Reference Ontology Design for a Neurovascular Knowledge Network

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 phenotype. 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. Gianluca Colombo Department of Computer Science Systems and Communication (DISCo), University of Milano-Bicocca , viale Sarca, 336 20126 Milan (Italy), e-mail: giacolos@gmail.com; gianluca.colombo@disco.unimib.it Daniele Merico Terrence Donnelly Centre for Cellular and Biomolecular Research (CCBR) Banting and Best Department of Medical Research, University of Toronto, 160 College St M5S 3E1 Toronto (Ontario, Canada) e-mail: daniele.merico@gmail.com Giancarlo Mauri Department of Computer Science Systems and Communication (DISCo), University of MilanoBicocca , viale Sarca, 336 20126 Milan (Italy), e-mail: giancarlo.mauri@disco.unimib.it

[1]  P. Johnson-Laird,et al.  Mental Models: Towards a Cognitive Science of Language, Inference, and Consciousness , 1985 .

[2]  Nicolaas J. I. Mars,et al.  Bottom-Up Construction of Ontologies , 1998, IEEE Trans. Knowl. Data Eng..

[3]  Giancarlo Guizzardi,et al.  On Ontology, ontologies, Conceptualizations, Modeling Languages, and (Meta)Models , 2007, DB&IS.

[4]  David Lee Gordon,et al.  Classification of Subtype of Acute Ischemic Stroke: Definitions for Use in a Multicenter Clinical Trial , 1993, Stroke.

[5]  Christopher Lueg,et al.  Knowledge Management and Information Technology: Relationship and Perspectives , 2002 .

[6]  Nicola Guarino,et al.  Formal ontology, conceptual analysis and knowledge representation , 1995, Int. J. Hum. Comput. Stud..

[7]  P. Simons.  Parts: A Study in Ontology , 1991 .

[8]  Chiara Ghidini,et al.  Contextual reasoning distilled , 2000, J. Exp. Theor. Artif. Intell..

[9]  Thomas R. Gruber,et al.  Toward principles for the design of ontologies used for knowledge sharing? , 1995, Int. J. Hum. Comput. Stud..

[10]  David B. Matchar,et al.  Improving the Reliability of Stroke Subgroup Classification Using the Trial of ORG 10172 in Acute Stroke Treatment (TOAST) Criteria , 2001, Stroke.

[11]  Olivier Bodenreider,et al.  Investigating subsumption in DL-based terminologies: A Case Study in SNOMED CT , 2004, KR-MED.

[12]  T. Kuhn,et al.  The Structure of Scientific Revolutions. , 1964 .

[13]  Sonia Bergamaschi,et al.  Extracting Relevant Attribute Values for Improved Search , 2007, IEEE Internet Computing.

[14]  Elena García Barriocanal,et al.  Knowledge representation issues in ontology-based clinical Knowledge Management systems , 2009, Int. J. Technol. Manag..

[15]  Balakrishnan Chandrasekaran,et al.  What are ontologies, and why do we need them? , 1999, IEEE Intell. Syst..

[16]  Mariano Fernández-López,et al.  Ontological Engineering , 2003, Encyclopedia of Database Systems.

[17]  Peter Szolovits,et al.  Artificial intelligence in medical diagnosis. , 1988, Annals of internal medicine.

[18]  Maurizio Vincini,et al.  Synthesizing an Integrated Ontology with MOMIS , 2004 .

[19]  Ramkrishnan V. Tenkasi,et al.  P ERSPECTIVE M AKING AND P ERSPECTIVE T AKING IN C OMMUNITIES OF K NOWING , 2000 .

[20]  Olivier Bodenreider,et al.  Investigating subsumption in SNOMED CT: An exploration into large description logic-based biomedical terminologies , 2007, Artif. Intell. Medicine.

[21]  J. Bard,et al.  Ontologies in biology: design, applications and future challenges , 2004, Nature Reviews Genetics.

[22]  K. Furie,et al.  An evidence‐based causative classification system for acute ischemic stroke , 2005, Annals of neurology.

[23]  Xuanjing Huang,et al.  From Web Directories to Ontologies: Natural Language Processing Challenges , 2007, ISWC/ASWC.

[24]  Riichiro Mizoguchi,et al.  Ontology-based description of functional design knowledge and its use in a functional way server , 2003, Expert Syst. Appl..