BioHackathon 2015: Semantics of data for life sciences and reproducible research

Toshiaki Katayama; Rutger A. Vos; Hiroyuki Mishima; Shin Kawano; Shuichi Kawashima; Jin Dong Kim; Yuki Moriya; Toshiaki Tokimatsu; Atsuko Yamaguchi; Yasunori Yamamoto; Hongyan Wu; Peter Amstutz; Erick Antezana; Nobuyuki P. Aoki; Kazuharu Arakawa; Jerven T. Bolleman; Evan Bolton; Raoul J.P. Bonnal; Hidemasa Bono; Kees Burger; Hirokazu Chiba; Kevin B. Cohen; Eric W. Deutsch; Jesualdo T. Fernández-Breis; Gang Fu; Takatomo Fujisawa; Atsushi Fukushima; Alexander García; Naohisa Goto; Tudor Groza; Colin Hercus; Robert Hoehndorf; Kotone Itaya; Nick Juty; Takeshi Kawashima; Jee Hyub Kim; Akira R. Kinjo; Masaaki Kotera; Kouji Kozaki; Sadahiro Kumagai; Tatsuya Kushida; Thomas Lütteke; Masaaki Matsubara; Joe Miyamoto; Attayeb Mohsen; Hiroshi Mori; Yuki Naito; Takeru Nakazato; Jeremy Nguyen-Xuan; Kozo Nishida; Naoki Nishida; Hiroyo Nishide; Soichi Ogishima; Tazro Ohta; Shujiro Okuda; Benedict Paten; Jean Luc Perret; Philip Prathipati; Pjotr Prins; Núria Queralt-Rosinach; Daisuke Shinmachi; Shinya Suzuki; Tsuyosi Tabata; Terue Takatsuki; Kieron Taylor; Mark Thompson; Ikuo Uchiyama; Bruno Vieira; Chih Hsuan Wei; Mark Wilkinson; Issaku Yamada; Ryota Yamanaka; Kazutoshi Yoshitake; Akiyasu C. Yoshizawa; Michel Dumontier; Kenjiro Kosaki; Toshihisa Takagi

doi:10.12688/f1000research.18236.1

BioHackathon 2015: Semantics of data for life sciences and reproducible research

Toshiaki Katayama, Rutger A. Vos, Hiroyuki Mishima, Shin Kawano, Shuichi Kawashima, Jin Dong Kim, Yuki Moriya, Toshiaki Tokimatsu, Atsuko Yamaguchi, Yasunori Yamamoto, Hongyan Wu, Peter Amstutz, Erick Antezana, Nobuyuki P. Aoki, Kazuharu Arakawa, Jerven T. Bolleman, Evan Bolton, Raoul J.P. Bonnal, Hidemasa Bono, Kees BurgerHirokazu Chiba, Kevin B. Cohen, Eric W. Deutsch, Jesualdo T. Fernández-Breis, Gang Fu, Takatomo Fujisawa, Atsushi Fukushima, Alexander García, Naohisa Goto, Tudor Groza, Colin Hercus, Robert Hoehndorf, Kotone Itaya, Nick Juty, Takeshi Kawashima, Jee Hyub Kim, Akira R. Kinjo, Masaaki Kotera, Kouji Kozaki, Sadahiro Kumagai, Tatsuya Kushida, Thomas Lütteke, Masaaki Matsubara, Joe Miyamoto, Attayeb Mohsen, Hiroshi Mori, Yuki Naito, Takeru Nakazato, Jeremy Nguyen-Xuan, Kozo Nishida, Naoki Nishida, Hiroyo Nishide, Soichi Ogishima, Tazro Ohta, Shujiro Okuda, Benedict Paten, Jean Luc Perret, Philip Prathipati, Pjotr Prins, Núria Queralt-Rosinach, Daisuke Shinmachi, Shinya Suzuki, Tsuyosi Tabata, Terue Takatsuki, Kieron Taylor, Mark Thompson, Ikuo Uchiyama, Bruno Vieira, Chih Hsuan Wei, Mark Wilkinson, Issaku Yamada, Ryota Yamanaka, Kazutoshi Yoshitake, Akiyasu C. Yoshizawa, Michel Dumontier, Kenjiro Kosaki, Toshihisa Takagi

