Abstract: With the rapidly accumulating knowledge of biological entities and
networks, there is a growing need for a general framework to understand this
information at a system level. In order to understand life as system, a formal
description of system dynamics with semantic validation will be necessary.
Within the context of biological pathways, several formats have been proposed,
e.g., SBML, CellML, and BioPAX. Unfortunately, these formats lack the formal
definitions of each term or fail to capture the system dynamics behavior. Thus,
we have developed a new system dynamics centered ontology called Cell System
Ontology (CSO). As an exchange format, the ontology is implemented in the Web
Ontology Language (OWL), which enables semantic validation and automatic
reasoning to check the consistency of biological pathway models. The features
of CSO are as follows: (1) manipulation of different levels of granularity and
abstraction of pathways, e.g., metabolic pathways, regulatory pathways, signal
transduction pathways, and cell-cell interactions; (2) capture of both
quantitative and qualitative aspects of biological function by using hybrid
functional Petri net with extension (HFPNe); and (3) encoding of biological
pathway data related to visualization and simulation, as well as modeling. The
new ontology also predefines mature core vocabulary, which will be necessary
for creating models with system dynamics. In addition, each of the core terms
has at least one standard icon for easy modeling and accelerating the
exchangeability among applications. In order to demonstrate the potential of
CSO-based pathway modeling, visualization, and simulation, we present an HFPNe
model for the ASEL and ASER regulatory networks in Caenorhabditis elegans.
Keywords: Cell system ontology, CSO, biological pathway, data exchange format, HFPNe, dynamic simulation, visualization
