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

Publication ,  Journal Article
Katayama, T; Wilkinson, MD; Aoki-Kinoshita, KF; Kawashima, S; Yamamoto, Y; Yamaguchi, A; Okamoto, S; Kawano, S; Kim, J-D; Wang, Y; Wu, H ...
Published in: Journal of biomedical semantics
February 2014
Published version (DOI) Open Access Copy (Duke)

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.

Duke Scholars

Hilmar Lapp
Author Hilmar Lapp  
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Published In

Journal of biomedical semantics

DOI

10.1186/2041-1480-5-5

EISSN

2041-1480

ISSN

2041-1480

Publication Date

February 2014

Volume

5

Issue

1

Start / End Page

5

Related Subject Headings

  • 46 Information and computing sciences
  • 0806 Information Systems
  • 0801 Artificial Intelligence and Image Processing
  • 0699 Other Biological Sciences
 

Citation

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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
Katayama, Toshiaki, Mark D. Wilkinson, Kiyoko F. Aoki-Kinoshita, Shuichi Kawashima, Yasunori Yamamoto, Atsuko Yamaguchi, Shinobu Okamoto, et al. “BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains.” Journal of Biomedical Semantics 5, no. 1 (February 2014): 5. https://doi.org/10.1186/2041-1480-5-5.
Katayama T, Wilkinson MD, Aoki-Kinoshita KF, Kawashima S, Yamamoto Y, Yamaguchi A, et al. BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains. Journal of biomedical semantics. 2014 Feb;5(1):5.
Katayama, Toshiaki, et al. “BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains.” Journal of Biomedical Semantics, vol. 5, no. 1, Feb. 2014, p. 5. Epmc, doi:10.1186/2041-1480-5-5.
Katayama T, Wilkinson MD, Aoki-Kinoshita KF, 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, Aranda B, Baran J, Bolleman J, Bonnal RJ, Buttigieg PL, Campbell MP, Chen Y-A, Chiba H, Cock PJ, 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 S-H, 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. BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains. Journal of biomedical semantics. 2014 Feb;5(1):5.
Journal cover image

Published In

Journal of biomedical semantics

DOI

10.1186/2041-1480-5-5

EISSN

2041-1480

ISSN

2041-1480

Publication Date

February 2014

Volume

5

Issue

1

Start / End Page

5

Related Subject Headings

  • 46 Information and computing sciences
  • 0806 Information Systems
  • 0801 Artificial Intelligence and Image Processing
  • 0699 Other Biological Sciences