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

T. Katayama; D.W. Wilkinson; G. Micklem; S. Kawashima; A. Yamaguchi; M. Nakao; T. Yamamoto; S. Okamoto; K. Oouchida; H. Chung; J. Aerts; H. Afzal; E. Antezana; K. Arakawa; B. Aranda; F. Belleau; J. Bolleman; R.J.P. Bonnal; B. Chapman; P.J.A. Cock; T. Eriksson; P.M.K. Gordon; N. Goto; K. Hayashida; H. Horn; R. Ishiwata; E. Kaminuma; A. Kasprzyk; H. Kawaji; N. Kido; Y. Kim; A.R. Kinjo; F. Konishi; K.H. Kwon; A. Labarga; A. Lamprecht; Y. Lin; P. Lindenbaum; L. McCarthy; H. Morita; K. Murakami; K. Nagao; K. Nishida; K. Nishimura; T. Nishizawa; S. Ogishima; K. Ono; K. Oshita; K. Park; J.C.P. Prins; T. Saito; M. Samwald; V.P. Satagopam; Y. Shigemoto; R. Smith; A. Splendiani; H. Sugawara; J. Taylor; R.A. Vos; D. Withers; C. Yamasaki; C.M. Zmasek; S. Kawamoto; K. Okubo; K. Asai; T. Takagi

doi:10.1186/2041-1480-4-6

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

T. Katayama, D.W. Wilkinson, G. Micklem, S. Kawashima, A. Yamaguchi, M. Nakao, T. Yamamoto, S. Okamoto, K. Oouchida, H. Chung, J. Aerts, H. Afzal, E. Antezana, K. Arakawa, B. Aranda, F. Belleau, J. Bolleman, R.J.P. Bonnal, B. Chapman, P.J.A. CockT. Eriksson, P.M.K. Gordon, N. Goto, K. Hayashida, H. Horn, R. Ishiwata, E. Kaminuma, A. Kasprzyk, H. Kawaji, N. Kido, Y. Kim, A.R. Kinjo, F. Konishi, K.H. Kwon, A. Labarga, A. Lamprecht, Y. Lin, P. Lindenbaum, L. McCarthy, H. Morita, K. Murakami, K. Nagao, K. Nishida, K. Nishimura, T. Nishizawa, S. Ogishima, K. Ono, K. Oshita, K. Park, J.C.P. Prins, T. Saito, M. Samwald, V.P. Satagopam, Y. Shigemoto, R. Smith, A. Splendiani, H. Sugawara, J. Taylor, R.A. Vos, D. Withers, C. Yamasaki, C.M. Zmasek, S. Kawamoto, K. Okubo, K. Asai, T. Takagi

Laboratory of Nematology

Research output: Contribution to journal › Article › Academic › 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. source provider, through middleware, to the end-consumer.

Original language	English
Article number	6
Journal	Journal of Biomedical Semantics
Volume	4
DOIs	https://doi.org/10.1186/2041-1480-4-6
Publication status	Published - 2013

Keywords

protein-interaction database
systems biology
ontology
bioinformatics
tool
representation
services
language
framework
networks

Access to Document

10.1186/2041-1480-4-6

Development and application of high throughput computational methods for the identification of biologically significant genome-wide variation in host-microbe interactions
Prins, P. (PhD candidate), Bakker, J. (Promotor) & Smant, G. (Co-promotor)
1/10/07 → 5/10/15
Project: PhD

Cite this

Katayama, T., Wilkinson, D. W., Micklem, G., Kawashima, S., Yamaguchi, A., Nakao, M., Yamamoto, T., Okamoto, S., Oouchida, K., Chung, H., 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, Article 6. https://doi.org/10.1186/2041-1480-4-6

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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. source provider, through middleware, to the end-consumer.",

