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

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. 208G .

Unifying heterogeneous and distributed information about marine species through the top level ontology MarineTLO

“…Similar approaches have been described also in different domains, i.e., in the medical domain. The Neuroweb Reference ontology (Colombo et al, 2009) is an upper level schema and enables a specific infrastructure to operate over different clinical repositories and to retrieve patients based on a set of specific criteria. This ontology acts as a vocabulary by encoding in a common way the phenotypes (the pathological condition of a patient) of different patients coming from different repositories.…”