Skip to main content
SpringerLink
Log in

Methodology for Biomedical Ontology Matching

  • Conference paper
  • First Online:
The Semantic Web: ESWC 2019 Satellite Events (ESWC 2019)

Part of the book series: Lecture Notes in Computer Science ((LNISA,volume 11762))

Included in the following conference series:

  • 972 Accesses

Abstract

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.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 39.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 54.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Notes

  1. 1.

    http://oaei.ontologymatching.org/.

  2. 2.

    https://bioportal.bioontology.org/.

  3. 3.

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

  4. 4.

    https://owl.vse.cz/OOSP/.

  5. 5.

    http://oaei.ontologymatching.org/2018/.

  6. 6.

    https://cbiit.cancer.gov/ncip/biomedical-informatics-resources/interoperability-and-semantics/terminology/.

  7. 7.

    http://sio.semanticscience.org/.

References

  1. Biomedicine. http://www.memidex.com/biomedicine. Accessed 10 Feb 2019

  2. Rubin, D.L., Shah, N.H., Noy, N.F.: Biomedical ontologies: a functional perspective. Briefings Bioinf. 9(1), 75–90 (2008)

    Article  Google Scholar 

  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. Staab, S., Studer, R.: Handbook on Ontologies, 2nd edn. Springer, Berlin (2009). https://doi.org/10.1007/978-3-540-92673-3

    Book  MATH  Google Scholar 

  5. Euzenat, J., Schvaiko, P.: Ontology Matching, 2nd edn. Springer, Berlin (2013)

    Book  Google Scholar 

  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. 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)

    Article  Google Scholar 

  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. 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). https://doi.org/10.1007/978-3-642-35176-1_33

    Chapter  Google Scholar 

  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. 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). https://doi.org/10.1007/978-3-642-41030-7_38

    Chapter  Google Scholar 

  12. PubChem., http://pubchemdocs.ncbi.nlm.nih.gov/rdf. Accessed 10 Feb 2019

  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). https://doi.org/10.1007/978-3-642-24794-1_12

    Chapter  Google Scholar 

Download references

Acknowledgement

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.

Author information

Authors and Affiliations

  1. University of Economics, nám. W. Churchilla 1938/4, 13067, Prague, Czech Republic

    Jana Vataščinová

Authors
  1. Jana Vataščinová
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Jana Vataščinová .

Editor information

Editors and Affiliations

  1. Kansas State University, Manhattan, KS, USA

    Pascal Hitzler

  2. Vienna University of Economics and Business, Vienna, Austria

    Sabrina Kirrane

  3. Linköping University, Linköping, Sweden

    Olaf Hartig

  4. Vrije Universiteit Amsterdam, Amsterdam, The Netherlands

    Victor de Boer

  5. Leibniz Information Centre for Science and Technology University Library (TIB), Hannover, Germany

    Maria-Esther Vidal

  6. University of Bonn, Bonn, Germany

    Maria Maleshkova

  7. Vrije Universiteit Amsterdam, Amsterdam, The Netherlands

    Stefan Schlobach

  8. Jönköping University, Jönköping, Sweden

    Karl Hammar

  9. F. Hoffmann-La Roche AG, Basel, Switzerland

    Nelia Lasierra

  10. Robert Bosch GmbH, Stuttgart, Germany

    Steffen Stadtmüller

  11. Aalborg University, Aalborg, Denmark

    Katja Hose

  12. IMEC, Ghent University, Ghent, Belgium

    Ruben Verborgh

Rights and permissions

Reprints and permissions

Copyright information

© 2019 Springer Nature Switzerland AG

About this paper

Check for updates. Verify currency and authenticity via CrossMark

Cite this paper

Vataščinová, J. (2019). Methodology for Biomedical Ontology Matching. In: Hitzler, P., et al. The Semantic Web: ESWC 2019 Satellite Events. ESWC 2019. Lecture Notes in Computer Science(), vol 11762. Springer, Cham. https://doi.org/10.1007/978-3-030-32327-1_43

Download citation

  • DOI: https://doi.org/10.1007/978-3-030-32327-1_43

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-030-32326-4

  • Online ISBN: 978-3-030-32327-1

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics

Search

Navigation