The goal of this paper is two-fold: first, to emphasize causality in disease ontology and knowledge representation, presenting a general and cursory discussion of causality and causal chains; and second, to clarify and develop the River Flow Model of Diseases (RFM). The RFM is an ontological account of disease, representing the causal structure of pathology. It applies general knowledge of causality using the concept of causal chains. The river analogy of disease is explained, formal descriptions are offered, and the RFM (...) disease definition is refined by describing causal chains in terms of causal relations. The definition is updated to coincide with the actual RFM classes found in its upper-level ontology, YAMATO, which brings to light some challenges in developing both YAMATO and the RFM. The RFM is also discussed in relation to another ontological account of disease. Strategies are offered toward interoperability between these theories. (shrink)

Many existing biomedical vocabulary standards rest on incomplete, inconsistent or confused accounts of basic terms pertaining to diseases, diagnoses, and clinical phenotypes. Here we outline what we believe to be a logically and biologically coherent framework for the representation of such entities and of the relations between them. We defend a view of disease as involving in every case some physical basis within the organism that bears a disposition toward the execution of pathological processes. We present our view in the (...) form of a list of terms and definitions designed to provide a consistent starting point for the representation of both disease and diagnosis in information systems in the future. (shrink)