Reasoning strategies are a key component in many medical tasks, including decision making, clinical problem solving, and understanding of medical texts. Identification of reasoning strategies used by clinicians may prove critical to the optimal design of decision support systems. This paper presents a formal method of cognitive-semantic analysis for the identification and characterization of reasoning strategies deployed in medical tasks and demonstrates its use through specific examples. Although semantic analysis was originally developed in the investigation of knowledge structures, it can also be applied to identify the reasoning and decision processes used by physicians and medical trainees in clinical tasks. Assumptions underlying the methods, as well as illustrations of their use in diagnostic explanation tasks, are presented. We discuss semantic analysis in the context of the current interests in developing medical ontologies and argue that a frame-based propositional analytic methodology can provide a systematic way of addressing the construction of such ontologies. Although the application of propositional analysis methods has some limitations, we show how such limitations are being addressed and present some examples of information tools that have been developed to ease, and make more systematic, the process of analysis.