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

5 Scopus citations

Abstract

We report on the activities of the 2015 edition of the BioHackathon, an annual event that brings together researchers and developers from around the world to develop tools and technologies that promote the reusability of biological data. We discuss issues surrounding the representation, publication, integration, mining and reuse of biological data and metadata across a wide range of biomedical data types of relevance for the life sciences, including chemistry, genotypes and phenotypes, orthology and phylogeny, proteomics, genomics, glycomics, and metabolomics. We describe our progress to address ongoing challenges to the reusability and reproducibility of research results, and identify outstanding issues that continue to impede the progress of bioinformatics research. We share our perspective on the state of the art, continued challenges, and goals for future research and development for the life sciences Semantic Web.

Original language	English (US)
Pages (from-to)	136
Journal	F1000Research
Volume	9
DOIs	https://doi.org/10.12688/f1000research.18236.1
State	Published - Feb 24 2020

Bibliographical note

KAUST Repository Item: Exported on 2020-10-01
Acknowledgements: BH15 is 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 support of the BioHackathons.

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10.12688/f1000research.18236.1

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Katayama, T., Vos, R. A., Mishima, H., Kawano, S., Kawashima, S., Kim, J. D., Moriya, Y., Tokimatsu, T., Yamaguchi, A., Yamamoto, Y., Wu, H., Amstutz, P., Antezana, E., Aoki, N. P., Arakawa, K., Bolleman, J. T., Bolton, E., Bonnal, R. J. P., Bono, H., ... Takagi, T. (2020). BioHackathon 2015: Semantics of data for life sciences and reproducible research. F1000Research, 9, 136. https://doi.org/10.12688/f1000research.18236.1

@article{571d5c9f5c714587b2fc38d412930514,

title = "BioHackathon 2015: Semantics of data for life sciences and reproducible research",

abstract = "We report on the activities of the 2015 edition of the BioHackathon, an annual event that brings together researchers and developers from around the world to develop tools and technologies that promote the reusability of biological data. We discuss issues surrounding the representation, publication, integration, mining and reuse of biological data and metadata across a wide range of biomedical data types of relevance for the life sciences, including chemistry, genotypes and phenotypes, orthology and phylogeny, proteomics, genomics, glycomics, and metabolomics. We describe our progress to address ongoing challenges to the reusability and reproducibility of research results, and identify outstanding issues that continue to impede the progress of bioinformatics research. We share our perspective on the state of the art, continued challenges, and goals for future research and development for the life sciences Semantic Web.",

author = "Toshiaki Katayama and Vos, {Rutger A.} and Hiroyuki Mishima and Shin Kawano and Shuichi Kawashima and Kim, {Jin Dong} and Yuki Moriya and Toshiaki Tokimatsu and Atsuko Yamaguchi and Yasunori Yamamoto and Hongyan Wu and Peter Amstutz and Erick Antezana and Aoki, {Nobuyuki P.} and Kazuharu Arakawa and Bolleman, {Jerven T.} and Evan Bolton and Bonnal, {Raoul J.P.} and Hidemasa Bono and Kees Burger and Hirokazu Chiba and Cohen, {Kevin B.} and Deutsch, {Eric W.} and Fern{\'a}ndez-Breis, {Jesualdo T.} and Gang Fu and Takatomo Fujisawa and Atsushi Fukushima and Alexander Garc{\'i}a and Naohisa Goto and Tudor Groza and Colin Hercus and Robert Hoehndorf and Kotone Itaya and Nick Juty and Takeshi Kawashima and Kim, {Jee Hyub} and Kinjo, {Akira R.} and Masaaki Kotera and Kouji Kozaki and Sadahiro Kumagai and Tatsuya Kushida and Thomas L{\"u}tteke and Masaaki Matsubara and Joe Miyamoto and Attayeb Mohsen and Hiroshi Mori and Yuki Naito and Takeru Nakazato and Jeremy Nguyen-Xuan and Kozo Nishida and Naoki Nishida and Hiroyo Nishide and Soichi Ogishima and Tazro Ohta and Shujiro Okuda and Benedict Paten and Perret, {Jean Luc} and Philip Prathipati and Pjotr Prins and N{\'u}ria Queralt-Rosinach and Daisuke Shinmachi and Shinya Suzuki and Tsuyosi Tabata and Terue Takatsuki and Kieron Taylor and Mark Thompson and Ikuo Uchiyama and Bruno Vieira and Wei, {Chih Hsuan} and Mark Wilkinson and Issaku Yamada and Ryota Yamanaka and Kazutoshi Yoshitake and Yoshizawa, {Akiyasu C.} and Michel Dumontier and Kenjiro Kosaki and Toshihisa Takagi",

