BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services. Katayama, T., Kawashima, S., Micklem, G., Kawano, S., Kim, J., Kocbek, S., Okamoto, S., Wang, Y., Wu, H., Yamaguchi, A., Yamamoto, Y., Antezana, E., Aoki-Kinoshita, K., F., Arakawa, K., Banno, M., Baran, J., Bolleman, J., T., Bonnal, R., J., Bono, H., Fernández-Breis, J., T., Buels, R., Campbell, M., P., Chiba, H., Cock, P., J., A., Cohen, K., B., Dumontier, M., Fujisawa, T., Fujiwara, T., Garcia, L., Gaudet, P., Hattori, E., Hoehndorf, R., Itaya, K., Ito, M., Jamieson, D., Jupp, S., Juty, N., Kalderimis, A., Kato, F., Kawaji, H., Kawashima, T., Kinjo, A., R., Komiyama, Y., Kotera, M., Kushida, T., Malone, J., Matsubara, M., Mizuno, S., Mizutani, S., Mori, H., Moriya, Y., Murakami, K., Nakazato, T., Nishide, H., Nishimura, Y., Ogishima, S., Ohta, T., Okuda, S., Ono, H., Perez-Riverol, Y., Shinmachi, D., Splendiani, A., Strozzi, F., Suzuki, S., Takehara, J., Thompson, M., Tokimatsu, T., Uchiyama, I., Verspoor, K., Wilkinson, M., D., Wimalaratne, S., Yamada, I., Yamamoto, N., Yarimizu, M., Kawamoto, S., & Takagi, T. F1000Research, 8:1677, 9, 2019.
BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services [link]Website  abstract   bibtex   
Publishing databases in the Resource Description Framework (RDF) model is becoming widely accepted to maximize the syntactic and semantic interoperability of open data in life sciences. Here we report advancements made in the 6th and 7th annual BioHackathons which were held in Tokyo and Miyagi respectively. This review consists of two major sections covering: 1) improvement and utilization of RDF data in various domains of the life sciences and 2) meta-data about these RDF data, the resources that store them, and the service quality of SPARQL Protocol and RDF Query Language (SPARQL) endpoints. The first section describes how we developed RDF data, ontologies and tools in genomics, proteomics, metabolomics, glycomics and by literature text mining. The second section describes how we defined descriptions of datasets, the provenance of data, and quality assessment of services and service discovery. By enhancing the harmonization of these two layers of machine-readable data and knowledge, we improve the way community wide resources are developed and published. Moreover, we outline best practices for the future, and prepare ourselves for an exciting and unanticipatable variety of real world applications in coming years.
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 title = {BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services},
 type = {article},
 year = {2019},
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 month = {9},
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 abstract = {Publishing databases in the Resource Description Framework (RDF) model is becoming widely accepted to maximize the syntactic and semantic interoperability of open data in life sciences. Here we report advancements made in the 6th and 7th annual BioHackathons which were held in Tokyo and Miyagi respectively. This review consists of two major sections covering: 1) improvement and utilization of RDF data in various domains of the life sciences and 2) meta-data about these RDF data, the resources that store them, and the service quality of SPARQL Protocol and RDF Query Language (SPARQL) endpoints. The first section describes how we developed RDF data, ontologies and tools in genomics, proteomics, metabolomics, glycomics and by literature text mining. The second section describes how we defined descriptions of datasets, the provenance of data, and quality assessment of services and service discovery. By enhancing the harmonization of these two layers of machine-readable data and knowledge, we improve the way community wide resources are developed and published. Moreover, we outline best practices for the future, and prepare ourselves for an exciting and unanticipatable variety of real world applications in coming years.},
 bibtype = {article},
 author = {Katayama, Toshiaki and Kawashima, Shuichi and Micklem, Gos and Kawano, Shin and Kim, Jin-Dong and Kocbek, Simon and Okamoto, Shinobu and Wang, Yue and Wu, Hongyan and Yamaguchi, Atsuko and Yamamoto, Yasunori and Antezana, Erick and Aoki-Kinoshita, Kiyoko F. and Arakawa, Kazuharu and Banno, Masaki and Baran, Joachim and Bolleman, Jerven T. and Bonnal, Raoul J.P. and Bono, Hidemasa and Fernández-Breis, Jesualdo T. and Buels, Robert and Campbell, Matthew P. and Chiba, Hirokazu and Cock, Peter J. A. and Cohen, Kevin B. and Dumontier, Michel and Fujisawa, Takatomo and Fujiwara, Toyofumi and Garcia, Leyla and Gaudet, Pascale and Hattori, Emi and Hoehndorf, Robert and Itaya, Kotone and Ito, Maori and Jamieson, Daniel and Jupp, Simon and Juty, Nick and Kalderimis, Alex and Kato, Fumihiro and Kawaji, Hideya and Kawashima, Takeshi and Kinjo, Akira R. and Komiyama, Yusuke and Kotera, Masaaki and Kushida, Tatsuya and Malone, James and Matsubara, Masaaki and Mizuno, Satoshi and Mizutani, Sayaka and Mori, Hiroshi and Moriya, Yuki and Murakami, Katsuhiko and Nakazato, Takeru and Nishide, Hiroyo and Nishimura, Yosuke and Ogishima, Soichi and Ohta, Tazro and Okuda, Shujiro and Ono, Hiromasa and Perez-Riverol, Yasset and Shinmachi, Daisuke and Splendiani, Andrea and Strozzi, Francesco and Suzuki, Shinya and Takehara, Junichi and Thompson, Mark and Tokimatsu, Toshiaki and Uchiyama, Ikuo and Verspoor, Karin and Wilkinson, Mark D. and Wimalaratne, Sarala and Yamada, Issaku and Yamamoto, Nozomi and Yarimizu, Masayuki and Kawamoto, Shoko and Takagi, Toshihisa},
 journal = {F1000Research}
}

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