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Ontological modeling at a domain interface: bridging clinical and biomolecular knowledge

Published online by Cambridge University Press:  01 September 2009

Gianluca Colombo ,
Daniele Merico ,
Zoltán Nagy ,
Flavio De Paoli ,
Marco Antoniotti  and
Giancarlo Mauri
Gianluca Colombo
Affiliation:
Department of Computer Science, Systems and Communication (DISCo), University of Milan—Bicocca, viale Sarca, 336/14, 20126 Milan, Italy; e-mail: [email protected], [email protected], [email protected], [email protected]
Daniele Merico
Affiliation:
Department of Computer Science, Systems and Communication (DISCo), University of Milan—Bicocca, viale Sarca, 336/14, 20126 Milan, Italy; e-mail: [email protected], [email protected], [email protected], [email protected] Department of Biomolecular Sciences and Biotechnologies (DSBB), University of Milan, Via Celoria, 26, 20133 Milan, Italy; e-mail: [email protected] Terrence Donnelly Centre for Cellular and Biomolecular Research (CCBR), Banting and Best Department of Medical Research, University of Toronto, 160, College Street, M5S 3E1 Toronto, Ontario, Canada
Zoltán Nagy
Affiliation:
Department of Vascular Neurology, Semmelweis University, Huvosvolgyi Street 116, 1021 Budapest, Hungary; e-mail: [email protected]
Flavio De Paoli
Affiliation:
Department of Computer Science, Systems and Communication (DISCo), University of Milan—Bicocca, viale Sarca, 336/14, 20126 Milan, Italy; e-mail: [email protected], [email protected], [email protected], [email protected]
Marco Antoniotti
Affiliation:
Department of Computer Science, Systems and Communication (DISCo), University of Milan—Bicocca, viale Sarca, 336/14, 20126 Milan, Italy; e-mail: [email protected], [email protected], [email protected], [email protected]
Giancarlo Mauri
Affiliation:
Department of Computer Science, Systems and Communication (DISCo), University of Milan—Bicocca, viale Sarca, 336/14, 20126 Milan, Italy; e-mail: [email protected], [email protected], [email protected], [email protected]
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Abstract

In this paper, we discuss the challenges posed by the NEUROWEB project, as a case study of ontological modeling at a knowledge interface between neurovascular medicine and genomics. The aim of the project is the development of a support system for association studies. We identify the notion of clinical phenotypes, that is, the pathological condition of a patient, as the central construct of the knowledge model. Clinical phenotypes are assessed through the diagnostic activity, performed by clinical experts operating within communities of practice; the different communities 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 develop a central model for the clinical phenotypes, able to reconcile the different methodologies into a common classificatory system. To bridge neurovascular medicine and genomics, we identify the general theory of biological function as the common ground between the two disciplines; therefore, we decompose the clinical phenotypes into elementary phenotypes with a homogeneous physiological background, and we connect them to the biological processes, acting as the elementary units of the genomic world.

Type
Original Article
Information
The Knowledge Engineering Review , Volume 24 , Special Issue 3: Software and system engineering – part 2 , September 2009 , pp. 205 - 224
Copyright
Copyright © Cambridge University Press 2009

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