The Role of Foundational Relations in the Alignment of Biomedical Ontologies

The Foundational Model of Anatomy (FMA) symbolically represents the structural organization of the human body from the macromolecular to the macroscopic levels, with the goal of providing a robust and consistent scheme for classifying anatomical entities on the basis of explicit definitions. This scheme also provides a template for modeling pathology, physiological function and genotype-phenotype correlations, and it can thus serve as a reference ontology in biomedical informatics. Here we articulate the need for formally clarifying the is-a and partof relations in the FMA and similar ontology and terminology systems. We diagnose certain characteristic errors in the treatment of these relations and show how these errors can be avoided through adoption of the formalism we describe. We then illustrate how a consistently applied formal treatment of taxonomy and partonomy can support the alignment of ontologies

The influence of medical expertise, case typicality and illness script component on case processing and disease probability estimates

The present study investigated the influence of medical expertise, case typicality, and illness script component (enabling conditions vs. consequences) on the speed of case informati

Expertise and the interpretation of computerized physiological data: implications for the design of computerized monitoring in neonatal intensive care

This paper presents the outcomes from a cognitive engineering project addressing the design problems of computerized monitoring in neonatal intensive care. Cognitive engineering is viewed, in this project, as a symbiosis between cognitive science and design practice. A range of methodologies has been used: interviews with neonatal staff, ward observations and experimental techniques. The results of these investigations are reported, focusing specifically on the differences between junior and senior physicians in their interpretation of monitored physiological data. It was found that the senior doctors made better use of the different knowledge sources available than the junior doctors. The senior doctors were able to identify more relevant physiological patterns and generated more and better inferences than did their junior colleagues. Expertise differences are discussed in the context of previous psychological research in medical expertise. Finally, the paper discusses the potential utility of these outcomes to inform the design of computerized decision support in neonatal intensive care

Ontologies, Disorders and Prototypes

As it emerged from philosophical analyses and cognitive research, most concepts exhibit typicality effects, and resist to the efforts of defining them in terms of necessary and sufficient conditions. This holds also in the case of many medical concepts. This is a problem for the design of computer science ontologies, since knowledge representation formalisms commonly adopted in this field (such as, in the first place, the Web Ontology Language - OWL) do not allow for the representation of concepts in terms of typical traits. The need of representing concepts in terms of typical traits concerns almost every domain of real world knowledge, including medical domains. In particular, in this article we take into account the domain of mental disorders, starting from the DSM-5 descriptions of some specific disorders. We favour a hybrid approach to concept representation, in which ontology oriented formalisms are combined to a geometric representation of knowledge based on conceptual space. As a preliminary step to apply our proposal to mental disorder concepts, we started to develop an OWL ontology of the schizophrenia spectrum, which is as close as possible to the DSM-5 descriptions