Building executable biological pathway models automatically from BioPAX

The amount of biological data exposed in semantic formats is steadily increasing. In particular, pathway information (a model of how molecules interact within a cell) from databases such as KEGG and WikiPathways are available in a standard RDF-based format BioPAX. However, these models are descriptive and not executable in nature. Being able to simulate or execute a pathway is one key mechanism for understanding the operation of a cell. The creation of executable models can take a significant amount of time and only relatively few such models currently exist. In this paper, we leverage the availability of semantically represented pathways, to bootstrap the creation of executable pathway models. We present an approach to automate the creation of executable models in the form of Petri-Nets from BioPAX represented pathways. This approach is encapsulated in an online tool, BioPax2PNML.