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Joint International Semantic Technology Conference

JIST 2019: Semantic Technology pp 182–190Cite as

Building Knowledge Graph Across Different Subdomains Using Interlinking Ontology for Biomedical Concepts

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Part of the book series: Communications in Computer and Information Science ((CCIS,volume 1157))

Abstract

This paper proposes a method for building knowledge graphs across different subdomains in life science using Interlinking Ontology for Biological Concepts (IOBC). IOBC provides wide range of concepts related to biomedical domains with relationships between concepts across different subdomains. The proposed method obtains some relationships according to interests of the users. Then, it combines these relationships with mappings from related concepts to other RDF datasets and construct new knowledge graphs using them. This paper introduces the building method which consist of 5 steps with some results of trial constructions of knowledge graphs.

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Notes

  1. 1.

    http://purl.bioontology.org/ontology/IOBC.

  2. 2.

    http://lod.hozo.jp/repositories/IOBC.

  3. 3.

    http://purl.jp/bio/4/id/200906082725054443.

  4. 4.

    http://purl.jp/bio/4/subject/System_cat.

  5. 5.

    https://www.ebi.ac.uk/ols/.

References

  1. Bodenreider, O., Nelson, S.J., et al.: Beyond synonymy: exploiting the UMLS semantics in mapping vocabularies. In: Proceedings of AMIA Symposium, pp. 815–819 (1998)

    Google Scholar 

  2. The UniProt Consortium: UniProt: the universal protein knowledgebase. Nucleic Acids Res. 45(D1), D158–D169 (2017)

    Article  Google Scholar 

  3. Gene Ontology Consortium: Creating the gene ontology resource: design and implementation. Genome Res. 11(8), 1425–1433 (2001)

    Article  Google Scholar 

  4. Kushida, T., et al.: Refined JST thesaurus extended with data from other open life science data sources. In: Wang, Z., Turhan, A.Y., Wang, K., Zhang, X. (eds.) JIST 2017. LNCS, vol. 10675, pp. 35–48. Springer, Cham (2017). https://doi.org/10.1007/978-3-319-70682-5_3

    Chapter  Google Scholar 

  5. Kushida, T., Kozaki, K., Tateisi, Y., et al.: Efficient construction of a new ontology for life sciences by sub-classifying related terms in the Japan science and technology agency thesaurus. In: Proceedings of ICBO 2017, vol. 2137, pp. 1–6. CEUR-WS.org, Newcastle (2017)

    Google Scholar 

  6. Kushida, T., Kozaki, K., Kawamura, T., Tateisi, Y., Yamamoto, Y., Takagi, T.: Inference of functions, roles, and applications of chemicals using linked open data and ontologies. In: Ichise, R., Lecue, F., Kawamura, T., Muggleton, S., Kozaki, K. (eds.) JIST 2018. LNCS, vol. 11341, pp. 385–397. Springer, Cham (2018). https://doi.org/10.1007/978-3-030-04284-4_26

    Chapter  Google Scholar 

  7. Noy, N.F., et al.: BioPortal: ontologies and integrated data resources at the click of a mouse. Nucleic Acids Res. 37(suppl 2), W170–W173 (2009)

    Article  Google Scholar 

  8. Ghazvinian, A., Noy, N.F., Musen, M.A.: Creating mappings for ontologies in biomedicine: simple methods work. In: AMIA Annual Symposium Proceedings, pp. 198–202. American Medical Informatics Association (2009)

    Google Scholar 

  9. Kushida, T., et al.: Refining JST thesaurus and discussing the effectiveness in life science research. In: Proceedings of 5th Intelligent Exploration of Semantic Data Workshop (IESD 2016, co-located with ISWC 2016), Kobe, pp. 1–14 (2016)

    Google Scholar 

  10. Hastings, J., de Matos, P., Dekker, A., Ennis, M., Harsha, B., Kale, N., et al.: The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013. Nucleic Acids Res. 41(D1), D456–D463 (2013)

    Article  Google Scholar 

  11. Kushida, T., Kozaki, K., Kawamura, T., Tateisi, Y., Yamamoto, Y., Takagi, T.: Interconnection of biological knowledge using NikkajiRDF and interlinking ontology for biological concepts: new generation computing. New Gener. Comput. 37, 525–549 (2019)

    Article  Google Scholar 

  12. Jupp, S., et al.: A new ontology lookup service at EMBL-EBI. In: Malone, J. et al. (eds.) Proceedings of SWAT4LS International Conference 2015 (2015)

    Google Scholar 

  13. Kamdar, M.R., Musen, M.A.: PhLeGrA: graph analytics in pharmacology over the web of life sciences linked open data. In: Proceedings of the 26th International Conference on World Wide Web, pp. 321–329 (2017)

    Google Scholar 

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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.

Author information

Authors and Affiliations

  1. Osaka Electro-Communication University, Osaka, Japan

    Kouji Kozaki

  2. RIKEN BioResource Research Center, Ibaraki, Japan

    Tatsuya Kushida

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

    Tatsuya Kushida & Toshihisa Takagi

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

    Yasunori Yamamoto

  5. Toyama University of International Studies, Toyama, Japan

    Toshihisa Takagi

Authors
  1. Kouji Kozaki
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  2. Tatsuya Kushida
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  3. Yasunori Yamamoto
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  4. Toshihisa Takagi
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Corresponding author

Correspondence to Kouji Kozaki .

Editor information

Editors and Affiliations

  1. Tianjin University, Tianjin, China

    Xin Wang

  2. University of Bari Aldo Moro, Bari, Italy

    Francesca A. Lisi

  3. Free University of Bozen-Bolzano, Bolzano, Italy

    Guohui Xiao

  4. Imperial College London, London, UK

    Elena Botoeva

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Kozaki, K., Kushida, T., Yamamoto, Y., Takagi, T. (2020). Building Knowledge Graph Across Different Subdomains Using Interlinking Ontology for Biomedical Concepts. In: Wang, X., Lisi, F., Xiao, G., Botoeva, E. (eds) Semantic Technology. JIST 2019. Communications in Computer and Information Science, vol 1157. Springer, Singapore. https://doi.org/10.1007/978-981-15-3412-6_18

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  • DOI: https://doi.org/10.1007/978-981-15-3412-6_18

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  • Publisher Name: Springer, Singapore

  • Print ISBN: 978-981-15-3411-9

  • Online ISBN: 978-981-15-3412-6

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