note = "KAUST Repository Item: Exported on 2020-10-01 Acknowledgements: BH15 is 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 support of the BioHackathons.",

year = "2020",

month = feb,

day = "24",

doi = "10.12688/f1000research.18236.1",

language = "English (US)",

volume = "9",

pages = "136",

journal = "F1000Research",

issn = "1759-796X",

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Katayama, T, Vos, RA, Mishima, H, Kawano, S, Kawashima, S, Kim, JD, Moriya, Y, Tokimatsu, T, Yamaguchi, A, Yamamoto, Y, Wu, H, Amstutz, P, Antezana, E, Aoki, NP, Arakawa, K, Bolleman, JT, Bolton, E, Bonnal, RJP, Bono, H, Burger, K, Chiba, H, Cohen, KB, Deutsch, EW, Fernández-Breis, JT, Fu, G, Fujisawa, T, Fukushima, A, García, A, Goto, N, Groza, T, Hercus, C, Hoehndorf, R, Itaya, K, Juty, N, Kawashima, T, Kim, JH, Kinjo, AR, Kotera, M, Kozaki, K, Kumagai, S, Kushida, T, Lütteke, T, Matsubara, M, Miyamoto, J, Mohsen, A, Mori, H, Naito, Y, Nakazato, T, Nguyen-Xuan, J, Nishida, K, Nishida, N, Nishide, H, Ogishima, S, Ohta, T, Okuda, S, Paten, B, Perret, JL, Prathipati, P, Prins, P, Queralt-Rosinach, N, Shinmachi, D, Suzuki, S, Tabata, T, Takatsuki, T, Taylor, K, Thompson, M, Uchiyama, I, Vieira, B, Wei, CH, Wilkinson, M, Yamada, I, Yamanaka, R, Yoshitake, K, Yoshizawa, AC, Dumontier, M, Kosaki, K & Takagi, T 2020, 'BioHackathon 2015: Semantics of data for life sciences and reproducible research', F1000Research, vol. 9, pp. 136. https://doi.org/10.12688/f1000research.18236.1

TY - JOUR

T1 - BioHackathon 2015: Semantics of data for life sciences and reproducible research

AU - Katayama, Toshiaki

AU - Vos, Rutger A.

AU - Mishima, Hiroyuki

AU - Kawano, Shin

AU - Kawashima, Shuichi

AU - Kim, Jin Dong

AU - Moriya, Yuki

AU - Tokimatsu, Toshiaki

AU - Yamaguchi, Atsuko

AU - Yamamoto, Yasunori

AU - Wu, Hongyan

AU - Amstutz, Peter

AU - Antezana, Erick

AU - Aoki, Nobuyuki P.

AU - Arakawa, Kazuharu

AU - Bolleman, Jerven T.

AU - Bolton, Evan

AU - Bonnal, Raoul J.P.

AU - Bono, Hidemasa

AU - Burger, Kees

AU - Chiba, Hirokazu

AU - Cohen, Kevin B.

AU - Deutsch, Eric W.

AU - Fernández-Breis, Jesualdo T.

