuma; Arek Kasprzyk; Hideya Kawaji; Nobuhiro Kido; Young Joo Kim; Akira R Kinjo; Fumikazu Konishi; Kyung-Hoon Kwon; Alberto Labarga; Anna-Lena Lamprecht; Yu Lin; Pierre Lindenbaum; Luke McCarthy; Hideyuki Morita; Katsuhiko Murakami; Koji Nagao; Kozo Nishida; Kunihiro Nishimura; Tatsuya Nishizawa; Soichi Ogishima; Keiichiro Ono; Kazuki Oshita; Keun-Joon Park; Pjotr Prins; Taro L Saito; Matthias Samwald; Venkata P Satagopam; Yasumasa Shigemoto; Richard Smith; Andrea Splendiani; Hideaki Sugawara; James Taylor; Rutger Vos; David Withers; Chisato Yamasaki; Christian M Zmasek; Shoko Kawamoto; Kosaku Okubo; Kiyoshi Asai; Toshihisa Takagi

doi:10.1186/2041-1480-4-6

The 3rd DBCLS BioHackathon: improving life science data integration with semantic Web technologies

Toshiaki Katayama, Mark D Wilkinson, Gos Micklem, Shuichi Kawashima, Atsuko Yamaguchi, Mitsuteru Nakao, Yasunori Yamamoto, Shinobu Okamoto, Kenta Oouchida, Hong-Woo Chun, Jan Aerts, Hammad Afzal, Erick Antezana, Kazuharu Arakawa, Bruno Aranda, Francois Belleau, Jerven Bolleman, Raoul Jean Bonnal, Brad Chapman, Peter CockTore Eriksson, Paul Gordon, Naohisa Goto, Kazuhiro Hayashi, Heiko Horn, Ryosuke Ishiwata, Eli Kaminuma, Arek Kasprzyk, Hideya Kawaji, Nobuhiro Kido, Young Joo Kim, Akira R Kinjo, Fumikazu Konishi, Kyung-Hoon Kwon, Alberto Labarga, Anna-Lena Lamprecht, Yu Lin, Pierre Lindenbaum, Luke McCarthy, Hideyuki Morita, Katsuhiko Murakami, Koji Nagao, Kozo Nishida, Kunihiro Nishimura, Tatsuya Nishizawa, Soichi Ogishima, Keiichiro Ono, Kazuki Oshita, Keun-Joon Park, Pjotr Prins, Taro L Saito, Matthias Samwald, Venkata P Satagopam, Yasumasa Shigemoto, Richard Smith, Andrea Splendiani, Hideaki Sugawara, James Taylor, Rutger Vos, David Withers, Chisato Yamasaki, Christian M Zmasek, Shoko Kawamoto, Kosaku Okubo, Kiyoshi Asai, Toshihisa Takagi

18 Citations (Scopus)

Abstract

Background: BioHackathon 2010 was the third in a series of meetings hosted by the Database Center for Life Sciences (DBCLS) in Tokyo, Japan. The overall goal of the BioHackathon series is to improve the quality and accessibility of life science research data on the Web by bringing together representatives from public databases, analytical tool providers, and cyber-infrastructure researchers to jointly tackle important challenges in the area of in silico biological research. Results: The theme of BioHackathon 2010 was the 'Semantic Web', and all attendees gathered with the shared goal of producing Semantic Web data from their respective resources, and/or consuming or interacting those data using their tools and interfaces. We discussed on topics including guidelines for designing semantic data and interoperability of resources. We consequently developed tools and clients for analysis and visualization. Conclusion: We provide a meeting report from BioHackathon 2010, in which we describe the discussions, decisions, and breakthroughs made as we moved towards compliance with Semantic Web technologies - from source provider, through middleware, to the end-consumer.

Original language	English
Journal	Journal of Biomedical Semantics
Volume	4
Issue number	1
Pages (from-to)	6
Number of pages	17
ISSN	2041-1480
DOIs	https://doi.org/10.1186/2041-1480-4-6
Publication status	Published - 11 Feb 2013

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Katayama, T., Wilkinson, M. D., Micklem, G., Kawashima, S., Yamaguchi, A., Nakao, M., Yamamoto, Y., Okamoto, S., Oouchida, K., Chun, H-W., Aerts, J., Afzal, H., Antezana, E., Arakawa, K., Aranda, B., Belleau, F., Bolleman, J., Bonnal, R. J., Chapman, B., ... Takagi, T. (2013). The 3rd DBCLS BioHackathon: improving life science data integration with semantic Web technologies. Journal of Biomedical Semantics, 4(1), 6. https://doi.org/10.1186/2041-1480-4-6

