BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services

Toshiaki Katayama; Shuichi Kawashima; Gos Micklem; Shin Kawano; Jin-Dong Kim; Simon Kocbek; Shinobu Okamoto; Yue Wang; Hongyan Wu; Atsuko Yamaguchi; Yasunori Yamamoto; Erick Antezana; Kiyoko F. Aoki-Kinoshita; Kazuharu Arakawa; Masaki Banno; Joachim Baran; Jerven T. Bolleman; Raoul J. P. Bonnal; Hidemasa Bono; Jesualdo T. Fernández-Breis; Robert Buels; Matthew P. Campbell; Hirokazu Chiba; Peter J. A. Cock; Kevin B. Cohen; Michel Dumontier; Takatomo Fujisawa; Toyofumi Fujiwara; Leyla Garcia; Pascale Gaudet; Emi Hattori; Robert Hoehndorf; Kotone Itaya; Maori Ito; Daniel Jamieson; Simon Jupp; Nick Juty; Alex Kalderimis; Fumihiro Kato; Hideya Kawaji; Takeshi Kawashima; Akira R. Kinjo; Yusuke Komiyama; Masaaki Kotera; Tatsuya Kushida; James Malone; Masaaki Matsubara; Satoshi Mizuno; Sayaka Mizutani; Hiroshi Mori; Yuki Moriya; Katsuhiko Murakami; Takeru Nakazato; Hiroyo Nishide; Yosuke Nishimura; Soichi Ogishima; Tazro Ohta; Shujiro Okuda; Hiromasa Ono; Yasset Perez-Riverol; Daisuke Shinmachi; Andrea Splendiani; Francesco Strozzi; Shinya Suzuki; Junichi Takehara; Mark Thompson; Toshiaki Tokimatsu; Ikuo Uchiyama; Karin Verspoor; Mark D. Wilkinson; Sarala Wimalaratne; Issaku Yamada; Nozomi Yamamoto; Masayuki Yarimizu; Shoko Kawamoto; Toshihisa Takagi

doi:10.12688/f1000research.18238.1

BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services

Toshiaki Katayama, Shuichi Kawashima, Gos Micklem, Shin Kawano, Jin-Dong Kim, Simon Kocbek, Shinobu Okamoto, Yue Wang, Hongyan Wu, Atsuko Yamaguchi, Yasunori Yamamoto, Erick Antezana, Kiyoko F. Aoki-Kinoshita, Kazuharu Arakawa, Masaki Banno, Joachim Baran, Jerven T. Bolleman, Raoul J. P. Bonnal, Hidemasa Bono, Jesualdo T. Fernández-BreisRobert Buels, Matthew P. Campbell, Hirokazu Chiba, Peter J. A. Cock, Kevin B. Cohen, Michel Dumontier, Takatomo Fujisawa, Toyofumi Fujiwara, Leyla Garcia, Pascale Gaudet, Emi Hattori, Robert Hoehndorf, Kotone Itaya, Maori Ito, Daniel Jamieson, Simon Jupp, Nick Juty, Alex Kalderimis, Fumihiro Kato, Hideya Kawaji, Takeshi Kawashima, Akira R. Kinjo, Yusuke Komiyama, Masaaki Kotera, Tatsuya Kushida, James Malone, Masaaki Matsubara, Satoshi Mizuno, Sayaka Mizutani, Hiroshi Mori, Yuki Moriya, Katsuhiko Murakami, Takeru Nakazato, Hiroyo Nishide, Yosuke Nishimura, Soichi Ogishima, Tazro Ohta, Shujiro Okuda, Hiromasa Ono, Yasset Perez-Riverol, Daisuke Shinmachi, Andrea Splendiani, Francesco Strozzi, Shinya Suzuki, Junichi Takehara, Mark Thompson, Toshiaki Tokimatsu, Ikuo Uchiyama, Karin Verspoor, Mark D. Wilkinson, Sarala Wimalaratne, Issaku Yamada, Nozomi Yamamoto, Masayuki Yarimizu, Shoko Kawamoto, Toshihisa Takagi

Research output: Contribution to journal › Article › peer-review

1 Scopus citations

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.

