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 J.P. Bonnal; Brad Chapman; Peter J.A. Cock; Tore Eriksson; Paul M.K. 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 A. 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 J.P. Bonnal, Brad Chapman, Peter J.A. CockTore Eriksson, Paul M.K. 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 A. Vos, David Withers, Chisato Yamasaki, Christian M. Zmasek, Shoko Kawamoto, Kosaku Okubo, Kiyoshi Asai, Toshihisa Takagi

Research Organization of Information and Systems

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

17 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
Article number	6
Journal	Journal of Biomedical Semantics
Volume	4
Issue number	1
DOIs	https://doi.org/10.1186/2041-1480-4-6
Publication status	Published - 2013 Feb 11

Keywords

BioHackathon
Data integration
Data visualization
Databases
Interfaces
Open source
Semantic Web
Software
Web services

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10.1186/2041-1480-4-6

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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. P., Chapman, B., ... Takagi, T. (2013). The 3rd DBCLS BioHackathon: Improving life science data integration with Semantic Web technologies. Journal of Biomedical Semantics, 4(1), Article 6. https://doi.org/10.1186/2041-1480-4-6

@article{70d579112a324bbfbf48d72da336f2f1,

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.",

keywords = "BioHackathon, Data integration, Data visualization, Databases, Interfaces, Open source, Semantic Web, Software, Web services",

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 Chun, {Hong Woo} and Jan Aerts and Hammad Afzal and Erick Antezana and Kazuharu Arakawa and Bruno Aranda and Francois Belleau and Jerven Bolleman and Bonnal, {Raoul J.P.} and Brad Chapman and Cock, {Peter J.A.} and Tore Eriksson and Gordon, {Paul M.K.} 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 Kwon, {Kyung Hoon} and Alberto Labarga and Lamprecht, {Anna Lena} 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 Park, {Keun Joon} 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 Vos, {Rutger A.} and David Withers and Chisato Yamasaki and Zmasek, {Christian M.} and Shoko Kawamoto and Kosaku Okubo and Kiyoshi Asai and Toshihisa Takagi",

note = "Funding Information: BioHackathon 2010 was supported by the Integrated Database Project (Ministry of Education, Culture, Sports, Science and Technology of Japan) and the Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, Japan. Publisher Copyright: {\textcopyright} 2013 Katayama et al; licensee BioMed Central Ltd.",

year = "2013",

month = feb,

day = "11",

doi = "10.1186/2041-1480-4-6",

language = "English",

volume = "4",

journal = "Journal of Biomedical Semantics",

issn = "2041-1480",

publisher = "BioMed Central Ltd.",

number = "1",

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Katayama, T, Wilkinson, MD, Micklem, G, Kawashima, S, Yamaguchi, A, Nakao, M, Yamamoto, Y, Okamoto, S, Oouchida, K, Chun, HW, Aerts, J, Afzal, H, Antezana, E, Arakawa, K, Aranda, B, Belleau, F, Bolleman, J, Bonnal, RJP, Chapman, B, Cock, PJA, Eriksson, T, Gordon, PMK, Goto, N, Hayashi, K, Horn, H, Ishiwata, R, Kaminuma, E, Kasprzyk, A, Kawaji, H, Kido, N, Kim, YJ, Kinjo, AR, Konishi, F, Kwon, KH, Labarga, A, Lamprecht, AL, 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, KJ, Prins, P, Saito, TL, Samwald, M, Satagopam, VP, Shigemoto, Y, Smith, R, Splendiani, A, Sugawara, H, Taylor, J, Vos, RA, 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, 6. https://doi.org/10.1186/2041-1480-4-6

TY - JOUR

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 J.P.

AU - Chapman, Brad

AU - Cock, Peter J.A.

AU - Eriksson, Tore

AU - Gordon, Paul M.K.

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 A.

AU - Withers, David

AU - Yamasaki, Chisato

AU - Zmasek, Christian M.

AU - Kawamoto, Shoko

AU - Okubo, Kosaku

AU - Asai, Kiyoshi

AU - Takagi, Toshihisa

N1 - Funding Information: BioHackathon 2010 was supported by the Integrated Database Project (Ministry of Education, Culture, Sports, Science and Technology of Japan) and the Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, Japan. Publisher Copyright: © 2013 Katayama et al; licensee BioMed Central Ltd.

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.

KW - BioHackathon

KW - Data integration

KW - Data visualization

KW - Databases

KW - Interfaces

KW - Open source

KW - Semantic Web

KW - Software

KW - Web services

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U2 - 10.1186/2041-1480-4-6

DO - 10.1186/2041-1480-4-6

M3 - Review article

AN - SCOPUS:84939564975

SN - 2041-1480

VL - 4

JO - Journal of Biomedical Semantics

JF - Journal of Biomedical Semantics

IS - 1

M1 - 6

ER -

The 3rd DBCLS BioHackathon: Improving life science data integration with Semantic Web technologies

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