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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: gianluca.colombo@disco.unimib.it, flavio.depaoli@disco.unimib.it, marco.antioniotti@disco.unimib.it, mauri@disco.unimib.it
Daniele Merico
Affiliation:
Department of Computer Science, Systems and Communication (DISCo), University of Milan—Bicocca, viale Sarca, 336/14, 20126 Milan, Italy; e-mail: gianluca.colombo@disco.unimib.it, flavio.depaoli@disco.unimib.it, marco.antioniotti@disco.unimib.it, mauri@disco.unimib.it Department of Biomolecular Sciences and Biotechnologies (DSBB), University of Milan, Via Celoria, 26, 20133 Milan, Italy; e-mail: daniele.merico@gmail.com 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: nagy@opni.hu
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: gianluca.colombo@disco.unimib.it, flavio.depaoli@disco.unimib.it, marco.antioniotti@disco.unimib.it, mauri@disco.unimib.it
Marco Antoniotti
Affiliation:
Department of Computer Science, Systems and Communication (DISCo), University of Milan—Bicocca, viale Sarca, 336/14, 20126 Milan, Italy; e-mail: gianluca.colombo@disco.unimib.it, flavio.depaoli@disco.unimib.it, marco.antioniotti@disco.unimib.it, mauri@disco.unimib.it
Giancarlo Mauri
Affiliation:
Department of Computer Science, Systems and Communication (DISCo), University of Milan—Bicocca, viale Sarca, 336/14, 20126 Milan, Italy; e-mail: gianluca.colombo@disco.unimib.it, flavio.depaoli@disco.unimib.it, marco.antioniotti@disco.unimib.it, mauri@disco.unimib.it
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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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