title: Ontology-based representation of simulation models of physiology.
abstract: Dynamic simulation models of physiology are often represented as a set of mathematical equations. Such models are very useful for studying and understanding the dynamic behavior of physiological variables. However, the sheer number of equations and variables can make these models unwieldy, difficult to under-stand, and challenging to maintain. We describe a symbolic, ontologically-guided methodology for representing a physiological model of the circulation. We created an ontology describing the types of equations in the model as well as the anatomic components and how they are connected to form a circulatory loop. The ontology provided an explicit representation of the model, both its mathematical and anatomic content, abstracting and hiding much of the mathematical complexity. The ontology also provided a framework to construct a graphical representation of the model, providing a simpler visualization than the large set of mathematical equations. Our approach may help model builders to maintain, debug, and extend simulation models.
authors.affiliation: Stanford Medical Informatics, Stanford University School of Medicine, Stanford, CA, USA.
authors.forename: Daniel L
authors.initials: DL
authors.lastname: Rubin
authors.forename: David
authors.initials: D
authors.lastname: Grossman
authors.forename: Maxwell
authors.initials: M
authors.lastname: Neal
authors.forename: Daniel L
authors.initials: DL
authors.lastname: Cook
authors.forename: James B
authors.initials: JB
authors.lastname: Bassingthwaighte
authors.forename: Mark A
authors.initials: MA
authors.lastname: Musen
mesh_terms: D001775:Blood Circulation / Q000502:physiology*; D002320:Cardiovascular Physiological Phenomena; D002319:Cardiovascular System / Q000033:anatomy & histology; D003198:Computer Simulation; D006801:Humans; D008955:Models, Cardiovascular; D012984:Software; D018875:Vocabulary, Controlled