Katayama, T, Wilkinson, MD, Micklem, G, Kawashima, S, Yamaguchi, A, Nakao, M, Yamamoto, Y, Okamoto, S, Oouchida, K, Chun, H-W, Aerts, J, Afzal, H, Antezana, E, Arakawa, K, Aranda, B, Belleau, F, Bolleman, J, Bonnal, RJ, Chapman, B, Cock, P, Eriksson, T, Gordon, P, Goto, N, Hayashi, K, Horn, H, Ishiwata, R, Kaminuma, E, Kasprzyk, A, Kawaji, H, Kido, N, Kim, YJ, Kinjo, AR, Konishi, F, Kwon, K-H, Labarga, A, Lamprecht, A-L, Lin, Y, Lindenbaum, P, McCarthy, L, Morita, H, Murakami, K, Nagao, K, Nishida, K, Nishimura, K, Nishizawa, T, Ogishima, S, Ono, K, Oshita, K, Park, K-J, Prins, P, Saito, TL, Samwald, M, Satagopam, VP, Shigemoto, Y, Smith, R, Splendiani, A, Sugawara, H, Taylor, J, Vos, R, Withers, D, Yamasaki, C, Zmasek, CM, Kawamoto, S, Okubo, K, Asai, K & Takagi, T 2013, 'The 3rd DBCLS BioHackathon: improving life science data integration with semantic Web technologies', Journal of Biomedical Semantics, vol. 4, no. 1, pp. 6. https://doi.org/10.1186/2041-1480-4-6

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title = "The 3rd DBCLS BioHackathon: improving life science data integration with semantic Web technologies",

abstract = "Background: BioHackathon 2010 was the third in a series of meetings hosted by the Database Center for Life Sciences (DBCLS) in Tokyo, Japan. The overall goal of the BioHackathon series is to improve the quality and accessibility of life science research data on the Web by bringing together representatives from public databases, analytical tool providers, and cyber-infrastructure researchers to jointly tackle important challenges in the area of in silico biological research. Results: The theme of BioHackathon 2010 was the 'Semantic Web', and all attendees gathered with the shared goal of producing Semantic Web data from their respective resources, and/or consuming or interacting those data using their tools and interfaces. We discussed on topics including guidelines for designing semantic data and interoperability of resources. We consequently developed tools and clients for analysis and visualization. Conclusion: We provide a meeting report from BioHackathon 2010, in which we describe the discussions, decisions, and breakthroughs made as we moved towards compliance with Semantic Web technologies - from source provider, through middleware, to the end-consumer.",

author = "Toshiaki Katayama and Wilkinson, {Mark D} and Gos Micklem and Shuichi Kawashima and Atsuko Yamaguchi and Mitsuteru Nakao and Yasunori Yamamoto and Shinobu Okamoto and Kenta Oouchida and Hong-Woo Chun and Jan Aerts and Hammad Afzal and Erick Antezana and Kazuharu Arakawa and Bruno Aranda and Francois Belleau and Jerven Bolleman and Bonnal, {Raoul Jean} and Brad Chapman and Peter Cock and Tore Eriksson and Paul Gordon and Naohisa Goto and Kazuhiro Hayashi and Heiko Horn and Ryosuke Ishiwata and Eli Kaminuma and Arek Kasprzyk and Hideya Kawaji and Nobuhiro Kido and Kim, {Young Joo} and Kinjo, {Akira R} and Fumikazu Konishi and Kyung-Hoon Kwon and Alberto Labarga and Anna-Lena Lamprecht and Yu Lin and Pierre Lindenbaum and Luke McCarthy and Hideyuki Morita and Katsuhiko Murakami and Koji Nagao and Kozo Nishida and Kunihiro Nishimura and Tatsuya Nishizawa and Soichi Ogishima and Keiichiro Ono and Kazuki Oshita and Keun-Joon Park and Pjotr Prins and Saito, {Taro L} and Matthias Samwald and Satagopam, {Venkata P} and Yasumasa Shigemoto and Richard Smith and Andrea Splendiani and Hideaki Sugawara and James Taylor and Rutger Vos and David Withers and Chisato Yamasaki and Zmasek, {Christian M} and Shoko Kawamoto and Kosaku Okubo and Kiyoshi Asai and Toshihisa Takagi",

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T1 - The 3rd DBCLS BioHackathon