Original language	English (US)
Pages (from-to)	1677
Journal	F1000Research
Volume	8
DOIs	https://doi.org/10.12688/f1000research.18238.1
State	Published - Sep 23 2019

Bibliographical note

KAUST Repository Item: Exported on 2021-03-05
Acknowledgements: BioHackathon 2013 and 2014 are supported by the Integrated Database Project (Ministry of Education, Culture, Sports, Science and Technology of Japan) and hosted by the National Bioscience Database Center (NBDC) and the Database Center for Life Science (DBCLS). We thank Yuji Kohara, the director of DBCLS, for his supporting the BioHackathons.

ASJC Scopus subject areas

General Biochemistry, Genetics and Molecular Biology
General Medicine
General Immunology and Microbiology
Pharmacology, Toxicology and Pharmaceutics(all)

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10.12688/f1000research.18238.1

https://repository.kaust.edu.sa/bitstream/10754/667841/1/d641b67c-4e85-42b4-91d7-02098a169622_18238_-_toshiaki_katayama.pdf

Cite this

Katayama, T., Kawashima, S., Micklem, G., Kawano, S., Kim, J.-D., 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. P., Bono, H., ... Takagi, T. (2019). BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services. F1000Research, 8, 1677. https://doi.org/10.12688/f1000research.18238.1

@article{1fb24eaba8b8417ca6faa8137eabbd9a,

title = "BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services",

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.",

author = "Toshiaki Katayama and Shuichi Kawashima and Gos Micklem and Shin Kawano and Jin-Dong Kim and Simon Kocbek and Shinobu Okamoto and Yue Wang and Hongyan Wu and Atsuko Yamaguchi and Yasunori Yamamoto and Erick Antezana and Aoki-Kinoshita, {Kiyoko F.} and Kazuharu Arakawa and Masaki Banno and Joachim Baran and Bolleman, {Jerven T.} and Bonnal, {Raoul J. P.} and Hidemasa Bono and Fern{\'a}ndez-Breis, {Jesualdo T.} and Robert Buels and Campbell, {Matthew P.} and Hirokazu Chiba and Cock, {Peter J. A.} and Cohen, {Kevin B.} and Michel Dumontier and Takatomo Fujisawa and Toyofumi Fujiwara and Leyla Garcia and Pascale Gaudet and Emi Hattori and Robert Hoehndorf and Kotone Itaya and Maori Ito and Daniel Jamieson and Simon Jupp and Nick Juty and Alex Kalderimis and Fumihiro Kato and Hideya Kawaji and Takeshi Kawashima and Kinjo, {Akira R.} and Yusuke Komiyama and Masaaki Kotera and Tatsuya Kushida and James Malone and Masaaki Matsubara and Satoshi Mizuno and Sayaka Mizutani and Hiroshi Mori and Yuki Moriya and Katsuhiko Murakami and Takeru Nakazato and Hiroyo Nishide and Yosuke Nishimura and Soichi Ogishima and Tazro Ohta and Shujiro Okuda and Hiromasa Ono and Yasset Perez-Riverol and Daisuke Shinmachi and Andrea Splendiani and Francesco Strozzi and Shinya Suzuki and Junichi Takehara and Mark Thompson and Toshiaki Tokimatsu and Ikuo Uchiyama and Karin Verspoor and Wilkinson, {Mark D.} and Sarala Wimalaratne and Issaku Yamada and Nozomi Yamamoto and Masayuki Yarimizu and Shoko Kawamoto and Toshihisa Takagi",

note = "KAUST Repository Item: Exported on 2021-03-05 Acknowledgements: BioHackathon 2013 and 2014 are supported by the Integrated Database Project (Ministry of Education, Culture, Sports, Science and Technology of Japan) and hosted by the National Bioscience Database Center (NBDC) and the Database Center for Life Science (DBCLS). We thank Yuji Kohara, the director of DBCLS, for his supporting the BioHackathons.",

year = "2019",

month = sep,

day = "23",

doi = "10.12688/f1000research.18238.1",

language = "English (US)",

volume = "8",

pages = "1677",

journal = "F1000Research",

issn = "2046-1402",

publisher = "F1000 Research Ltd.",

}

Katayama, T, Kawashima, S, Micklem, G, Kawano, S, Kim, J-D, Kocbek, S, Okamoto, S, Wang, Y, Wu, H, Yamaguchi, A, Yamamoto, Y, Antezana, E, Aoki-Kinoshita, KF, Arakawa, K, Banno, M, Baran, J, Bolleman, JT, Bonnal, RJP, Bono, H, Fernández-Breis, JT, Buels, R, Campbell, MP, Chiba, H, Cock, PJA, Cohen, KB, 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, AR, 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, MD, Wimalaratne, S, Yamada, I, Yamamoto, N, Yarimizu, M, Kawamoto, S & Takagi, T 2019, 'BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services', F1000Research, vol. 8, pp. 1677. https://doi.org/10.12688/f1000research.18238.1

