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

  • Tatsuya KushidaEmail author
  • Kouji Kozaki
  • Takahiro Kawamura
  • Yuka Tateisi
  • Yasunori Yamamoto
  • Toshihisa Takagi
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 11341)


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.


Chemical Disease Drug Inference Knowledge graph LOD Ontology RDF SPARQL 



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.


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Copyright information

© Springer Nature Switzerland AG 2018

Authors and Affiliations

  1. 1.National Bioscience Database CenterJapan Science and Technology AgencyKawaguchiJapan
  2. 2.The Institute of Scientific and Industrial ResearchOsaka UniversitySuitaJapan
  3. 3.Japan Science and Technology AgencyKawaguchiJapan
  4. 4.Database Center for Life Science, Research Organization of Information and SystemsKashiwaJapan
  5. 5.Department of Biological Sciences, Graduate School of ScienceThe University of TokyoBunkyōJapan

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