AU - Fu, Gang

AU - Fujisawa, Takatomo

AU - Fukushima, Atsushi

AU - García, Alexander

AU - Goto, Naohisa

AU - Groza, Tudor

AU - Hercus, Colin

AU - Hoehndorf, Robert

AU - Itaya, Kotone

AU - Juty, Nick

AU - Kawashima, Takeshi

AU - Kim, Jee Hyub

AU - Kinjo, Akira R.

AU - Kotera, Masaaki

AU - Kozaki, Kouji

AU - Kumagai, Sadahiro

AU - Kushida, Tatsuya

AU - Lütteke, Thomas

AU - Matsubara, Masaaki

AU - Miyamoto, Joe

AU - Mohsen, Attayeb

AU - Mori, Hiroshi

AU - Naito, Yuki

AU - Nakazato, Takeru

AU - Nguyen-Xuan, Jeremy

AU - Nishida, Kozo

AU - Nishida, Naoki

AU - Nishide, Hiroyo

AU - Ogishima, Soichi

AU - Ohta, Tazro

AU - Okuda, Shujiro

AU - Paten, Benedict

AU - Perret, Jean Luc

AU - Prathipati, Philip

AU - Prins, Pjotr

AU - Queralt-Rosinach, Núria

AU - Shinmachi, Daisuke

AU - Suzuki, Shinya

AU - Tabata, Tsuyosi

AU - Takatsuki, Terue

AU - Taylor, Kieron

AU - Thompson, Mark

AU - Uchiyama, Ikuo

AU - Vieira, Bruno

AU - Wei, Chih Hsuan

AU - Wilkinson, Mark

AU - Yamada, Issaku

AU - Yamanaka, Ryota

AU - Yoshitake, Kazutoshi

AU - Yoshizawa, Akiyasu C.

AU - Dumontier, Michel

AU - Kosaki, Kenjiro

AU - Takagi, Toshihisa

N1 - KAUST Repository Item: Exported on 2020-10-01 Acknowledgements: BH15 is 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 support of the BioHackathons.

PY - 2020/2/24

Y1 - 2020/2/24

N2 - We report on the activities of the 2015 edition of the BioHackathon, an annual event that brings together researchers and developers from around the world to develop tools and technologies that promote the reusability of biological data. We discuss issues surrounding the representation, publication, integration, mining and reuse of biological data and metadata across a wide range of biomedical data types of relevance for the life sciences, including chemistry, genotypes and phenotypes, orthology and phylogeny, proteomics, genomics, glycomics, and metabolomics. We describe our progress to address ongoing challenges to the reusability and reproducibility of research results, and identify outstanding issues that continue to impede the progress of bioinformatics research. We share our perspective on the state of the art, continued challenges, and goals for future research and development for the life sciences Semantic Web.

AB - We report on the activities of the 2015 edition of the BioHackathon, an annual event that brings together researchers and developers from around the world to develop tools and technologies that promote the reusability of biological data. We discuss issues surrounding the representation, publication, integration, mining and reuse of biological data and metadata across a wide range of biomedical data types of relevance for the life sciences, including chemistry, genotypes and phenotypes, orthology and phylogeny, proteomics, genomics, glycomics, and metabolomics. We describe our progress to address ongoing challenges to the reusability and reproducibility of research results, and identify outstanding issues that continue to impede the progress of bioinformatics research. We share our perspective on the state of the art, continued challenges, and goals for future research and development for the life sciences Semantic Web.

UR - http://hdl.handle.net/10754/662837

UR - https://f1000research.com/articles/9-136/v1

UR - http://www.scopus.com/inward/record.url?scp=85083755264&partnerID=8YFLogxK

U2 - 10.12688/f1000research.18236.1

DO - 10.12688/f1000research.18236.1

M3 - Article

C2 - 32308977

SN - 1759-796X

VL - 9

SP - 136

JO - F1000Research

JF - F1000Research

ER -

BioHackathon 2015: Semantics of data for life sciences and reproducible research

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Bibliographical note

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