In this paper we describe the ontological model developed within the NEUROWEB project, a consortium of four European excellence centers for the diagnosis and treatment of the Ischemic Stroke pathology. The aim of the project is the development of a support system for association studies, intended as the search for statistical correlations between a feature (e.g., a genotype) and the clinical phe-notype. Clinical phenotypes are assessed through the diagnostic activity, performed by clinical experts operating within different neurovascular sites. These sites operate according to specific procedures, but they also conform to the minimal requirements of international guidelines, displayed by the adoption of a common standard for the patient classification. We developed a central model for the clinical phenotypes (the NEUROWEB Reference Ontology), able to reconcile the different methodologies into a common classificatory system. To support the integrative analysis of genotype-phenotype relations, the Reference Ontology was extended to handle concepts of the genomic world. We identified the general theory of biological function as the common ground between the clinical medicine and molecular biosciences; therefore we decomposed the clinical phenotypes into elementary phenotypes with a homogeneous physiological background, and we connected them to the biological processes, acting as the elementary units of the genomic world.
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References
Y. Kitamura, R. Mizoguchi. 2003. Ontology-based description of functional design knowledge and its use in a functional way server. International Journal of Expert System with Application 2:153–166.
Bouquet, P., Don, V., Serafini, A. 2002 ConTeXtualizedlocal ontology specification via ctxml. Proceedings of AAAI workshop on Meaning Negotiation, Edmonton Alberta, Canada, 2002.
Simons, P., 1987, Parts: A study in ontology, Oxford University Press, Oxford, 1987.
Zaihrayeu, I., Sun, L., Giunchiglia, F., et al. 2007 From Web Directories to Ontologies: Natural Language Processing Challenges.In proceedings The 6th International Semantic Web Conference and the 2nd Asian Semantic Web Conference, 2007, Busan, Korea, 11 -15 November, 2007, pp 623–636.
Benassi, R., Beneventano, D., Bergamaschi, S., Guerra, F., Vincini, M., 2004, Synthesizing an Integrated Ontology with MOMIS, International Conference on Knowledge Engineering and Decision Support (ICKEDS). Porto, Portugal, 21–23 July 2004.
Bergamaschi, S., Guerra, F., Orsini, M.,Sartori, C., 2007 Extracting Relevant Attribute Values for Improved Search, IEEE Internet Computing, vol. 11, no. 5, pp 26–35, Sept/Oct, 2007.
ueg, C., 2002, Knowledge Management and Information Technology: Relationship and Perspective, Upgrade — Knowledge Management and Information Technology, 2002.
Chandrasekaran, B., Josephson, J.R., Benjamins, V.R., 1999, What are ontologies, and why do we need them? Intelligent Systems and Their Applications, IEEE Volume 14, Issue 1, Jan/Feb 1999, pp 20–26.
Kuhn, T., 1970 The Structure of Scientific Revolutions, 1970, Chicago, University of Chicago Press, 1970.
Gomez-Perez, A., Corcho-Garcia, O., Fernandez-Lopez, M. 2003, Ontological Engineering, New York, Springer-Verlag, 2003.
Van der Vet, P.E., Mars, N.J.I., 1998, Bottom-Up Construction of Ontologies, IEEE Trans. Knowl. Data Eng. 1998, 10(4), pp 513–526.
Guizzardi, G. 2007, On Ontology, ontologies, Conceptualizations, Modeling Languages, and (Meta)Models, Frontiers in Artificial Intelligence and Applications, Databases and Information Systems IV, IOS Press, Amsterdam, 2007.
SNOMED-CT,http : //www.snomed.org/
Bodenreider, O., Smith, B., Kumar, A., Burgun, A., 2007, Investigating Subsumption in DL-Based Terminologies: A Case Study in SNOMED CT, Artif. Intell. Med. 2007, 39(3), pp 183–195.
OBO, Open Biomedical Ontologies http : //obo.sourceforge.net /
The Gene Ontology Consortium,http : //www.geneontology.org.
The National Center for Biomedical Ontologies, http : //www.bioontology.org/wiki/index.php/MainPage.
W3C - Web Ontology Language http : //www.w3.org/TR/owl -guide/
Protg, User Documentation http : //prot ege.stanford.edu/doc/users.html.
Bard, J. B., Rhee, L., Seung, Y., 2004 Ontology in Biology: design, application and future challanges, Nature Reviews Genetics, 2004/3, pp 213–222.
Smith, B., 2004, Beyond Concepts: Ontology as reality represenation, 2004, in Procedeengs FOIS 2004.
Guarino, N., 1995, Formal Ontology, Conceptual Analysis and Knowledge Representation, in International Journal of Human and Computer Studies, 43(5/6), pp 625–640.
Guarino, N., 1998, Formal Ontology in Information Systems, In Formal Ontology in Information Systems, Proceedings of FOIS'98, Trento, Italy, June 6–8, 1998. IOS Press, Amsterdam, pp 3–15.
Gruber, T. R., 1995, Toward principles for the design of ontologies used for knowledge sharing, International Journal of Human-Computer Studies, Vol. 43, Issues 4–5, November 1995, pp 907–928.
Amie L., Thomasson, 2004, Methods of Categorization, Proceedings of the third International Conference (FOIS-2004) IOS Press, pp 3–16, 2004.
Szolovits, P., Patil, R.S., Schwartz, W.B., Artificial intelligence in medical diagnosis, 1988, Annals of internal medicine, 1988.
Goldstein, L.B., Jones, M.R., Matchar D.B., et al., 2001 Improving the reliability of Stroke subgroup classification using the Trial of ORG 10172 in Acute Stroke Treatment (TOAST) criteria, Stroke 2001; 32: 1091–1097.
Adams, H.P. Jr., et al., 1993 Classification of Subtype of Acute Ischemic Stroke, Definition for Use in a Multicenter Clinical Trial, TOAST. Trial of Org 10172 in Acute Stroke Treatment, Stroke 1993, 24, pp 35–41.
Ay, H., Furie, K.L., Singhal, A., Smith, W.S., Sorensen, A.G., Koroshetz, W.J., 2005 An evidence-Based Causative Classification System for Acute Ischemic Stroke, Annals of Neurology, 2005, (58), pp 688–697.
Johnson-Laird, P. N. 1983, Mental models: Towards a cognitive science of language, inference, and consciousness, Cambridge, MA, Harvard University Press, 1983.
Boland, J., Tenkasi, R.V., 1995, Perspective making and perspective taking in communities of knowing, Organizational Science 6(4) pp 350–372.
Benerecetti, M., Bouquet P., Ghidini C., 2000, Contextual Reasoning Distilled, Journal of Theoretical and Artificial Intelligence (JETAI), 12(2000), pp 279–305.
Sicilia, J.J., Sicilia, M.A., Snchez-Alonso, S., et al., 2007, Knowledge Representation Issues in Ontology-based Clinical Knowledge Management Systems, International Journal of Technology Management, 2007.
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Colombo, G., Merico, D., Mauri, G. (2009). Reference Ontology Design for a Neurovascular Knowledge Network. In: Sicilia, MA., Lytras, M.D. (eds) Metadata and Semantics. Springer, Boston, MA. https://doi.org/10.1007/978-0-387-77745-0_39
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