An ontology-based application in heart electrophysiology: representation, reasoning and visualization on the web

ABSTRACT

Computational technologies have been increasingly explored to make biomedical knowledge and data more accessible for human understanding, comparison, analysis and communication. In this context, ontology has been recognized in the bioinformatics literature as a suitable technique for advancing knowledge and data representations in Biomedicine. Moreover, automated reasoning and visualization mechanisms can favor in providing support for human comprehensibility as well as in dealing with the complexity inherent to this domain. This paper elaborates on the application of ontology for heart electrophysiology representation, reasoning and visualization on the web. The ontology-based application we propose can be used to offer support for interactive learning in heart electrophysiology.

REFERENCES

• 1: Franz Baader , Diego Calvanese , Deborah L. McGuinness , Daniele Nardi , Peter F. Patel-Schneider, The description logic handbook: theory, implementation, and applications, Cambridge University Press, New York, NY, 2003
• 2: Anita Burgun, Desiderata for domain reference ontologies in biomedicine, Journal of Biomedical Informatics, v.39 n.3, p.307-313, June 2006 [doi>10.1016/j.jbi.2005.09.002]
• 3: Cavusoglu, M., et al. 2006. Gipsi: a Framework for Open Source /Open Architecture Software Development for Organ Level Surgical Simulation. IEEE Transactions on Information Technology in Biomedicine, 10(2): 312--322. {DOI: 10.1109/TITB.2006.864479}
• 4: Ramón Rubio García , Javier Suárez Quirós , Ramón Gallego Santos , Santiago Martín González , Samuel Morán Fernanz, Interactive multimedia animation with Macromedia Flash in Descriptive Geometry teaching, Computers & Education, v.49 n.3, p.615-639, November, 2007 [doi>10.1016/j.compedu.2005.11.005]
• 5: Geselowitz, D. 1989. On the Theory of the Electrocardiogram. Proceedings of the IEEE, 77(6): 857--876. {DOI: 10.1109/5.29327}
• 6: Gonçalves, B., Guizzardi, G., et al. 2007. An Electrocardiogram (ECG) Domain Ontology. In Proc. of the 2^nd Workshop on Ontologies and Metamodels for Software and Data Engineering, João Pessoa, Brazil.
• 7: Nicola Guarino , Christopher Welty, Evaluating ontological decisions with OntoClean, Communications of the ACM, v.45 n.2, February 2002 [doi>10.1145/503124.503150]
• 8: Guizzardi, G. 2005. Ontological Foundations for Structural Conceptual Models. Ph.D. Thesis, University of Twente, The Netherlands.
• 9: Guizzardi G.; Wagner, G. Towards Ontological Foundations for Agent Modelling Concepts using the Unified Foundational Ontology (UFO). Lecture Notes in Computer Science (LNCS), Springer-Verlag, Vol. 3508, 2005. {DOI: 10.1007/11426714_8}
• 10: Giancarlo Guizzardi , Terry Halpin, Ontological foundations for conceptual modelling, Applied Ontology, v.3 n.1-2, p.1-12, January 2008
• 11: Udo Hahn , Stefan Schulz, Guest editorial: Ontological foundations for biomedical sciences, Arificial Intelligence in Medicine, v.39 n.3, p.179-182, March, 2007 [doi>10.1016/j.artmed.2006.12.006]
• 12: Horrocks, I. et al. 2005. OWL Rules: a Proposal and Prototype Implementation. Journal of Web Semantics, 3(1): 23--40. {DOI: 10.1016/j.websem.2005.05.003}
• 13: Ingvar Johansson, Bioinformatics and biological reality, Journal of Biomedical Informatics, v.39 n.3, p.274-287, June 2006 [doi>10.1016/j.jbi.2005.08.005]
• 14: Brian McBride, Jena: A Semantic Web Toolkit, IEEE Internet Computing, v.6 n.6, p.55-59, November 2002 [doi>10.1109/MIC.2002.1067737]
• 15: Motik, B. et al. 2005. Query Answering for OWL-DL with Rules. Journal of Web Semantics, 3(1): 41--60.{DOI:10.1016/j.websem.2005.05.001}
• 16: Rubin, D., et al. 2006. Using Ontologies Linked with Geometric Models to Reason about Penetrating Injuries. Artificial Intelligence in Medicine, 37(3): 167--176. {DOI: 10.1016/j.artmed.2006.03.006}
• 17: Evren Sirin , Bijan Parsia , Bernardo Cuenca Grau , Aditya Kalyanpur , Yarden Katz, Pellet: A practical OWL-DL reasoner, Web Semantics: Science, Services and Agents on the World Wide Web, v.5 n.2, p.51-53, June, 2007 [doi>10.1016/j.websem.2007.03.004]
• 18: Smith, B. et al. 2007. The OBO Foundry: Coordinated Evolution of Ontologies to Support Biomedical Data Integration. Nature Biotechnology, 25(11): 1251--1255. {DOI: 10.1038/nbt1346}
• 19: Smith, B., et al. 2005. Relations in Biomedical Ontologies. Genome Biology, 6(5):R46. {DOI: 10.1186/gb-2005-6-5-r46}
• 20: Alexander C. Yu, Methods in biomedical ontology, Journal of Biomedical Informatics, v.39 n.3, p.252-266, June 2006 [doi>10.1016/j.jbi.2005.11.006]
• 21: Zamborlini, V., Gonçalves, B., Guizzardi, G. 2008. Codification and Application of a Well-Founded Heart-ECG Ontology. In Proc. of the 3^rd Workshop on Ontologies and Metamodels for Software and Data Engineering (WOMSDE'08), Campinas, Brazil.

INDEX TERMS

Primary Classification:
  H. Information Systems
  H.3 INFORMATION STORAGE AND RETRIEVAL
      H.3.5 On-line Information Services
          Subjects: Web-based services

Additional Classification:
  I. Computing Methodologies
  I.2 ARTIFICIAL INTELLIGENCE
      I.2.1 Applications and Expert Systems
          Subjects: Medicine and science

General Terms:
Design, Languages, Standardization

Keywords:
OWL DL + SWRL, biomedical ontology, heart electrophysiology and ECG, medical education, web animations