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

Rutger A Vos^{1

2}, Toshiaki Katayama³, Hiroyuki Mishima⁴, Shin Kawano³, Shuichi Kawashima³, Jin-Dong Kim³, Yuki Moriya³, Toshiaki Tokimatsu⁵, Atsuko Yamaguchi³, Yasunori Yamamoto³, Hongyan Wu⁶, Peter Amstutz⁷, Erick Antezana⁸, Nobuyuki P Aoki⁹, Kazuharu Arakawa¹⁰, Jerven T Bolleman¹¹, Evan Bolton¹², Raoul J P Bonnal¹³, Hidemasa Bono³, Kees Burger¹⁴, Hirokazu Chiba¹⁵, Kevin B Cohen^{16

17}, Eric W Deutsch¹⁸, Jesualdo T Fernández-Breis¹⁹, Gang Fu¹², Takatomo Fujisawa²⁰, Atsushi Fukushima²¹, Alexander García²², Naohisa Goto²³, Tudor Groza^{24

25}, Colin Hercus²⁶, Robert Hoehndorf²⁷, Kotone Itaya¹⁰, Nick Juty²⁸, Takeshi Kawashima²⁰, Jee-Hyub Kim²⁸, Akira R Kinjo²⁹, Masaaki Kotera³⁰, Kouji Kozaki³¹, Sadahiro Kumagai³², Tatsuya Kushida³³, Thomas Lütteke^{34

35}, Masaaki Matsubara³⁶, Joe Miyamoto³⁷, Attayeb Mohsen³⁸, Hiroshi Mori³⁹, Yuki Naito³, Takeru Nakazato³, Jeremy Nguyen-Xuan⁴⁰, Kozo Nishida⁴¹, Naoki Nishida⁴², Hiroyo Nishide¹⁵, Soichi Ogishima⁴³, Tazro Ohta³, Shujiro Okuda⁴⁴, Benedict Paten⁴⁵, Jean-Luc Perret⁴⁶, Philip Prathipati³⁸, Pjotr Prins^{47

48}, Núria Queralt-Rosinach⁴⁹, Daisuke Shinmachi⁹, Shinya Suzuki³⁰, Tsuyosi Tabata⁵⁰, Terue Takatsuki⁵¹, Kieron Taylor²⁸, Mark Thompson⁵², Ikuo Uchiyama¹⁵, Bruno Vieira⁵³, Chih-Hsuan Wei¹², Mark Wilkinson⁵⁴, Issaku Yamada³⁶, Ryota Yamanaka⁵⁵, Kazutoshi Yoshitake⁵⁶, Akiyasu C Yoshizawa⁵⁰, Michel Dumontier⁵⁷, Kenjiro Kosaki⁵⁸, Toshihisa Takagi^{33

