Methodology for Biomedical Ontology Matching

  • Jana VataščinováEmail author
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 11762)


This paper introduces a dissertation project in the field of ontology matching. Ontology matching plays an important role in integration of various systems or in connecting data which use different ontologies. One of the domains where different ontologies are used and where large amount of data is being continuously generated is biomedicine. The goal of the dissertation project is to propose a methodology for matching of biomedical ontologies. The existing projects do not address the topic as a whole. The related projects provide a methodology for ontology matching in general or talk about matching of biomedical ontologies (solely receiving a set of mappings). The thesis should define and address this gap. As biomedical ontologies can be quite specific, the need for a methodology for matching of these ontologies arises. To achieve the goal of the dissertation, the analytic steps come first - literature review of the field of matching of biomedical ontologies, use of the current methodologies and evaluation of their efficiency and their limitations, research of characteristics of biomedical ontologies, evaluation of different matching tools, and evaluation of combined results from multiple matching tools. Then, the formulation of the methodology steps will follow. After the formulation of the methodology, it needs to be evaluated. The evaluation should compare results from the matching process which follows the proposed methodology with the result from another methodology. At the end, some results of the analytic steps are drafted and current work to follow is described.


Ontology Ontology matching Biomedical ontology 



The research has been partially supported by IGA VSE 33/2019. Additionally, I would like to thank my PhD supervisor Vojtěch Svátek, my PhD adviser Ondřej Zamazal and all the ESWC 2019 reviewers for their valuable comments and feedback.


  1. 1.
    Biomedicine. Accessed 10 Feb 2019
  2. 2.
    Rubin, D.L., Shah, N.H., Noy, N.F.: Biomedical ontologies: a functional perspective. Briefings Bioinf. 9(1), 75–90 (2008)CrossRefGoogle Scholar
  3. 3.
    Gross, A., Hartung, M., Kirsten, T., Rahm, E.: Mapping composition for matching large life science ontologies. In: Proceedings of the Second International Conference on Biomedical Ontology, pp. 109–116, Buffalo, NY (2011)Google Scholar
  4. 4.
    Staab, S., Studer, R.: Handbook on Ontologies, 2nd edn. Springer, Berlin (2009). Scholar
  5. 5.
    Euzenat, J., Schvaiko, P.: Ontology Matching, 2nd edn. Springer, Berlin (2013)CrossRefGoogle Scholar
  6. 6.
    Algergawy, A., Cheatham, M., Faria, D., et al.: Results of the ontology alignment evaluation initiative 2018. In: Ontology Matching OM2018, pp. 76–116. CEUR-WS, Cáchy (2018)Google Scholar
  7. 7.
    Faria, D., Pesquita, C., Mott, I., Martins, C., Couto, F.M.: Tackling the challenges of matching biomedical ontologies. J. Biomed. Semant. 9(1), 4 (2018)CrossRefGoogle Scholar
  8. 8.
    Zaveri, A., Dumontier, M.: Ontology mapping for life science linked data. In: Proceedings of the First International Workshop on Biomedical Data Integration and Discovery. CEUR-WS, Japan (2016)Google Scholar
  9. 9.
    Sarasua, C., Simperl, E., Noy, N.F.: CrowdMap: crowdsourcing ontology alignment with microtasks. In: Cudré-Mauroux, P., et al. (eds.) ISWC 2012. LNCS, vol. 7649, pp. 525–541. Springer, Heidelberg (2012). Scholar
  10. 10.
    Jiménez-Ruiz, E., Grau, B.C., Zhou, Y., Horrocks, I.: Large-scale interactive ontology matching: algorithms and implementation. In: Proceedings of the 20th European Conference on Artificial Intelligence, pp. 444–449 (2012)Google Scholar
  11. 11.
    Faria, D., Pesquita, C., Santos, E., Palmonari, M., Cruz, I.F., Couto, F.M.: The agreementmakerlight ontology matching system. In: Meersman, R., et al. (eds.) OTM 2013. LNCS, vol. 8185, pp. 527–541. Springer, Heidelberg (2013). Scholar
  12. 12.
    PubChem., Accessed 10 Feb 2019
  13. 13.
    Euzenat, J., Le Duc, C.: Methodological guidelines for matching ontologies. In: Suárez-Figueroa, M.C., Gómez-Pérez, A., Motta, E., Gangemi, A. (eds.) Ontology Engineering in a Networked World, pp. 257–278. Springer, Heidelberg (2012). Scholar

Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  1. 1.University of EconomicsPragueCzech Republic

Personalised recommendations