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author = "T. Katayama and D.W. Wilkinson and G. Micklem and S. Kawashima and A. Yamaguchi and M. Nakao and T. Yamamoto and S. Okamoto and K. Oouchida and H. Chung and J. Aerts and H. Afzal and E. Antezana and K. Arakawa and B. Aranda and F. Belleau and J. Bolleman and R.J.P. Bonnal and B. Chapman and P.J.A. Cock and T. Eriksson and P.M.K. Gordon and N. Goto and K. Hayashida and H. Horn and R. Ishiwata and E. Kaminuma and A. Kasprzyk and H. Kawaji and N. Kido and Y. Kim and A.R. Kinjo and F. Konishi and K.H. Kwon and A. Labarga and A. Lamprecht and Y. Lin and P. Lindenbaum and L. McCarthy and H. Morita and K. Murakami and K. Nagao and K. Nishida and K. Nishimura and T. Nishizawa and S. Ogishima and K. Ono and K. Oshita and K. Park and J.C.P. Prins and T. Saito and M. Samwald and V.P. Satagopam and Y. Shigemoto and R. Smith and A. Splendiani and H. Sugawara and J. Taylor and R.A. Vos and D. Withers and C. Yamasaki and C.M. Zmasek and S. Kawamoto and K. Okubo and K. Asai and T. Takagi",

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Katayama, T, Wilkinson, DW, Micklem, G, Kawashima, S, Yamaguchi, A, Nakao, M, Yamamoto, T, Okamoto, S, Oouchida, K, Chung, H, 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, Hayashida, K, Horn, H, Ishiwata, R, Kaminuma, E, Kasprzyk, A, Kawaji, H, Kido, N, Kim, Y, Kinjo, AR, Konishi, F, Kwon, KH, Labarga, A, Lamprecht, A, 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, Prins, JCP, Saito, T, 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, 6. https://doi.org/10.1186/2041-1480-4-6

TY - JOUR

T1 - The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies

AU - Katayama, T.

AU - Wilkinson, D.W.

AU - Micklem, G.

AU - Kawashima, S.

AU - Yamaguchi, A.

AU - Nakao, M.

AU - Yamamoto, T.

AU - Okamoto, S.

AU - Oouchida, K.

AU - Chung, H.

AU - Aerts, J.

AU - Afzal, H.

AU - Antezana, E.

AU - Arakawa, K.

AU - Aranda, B.

AU - Belleau, F.

AU - Bolleman, J.

AU - Bonnal, R.J.P.

AU - Chapman, B.

AU - Cock, P.J.A.

AU - Eriksson, T.

AU - Gordon, P.M.K.

AU - Goto, N.

AU - Hayashida, K.

AU - Horn, H.

AU - Ishiwata, R.

AU - Kaminuma, E.

AU - Kasprzyk, A.

AU - Kawaji, H.

AU - Kido, N.

AU - Kim, Y.

AU - Kinjo, A.R.

AU - Konishi, F.

AU - Kwon, K.H.

AU - Labarga, A.

AU - Lamprecht, A.

AU - Lin, Y.

AU - Lindenbaum, P.

AU - McCarthy, L.

AU - Morita, H.

AU - Murakami, K.

AU - Nagao, K.

AU - Nishida, K.

AU - Nishimura, K.

AU - Nishizawa, T.

AU - Ogishima, S.

AU - Ono, K.

AU - Oshita, K.

AU - Park, K.

AU - Prins, J.C.P.

AU - Saito, T.

AU - Samwald, M.

AU - Satagopam, V.P.

AU - Shigemoto, Y.

AU - Smith, R.

AU - Splendiani, A.

AU - Sugawara, H.

AU - Taylor, J.

AU - Vos, R.A.

AU - Withers, D.

AU - Yamasaki, C.

AU - Zmasek, C.M.

AU - Kawamoto, S.

AU - Okubo, K.

AU - Asai, K.

AU - Takagi, T.

N1 - http://www.jbiomedsem.com/content/4/1/6

PY - 2013

Y1 - 2013

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. 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. source provider, through middleware, to the end-consumer.

KW - protein-interaction database

KW - systems biology

KW - ontology

KW - bioinformatics

KW - tool

KW - representation

KW - services

KW - language

KW - framework

KW - networks

U2 - 10.1186/2041-1480-4-6

DO - 10.1186/2041-1480-4-6

M3 - Article

SN - 2041-1480

VL - 4

JO - Journal of Biomedical Semantics

JF - Journal of Biomedical Semantics

M1 - 6

ER -

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

Abstract

Keywords

Access to Document

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Projects

Development and application of high throughput computational methods for the identification of biologically significant genome-wide variation in host-microbe interactions

Cite this