59}

Affiliations

¹ Institute of Biology Leiden, Leiden University, Leiden, The Netherlands.
² Naturalis Biodiversity Center, Leiden, The Netherlands.
³ Database Center for Life Science, Tokyo, Japan.
⁴ Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan.
⁵ DDBJ Center, National Institute of Genetics, Mishima, Japan.
⁶ Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
⁷ Curoverse, Somerville, USA.
⁸ Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway.
⁹ Faculty of Science and Engineering, SOKA University, Tokyo, Japan.
¹⁰ Institute for Advanced Biosciences, Keio University, Tokyo, Japan.
¹¹ SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, Lausanne, Switzerland.
¹² National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, USA.
¹³ Istituto Nazionale Genetica Molecolare, Romeo ed Enrica Invernizzi, Milan, Italy.
¹⁴ Dutch Techcentre for Life Sciences, Utrecht, The Netherlands.
¹⁵ National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Japan.
¹⁶ Computational Bioscience Program, University of Colorado School of Medicine, Denver, USA.
¹⁷ Université Paris-Saclay, LIMSI, CNRS, Paris, France.
¹⁸ Institute for Systems Biology, Seattle, USA.
¹⁹ Universidad de Murcia, IMIB-Arrixaca, Murcia, Spain.
²⁰ National Institute of Genetics, Mishima, Japan.
²¹ RIKEN Center for Sustainable Resource Science, Yokohama, Japan.
²² Polytechnic University of Madrid, Madrid, Spain.
²³ Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.
²⁴ St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Darlinghurst, Australia.
²⁵ Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, Australia.
²⁶ Novocraft Technologies Sdn. Bhd., Selangor, Malaysia.
²⁷ Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.
²⁸ European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK.
²⁹ Institute for Protein Research, Osaka University, Osaka, Japan.
³⁰ School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan.
³¹ The Institute of Scientific and Industrial Research, Osaka University, Osaka, Japan.
³² Hitachi Ltd., Tokyo, Japan.
³³ National Bioscience Database Center, Japan Science and Technology Agency, Tokyo, Japan.
³⁴ Institute of Veterinary Physiology and Biochemistry, Justus-Liebig University Giessen, Giessen, Germany.
³⁵ Gesellschaft für innovative Personalwirtschaftssysteme mbH (GIP GmbH), Offenbach, Germany.
³⁶ The Noguchi Institute, Tokyo, Japan.
³⁷ National Cancer Center Japan, Tokyo, Japan.
³⁸ National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan.
³⁹ Center for Information Biology, National Institute of Genetics, Mishima, Japan.
⁴⁰ Lawrence Berkeley National Laboratory, Berkeley, USA.
⁴¹ RIKEN Quantitative Biology Center, Osaka, Japan.
⁴² Department of Systems Science, Osaka University, Osaka, Japan.
⁴³ Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.
⁴⁴ Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan.
⁴⁵ UC Santa Cruz Genomics Institute, University of California, Santa Cruz, USA.
⁴⁶ INVENesis, Neuchâtel, Switzerland.
⁴⁷ University Medical Center Utrecht, Utrecht, The Netherlands.
⁴⁸ University of Tennessee Health Science Center, Memphis, USA.
⁴⁹ Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA.
⁵⁰ Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan.
⁵¹ RIKEN BioResource Center, Ibaraki, Japan.
⁵² Leiden University Medical Center, Leiden, The Netherlands.
⁵³ WurmLab, School of Biological & Chemical Sciences, Queen Mary University of London, London, UK.
⁵⁴ Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain.
⁵⁵ Oracle Corporation, Tokyo, Japan.
⁵⁶ Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.
⁵⁷ Institute of Data Science, Maastricht University, Maastricht, The Netherlands.
⁵⁸ Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan.
⁵⁹ Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.

PMID: 32308977
PMCID: PMC7141167
DOI: 10.12688/f1000research.18236.1

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

Rutger A Vos et al. F1000Res. 2020.

. 2020 Feb 24:9:136.

doi: 10.12688/f1000research.18236.1. eCollection 2020.

