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Inference of Functions, Roles, and Applications of Chemicals Using Linked Open Data and Ontologies

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Semantic Technology (JIST 2018)

Part of the book series: Lecture Notes in Computer Science ((LNISA,volume 11341))

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Abstract

A simple method to efficiently collect reliable chemical information was studied for developing an ontological foundation. Even ChEBI, a major chemical ontology, which consists of approximately 90,000 chemicals and information about 1,000 biological and chemical roles, and applications, lacks information regarding the roles of most of the chemicals. NikkajiRDF, linked open data which provide information of approximately 3.5 million chemicals and 694 application examples, is also being developed. NikkajiRDF was integrated with Interlinking Ontology for Biological Concepts (IOBC), which includes 80,000 concepts, including information on a number of diseases and drugs. As a result, it was possible to infer new information on at least one of the 432 biological and chemical functions, applications and involvements with biological phenomena, including diseases to 5,038 chemicals using IOBC’s ontological structure. Furthermore, seven chemicals and drugs, which would be involved in 16 diseases, were discovered using knowledge graphs that were developed from IOBC.

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Notes

  1. 1.

    sio: <http://semanticscience.org/resource/>.

  2. 2.

    dcterms: <http://purl.org/dc/terms/>.

  3. 3.

    rdfs: <http://www.w3.org/2000/01/rdf-schema#>.

  4. 4.

    wdt: <http://www.wikidata.org/prop/direct/>.

  5. 5.

    iobc: <http://purl.jp/bio/4/id/>.

  6. 6.

    xkos: <http://rdf-vocabulary.ddialliance.org/xkos#>.

  7. 7.

    mesh: <http://id.nlm.nih.gov/mesh/>.

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Acknowledgments

This study was supported by an operating grant from the Japan Science and Technology Agency and JSPS KAKENHI Grant Number JP17H01789. A part of this study was progressed and discussed in Japan BioHackathon 2016 (BH16.12), which served as a research and development meeting. We are grateful to all participants who gave us their valuable advice and constructive comments.

Author information

Authors and Affiliations

  1. National Bioscience Database Center, Japan Science and Technology Agency, Kawaguchi, Tokyo, Japan

    Tatsuya Kushida, Yuka Tateisi & Toshihisa Takagi

  2. The Institute of Scientific and Industrial Research, Osaka University, Suita, Japan

    Kouji Kozaki

  3. Japan Science and Technology Agency, Kawaguchi, Tokyo, Japan

    Takahiro Kawamura

  4. Database Center for Life Science, Research Organization of Information and Systems, Kashiwa, Japan

    Yasunori Yamamoto

  5. Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyō, Japan

    Toshihisa Takagi

Authors
  1. Tatsuya Kushida
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  2. Kouji Kozaki
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  3. Takahiro Kawamura
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  4. Yuka Tateisi
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  5. Yasunori Yamamoto
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  6. Toshihisa Takagi
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Corresponding author

Correspondence to Tatsuya Kushida .

Editor information

Editors and Affiliations

  1. National Institute of Informatics, Tokyo, Japan

    Ryutaro Ichise

  2. Accenture Labs, Dublin, Ireland

    Freddy Lecue

  3. Japan Science and Technology Agency, Tokyo, Japan

    Takahiro Kawamura

  4. Peking University, Beijing, China

    Dongyan Zhao

  5. Imperial College London, London, UK

    Stephen Muggleton

  6. Osaka University, Osaka, Japan

    Kouji Kozaki

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Kushida, T., Kozaki, K., Kawamura, T., Tateisi, Y., Yamamoto, Y., Takagi, T. (2018). Inference of Functions, Roles, and Applications of Chemicals Using Linked Open Data and Ontologies. In: Ichise, R., Lecue, F., Kawamura, T., Zhao, D., Muggleton, S., Kozaki, K. (eds) Semantic Technology. JIST 2018. Lecture Notes in Computer Science(), vol 11341. Springer, Cham. https://doi.org/10.1007/978-3-030-04284-4_26

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  • DOI: https://doi.org/10.1007/978-3-030-04284-4_26

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  • Online ISBN: 978-3-030-04284-4

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