T2 - improving life science data integration with semantic Web technologies

AU - Katayama, Toshiaki

AU - Wilkinson, Mark D

AU - Micklem, Gos

AU - Kawashima, Shuichi

AU - Yamaguchi, Atsuko

AU - Nakao, Mitsuteru

AU - Yamamoto, Yasunori

AU - Okamoto, Shinobu

AU - Oouchida, Kenta

AU - Chun, Hong-Woo

AU - Aerts, Jan

AU - Afzal, Hammad

AU - Antezana, Erick

AU - Arakawa, Kazuharu

AU - Aranda, Bruno

AU - Belleau, Francois

AU - Bolleman, Jerven

AU - Bonnal, Raoul Jean

AU - Chapman, Brad

AU - Cock, Peter

AU - Eriksson, Tore

AU - Gordon, Paul

AU - Goto, Naohisa

AU - Hayashi, Kazuhiro

AU - Horn, Heiko

AU - Ishiwata, Ryosuke

AU - Kaminuma, Eli

AU - Kasprzyk, Arek

AU - Kawaji, Hideya

AU - Kido, Nobuhiro

AU - Kim, Young Joo

AU - Kinjo, Akira R

AU - Konishi, Fumikazu

AU - Kwon, Kyung-Hoon

AU - Labarga, Alberto

AU - Lamprecht, Anna-Lena

AU - Lin, Yu

AU - Lindenbaum, Pierre

AU - McCarthy, Luke

AU - Morita, Hideyuki

AU - Murakami, Katsuhiko

AU - Nagao, Koji

AU - Nishida, Kozo

AU - Nishimura, Kunihiro

AU - Nishizawa, Tatsuya

AU - Ogishima, Soichi

AU - Ono, Keiichiro

AU - Oshita, Kazuki

AU - Park, Keun-Joon

AU - Prins, Pjotr

AU - Saito, Taro L

AU - Samwald, Matthias

AU - Satagopam, Venkata P

AU - Shigemoto, Yasumasa

AU - Smith, Richard

AU - Splendiani, Andrea

AU - Sugawara, Hideaki

AU - Taylor, James

AU - Vos, Rutger

AU - Withers, David

AU - Yamasaki, Chisato

AU - Zmasek, Christian M

AU - Kawamoto, Shoko

AU - Okubo, Kosaku

AU - Asai, Kiyoshi

AU - Takagi, Toshihisa

PY - 2013/2/11

Y1 - 2013/2/11

N2 - Background: BioHackathon 2010 was the third in a series of meetings hosted by the Database Center for Life Sciences (DBCLS) in Tokyo, Japan. The overall goal of the BioHackathon series is to improve the quality and accessibility of life science research data on the Web by bringing together representatives from public databases, analytical tool providers, and cyber-infrastructure researchers to jointly tackle important challenges in the area of in silico biological research. Results: The theme of BioHackathon 2010 was the 'Semantic Web', and all attendees gathered with the shared goal of producing Semantic Web data from their respective resources, and/or consuming or interacting those data using their tools and interfaces. We discussed on topics including guidelines for designing semantic data and interoperability of resources. We consequently developed tools and clients for analysis and visualization. Conclusion: We provide a meeting report from BioHackathon 2010, in which we describe the discussions, decisions, and breakthroughs made as we moved towards compliance with Semantic Web technologies - from source provider, through middleware, to the end-consumer.

AB - Background: BioHackathon 2010 was the third in a series of meetings hosted by the Database Center for Life Sciences (DBCLS) in Tokyo, Japan. The overall goal of the BioHackathon series is to improve the quality and accessibility of life science research data on the Web by bringing together representatives from public databases, analytical tool providers, and cyber-infrastructure researchers to jointly tackle important challenges in the area of in silico biological research. Results: The theme of BioHackathon 2010 was the 'Semantic Web', and all attendees gathered with the shared goal of producing Semantic Web data from their respective resources, and/or consuming or interacting those data using their tools and interfaces. We discussed on topics including guidelines for designing semantic data and interoperability of resources. We consequently developed tools and clients for analysis and visualization. Conclusion: We provide a meeting report from BioHackathon 2010, in which we describe the discussions, decisions, and breakthroughs made as we moved towards compliance with Semantic Web technologies - from source provider, through middleware, to the end-consumer.

U2 - 10.1186/2041-1480-4-6

DO - 10.1186/2041-1480-4-6

M3 - Journal article

C2 - 23398680

SN - 2041-1480

VL - 4

SP - 6

JO - Journal of Biomedical Semantics

JF - Journal of Biomedical Semantics

IS - 1

ER -

The 3rd DBCLS BioHackathon: improving life science data integration with semantic Web technologies

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