Role-based representation and inference of biochemical processes

We present a streamlined data model for representation of biochemical processes which consistently adopts a perspective on these processes as molecular events. Our model references a small number of established foundational relations predominantly from RO and employs BFO as upper ontology. It addresses some of the limitations in terms of interoperability, semantic compatibility and expressivity encountered in other approaches to modeling biochemical processes. Using a role-based approach we demonstrate how from this perspective various metabolic and transport processes can be consistently represented across different levels of granularity and how relations between processes like sequence of events can be inferred.