Conversion from BioPAX to CSO for system dynamics and visualization of biological pathway.

The vast accumulation of biological pathway data scattered in various sources presents challenges in the exchange and integration of these data. Major new standards for representation of pathway data and the ability to check inconsistency in pathways are inevitable for the development of a reliable pathway data repository. Within the context of biological pathways, the cell system ontology (CSO) had been developed as a general framework to model system dynamics and visualization of diverse biological pathways. CSO provides an excellent environment for modeling, visualizing, and simulating complex molecular mechanisms at different levels of details. This paper examines whether CSO addresses the integration capability of pathway data with system dynamics. We present a conversion tool for converting BioPAX to CSO. Transforming the data from BioPAX to CSO not only allows an analysis of the dynamic behaviors in molecular interactions but also allows the results to be stored for further biological investigations, which is not possible in BioPAX. The conversion is done using simple inference algorithms with the addition of view- and simulation-related properties. We demonstrate how CSO can be used to build a complete and consistent pathway repository and enhance the interoperability among applications.