Short Communication on Semantics for Biological Processes

Models as abstract representations of observed or hypothesized phenomena are not new to the life sciences. They have long been used as tools for organizing and communicating information. However, these models take in systems biology has changed dramatically. Traditional representations of biomolecular networks have been used for natural language narratives augmented with block-and-arrow diagrams. While useful for describing hypotheses about a system's components and their interactions, those representations are increasingly recognized as inadequate vehicles for understanding complex systems Instead, formal, quantitative models replace these static diagrams as integrators of knowledge, and serve as the centerpiece of the scientific modeling and simulation cycle