TY - JOUR

T1 - BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services

AU - Katayama, Toshiaki

AU - Kawashima, Shuichi

AU - Micklem, Gos

AU - Kawano, Shin

AU - Kim, Jin-Dong

AU - Kocbek, Simon

AU - Okamoto, Shinobu

AU - Wang, Yue

AU - Wu, Hongyan

AU - Yamaguchi, Atsuko

AU - Yamamoto, Yasunori

AU - Antezana, Erick

AU - Aoki-Kinoshita, Kiyoko F.

AU - Arakawa, Kazuharu

AU - Banno, Masaki

AU - Baran, Joachim

AU - Bolleman, Jerven T.

AU - Bonnal, Raoul J. P.

AU - Bono, Hidemasa

AU - Fernández-Breis, Jesualdo T.

AU - Buels, Robert

AU - Campbell, Matthew P.

AU - Chiba, Hirokazu

AU - Cock, Peter J. A.

AU - Cohen, Kevin B.

AU - Dumontier, Michel

AU - Fujisawa, Takatomo

AU - Fujiwara, Toyofumi

AU - Garcia, Leyla

AU - Gaudet, Pascale

AU - Hattori, Emi

AU - Hoehndorf, Robert

AU - Itaya, Kotone

AU - Ito, Maori

AU - Jamieson, Daniel

AU - Jupp, Simon

AU - Juty, Nick

AU - Kalderimis, Alex

AU - Kato, Fumihiro

AU - Kawaji, Hideya

AU - Kawashima, Takeshi

AU - Kinjo, Akira R.

AU - Komiyama, Yusuke

AU - Kotera, Masaaki

AU - Kushida, Tatsuya

AU - Malone, James

AU - Matsubara, Masaaki

AU - Mizuno, Satoshi

AU - Mizutani, Sayaka

AU - Mori, Hiroshi

AU - Moriya, Yuki

AU - Murakami, Katsuhiko

AU - Nakazato, Takeru

AU - Nishide, Hiroyo

AU - Nishimura, Yosuke

AU - Ogishima, Soichi

AU - Ohta, Tazro

AU - Okuda, Shujiro

AU - Ono, Hiromasa

AU - Perez-Riverol, Yasset

AU - Shinmachi, Daisuke

AU - Splendiani, Andrea

AU - Strozzi, Francesco

AU - Suzuki, Shinya

AU - Takehara, Junichi

AU - Thompson, Mark

AU - Tokimatsu, Toshiaki

AU - Uchiyama, Ikuo

AU - Verspoor, Karin

AU - Wilkinson, Mark D.

AU - Wimalaratne, Sarala

AU - Yamada, Issaku

AU - Yamamoto, Nozomi

AU - Yarimizu, Masayuki

AU - Kawamoto, Shoko

AU - Takagi, Toshihisa

N1 - KAUST Repository Item: Exported on 2021-03-05 Acknowledgements: BioHackathon 2013 and 2014 are supported by the Integrated Database Project (Ministry of Education, Culture, Sports, Science and Technology of Japan) and hosted by the National Bioscience Database Center (NBDC) and the Database Center for Life Science (DBCLS). We thank Yuji Kohara, the director of DBCLS, for his supporting the BioHackathons.

PY - 2019/9/23

Y1 - 2019/9/23

N2 - 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.

AB - 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.

UR - http://hdl.handle.net/10754/667841

UR - https://f1000research.com/articles/8-1677/v1

U2 - 10.12688/f1000research.18238.1

DO - 10.12688/f1000research.18238.1

M3 - Article

SN - 2046-1402

VL - 8

SP - 1677

JO - F1000Research

JF - F1000Research

ER -

BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services

Abstract

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