Authors

Affiliations

¹ Institute of Biology Leiden, Leiden University, Leiden, The Netherlands.
² Naturalis Biodiversity Center, Leiden, The Netherlands.
³ Database Center for Life Science, Tokyo, Japan.
⁴ Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan.
⁵ DDBJ Center, National Institute of Genetics, Mishima, Japan.
⁶ Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
⁷ Curoverse, Somerville, USA.
⁸ Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway.
⁹ Faculty of Science and Engineering, SOKA University, Tokyo, Japan.
¹⁰ Institute for Advanced Biosciences, Keio University, Tokyo, Japan.
¹¹ SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, Lausanne, Switzerland.
¹² National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, USA.
¹³ Istituto Nazionale Genetica Molecolare, Romeo ed Enrica Invernizzi, Milan, Italy.
¹⁴ Dutch Techcentre for Life Sciences, Utrecht, The Netherlands.
¹⁵ National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Japan.
¹⁶ Computational Bioscience Program, University of Colorado School of Medicine, Denver, USA.
¹⁷ Université Paris-Saclay, LIMSI, CNRS, Paris, France.
¹⁸ Institute for Systems Biology, Seattle, USA.
¹⁹ Universidad de Murcia, IMIB-Arrixaca, Murcia, Spain.
²⁰ National Institute of Genetics, Mishima, Japan.
²¹ RIKEN Center for Sustainable Resource Science, Yokohama, Japan.
²² Polytechnic University of Madrid, Madrid, Spain.
²³ Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.
²⁴ St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Darlinghurst, Australia.
²⁵ Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, Australia.
²⁶ Novocraft Technologies Sdn. Bhd., Selangor, Malaysia.
²⁷ Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.
²⁸ European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK.
²⁹ Institute for Protein Research, Osaka University, Osaka, Japan.
³⁰ School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan.
³¹ The Institute of Scientific and Industrial Research, Osaka University, Osaka, Japan.
³² Hitachi Ltd., Tokyo, Japan.
³³ National Bioscience Database Center, Japan Science and Technology Agency, Tokyo, Japan.
³⁴ Institute of Veterinary Physiology and Biochemistry, Justus-Liebig University Giessen, Giessen, Germany.
³⁵ Gesellschaft für innovative Personalwirtschaftssysteme mbH (GIP GmbH), Offenbach, Germany.
³⁶ The Noguchi Institute, Tokyo, Japan.
³⁷ National Cancer Center Japan, Tokyo, Japan.
³⁸ National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan.
³⁹ Center for Information Biology, National Institute of Genetics, Mishima, Japan.
⁴⁰ Lawrence Berkeley National Laboratory, Berkeley, USA.
⁴¹ RIKEN Quantitative Biology Center, Osaka, Japan.
⁴² Department of Systems Science, Osaka University, Osaka, Japan.
⁴³ Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.
⁴⁴ Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan.
⁴⁵ UC Santa Cruz Genomics Institute, University of California, Santa Cruz, USA.
⁴⁶ INVENesis, Neuchâtel, Switzerland.
⁴⁷ University Medical Center Utrecht, Utrecht, The Netherlands.
⁴⁸ University of Tennessee Health Science Center, Memphis, USA.
⁴⁹ Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA.
⁵⁰ Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan.
⁵¹ RIKEN BioResource Center, Ibaraki, Japan.
⁵² Leiden University Medical Center, Leiden, The Netherlands.
⁵³ WurmLab, School of Biological & Chemical Sciences, Queen Mary University of London, London, UK.
⁵⁴ Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain.
⁵⁵ Oracle Corporation, Tokyo, Japan.
⁵⁶ Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.
⁵⁷ Institute of Data Science, Maastricht University, Maastricht, The Netherlands.
⁵⁸ Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan.
⁵⁹ Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.

PMID: 32308977
PMCID: PMC7141167
DOI: 10.12688/f1000research.18236.1

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.

Keywords: BioHackathon; Bioinformatics; Databases; Linked Open Data; Metadata; Ontology; Semantic Web; Visualization; Web Services; Workflows.

PubMed Disclaimer

Conflict of interest statement

No competing interests were disclosed.

Figures

**Figure 1.. Main themes and topics of the BioHackathon 2015.**

**Figure 2.. Substitution rates as a function of evolutionary distance since the age of the most recent gene duplication observed in *Caenorhabditis* genomes.**

**Figure 3.. RDF schema for jPOST metadata.**

**Figure 4.. The graphical interface of Crick-chan as it answers which genes are associated with Alzheimer’s disease.**

**Figure 5.. Disease coverage for top-level categories in DO of the diseases only annotated in the Hoehndorf2015 DPA dataset in comparison to the HPO2015 annotation.**

**Figure 6.. From a General Process Model to an executable workflow.**

See this image and copyright information in PMC

References

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

Affiliations

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

Authors

Affiliations

Abstract

Conflict of interest statement

Figures

References

Publication types

MeSH terms

LinkOut - more resources

Full Text Sources