Development and Population of an Elaborate Formal Ontology for Clinical Practice Knowledge Representation

David Mendes, Irene Rodrigues, Carlos Fernandes Baeta

Abstract

The Ontology for General Medical Science (OGMS) complemented with the Computer-Based Patient Record Ontology (CPR)is based on several upper ontologies which may have formal ontological relations according to the OBO Foundry principles. These ontologies accordant to the underlying Ontological Realism render a structure with reasoning capabilities that reach further than those possible with logical formalisms alone. We propose to extend carefully the OGMS taking into account the diverse ontological relations found in the recently proposed Basic Formal Ontology V2, FMA and SNOMED-CT as foundational ontologies in order to extract axioms for ontology enrichment from natural language text. With these cautions in mind, using careful instantiation we improve largely the reasoning capabilities over the resulting OWL knowledge base. Most of the clinical practice knowledge is currently recorded in SOAP text format. We extend the OGMS with the CPR structure into an Ontology for General Clinical Practice (OGCP) for the generation of adequate ontologically rich axioms from the SOAP text segments.

References

  1. Bail, S., Horridge, M., Parsia, B., and Sattler, U. (2011). The justificatory structure of the ncbo bioportal ontologies. In Aroyo, L., Welty, C., Alani, H., Taylor, J., Bernstein, A., Kagal, L., Noy, N. F., and Blomqvist, E., editors, International Semantic Web Conference (1), volume 7031 of Lecture Notes in Computer Science, page 67ÃcâC n?âA? IJ82. Springer.
  2. BFO (2012). Basic formal ontology 2.0.
  3. Brochhausen, M., Burgun, A., Ceusters, W., Hasman, A., Leong, T., Musen, M., Oliveira, J., Peleg, M., Rector, A., Schulz, S., et al. (2011). Discussion of" biomedical ontologies: Toward scientific debate". Methods of information in medicine, 50(3):217.
  4. Hoehndorf, R., Dumontier, M., Oellrich, A., RebholzSchuhmann, D., Schofield, P., and Gkoutos, G. (2011). Interoperability between biomedical ontologies through relation expansion, upper-level ontologies and automatic reasoning. PloS one, 6(7):e22006.
  5. IFOMIS (2004). Basic formal ontology.
  6. Kaljurand, K. (2010). Owl verbalizer: making machinereadable knowledge also human-readable. Available Online: https://code.google.com/p/owlverbalizer/.
  7. Kaljurand, K. and Fuchs, N. E. (2007). Verbalizing owl in attempto controlled english. Proceedings of OWLED07.
  8. Kazakov, Y. (2009). Consequence-Driven Reasoning for Horn SHIQ Ontologies. In Boutilier, C., editor, IJCAI, pages 2040-2045. IJCAI Distinguished Paper Award Winner.
  9. Kazakov, Y., Krötzsch, M., and Simancík, F. (2011). Concurrent classification of el ontologies. In Proceedings of the 10th international conference on The semantic web - Volume Part I, ISWC'11, pages 305-320, Berlin, Heidelberg. Springer-Verlag.
  10. Melo, D., Rodrigues, I., and Nogueira, V. (2012). Work out the semantic web search: The cooperative way. Advances in Artificial Intelligence, 2012.
  11. Mendes, D. and Rodrigues, I. P. (2012a). A Semantic Web pragmatic approach to develop Clinical Ontologies, and thus Semantic Interoperability, based in HL7 v2.xml messaging. In Information Systems and Technologies for Enhancing Health and Social Care. IGI Global.
  12. Mendes, D. and Rodrigues, I. P. (2012b). Advances to semantic interoperability through cpr ontology extracting from soap framework reports. electronic Journal of Health Informatics.
  13. Noy, N. F., Shah, N. H., Whetzel, P. L., Dai, B., Dorf, M., Griffith, N., Jonquet, C., Rubin, D. L., Storey, M.-A., Chute, C. G., and Musen, M. a. (2009). BioPortal: ontologies and integrated data resources at the click of a mouse. Nucleic acids research, 37(Web Server issue):W170-3.
  14. Ogbuji, C. (2011). A Framework Ontology for ComputerBased Patient Record Systems. In Proceedings of the ICBO: International Conference on Biomedical Ontology, pages 217-223, Buffalo, NY, USA.
  15. OGMS (2010). Ontology for general medical science.
  16. OMIM (2012). Omim, online mendelian inheritance in man. Available Online: http://www.ncbi.nlm.nih.gov/ omim.
  17. RO, O. F. (2012). Relations ontology.
  18. Schriml, L., Arze, C., Nadendla, S., Chang, Y., Mazaitis, M., Felix, V., Feng, G., and Kibbe, W. (2012). Disease ontology: a backbone for disease semantic integration. Nucleic Acids Research, 40(D1):D940-D946.
  19. Simancik, F., Kazakov, Y., and Horrocks, I. (2011). Consequence-Based Reasoning beyond Horn Ontologies. In Walsh, T., editor, IJCAI, pages 1093-1098. IJCAI/AAAI.
  20. Smith, B. and Brochhausen, M. (2010). Putting Biomedical Ontologies to Work. Methods Inf Med, 49.
  21. Smith, B. and Ceusters, W. (2010). Ontological realism: A methodology for coordinated evolution of scientific ontologies. Applied ontology, 5(3-4):139-188.
  22. Smith, B., Ceusters, W., Klagges, B., KÃu?hler, J., Kumar, A., Lomax, J., Mungall, C., Neuhaus, F., Rector, A. L., and Rosse, C. (2005). Relations in biomedical ontologies. Genome Biol, 6(5):R46.
  23. W3C (2009). Computer-based patient record ontology. http://code.google.com/p/cprontology. http://code. google.com/p/cprontology.
  24. Wiki-DO (2012). Disease ontology wiki page. Available Online: http://do-wiki.nubic.northwestern.edu/ do-wiki/index.php/Main_Page.
  25. Wong, W., Liu, W., and Bennamoun, M. (2012). Ontology learning from text: A look back and into the future. ACM Comput. Surv., 44(4):20:1-20:36.
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Paper Citation


in Harvard Style

Mendes D., Rodrigues I. and Fernandes Baeta C. (2013). Development and Population of an Elaborate Formal Ontology for Clinical Practice Knowledge Representation . In Proceedings of the International Conference on Knowledge Engineering and Ontology Development - Volume 1: KEOD, (IC3K 2013) ISBN 978-989-8565-81-5, pages 286-292. DOI: 10.5220/0004548602860292


in Bibtex Style

@conference{keod13,
author={David Mendes and Irene Rodrigues and Carlos Fernandes Baeta},
title={Development and Population of an Elaborate Formal Ontology for Clinical Practice Knowledge Representation},
booktitle={Proceedings of the International Conference on Knowledge Engineering and Ontology Development - Volume 1: KEOD, (IC3K 2013)},
year={2013},
pages={286-292},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0004548602860292},
isbn={978-989-8565-81-5},
}


in EndNote Style

TY - CONF
JO - Proceedings of the International Conference on Knowledge Engineering and Ontology Development - Volume 1: KEOD, (IC3K 2013)
TI - Development and Population of an Elaborate Formal Ontology for Clinical Practice Knowledge Representation
SN - 978-989-8565-81-5
AU - Mendes D.
AU - Rodrigues I.
AU - Fernandes Baeta C.
PY - 2013
SP - 286
EP - 292
DO - 10.5220/0004548602860292