A Method to Support Cell Physiological Modelling Using Description Language and Ontology

Abstract

The development of physiological cell models to support the understanding of biological mechanisms gains increasingly importance. Due to the complexity of biological systems, whole cell models, which are composed of many imported component models of functional elements, get quite complex, making modifications difficult. Here, we propose a method to enhance structural changes of cell models, employing the markup languages of CellML and our original PMSML (Physiological Model Structure Markup Language), in addition to a new ontology for cell physiological modelling, the Cell Model Ontology. In particular, a method to make references from CellML files to the ontology and a method to assist with manipulation of model structures using PMSML together with the Cell Model Ontology are reported. Using these methods two software utilities, an interactive ontology ID assigner, the CellML Ontologizer, and a graphical cell model editor, the Cell Structure Editor, are implemented. Experimental results proved that the proposed method and the implemented software are useful for the modification of physiological models.