The Systems Biology Graphical Notation: Current Status and Applications in Systems Medicine

Abstract

The Systems Biology Graphical Notation (SBGN) is a community standard developed to reduce ambiguity in the visual representation of biomolecular networks by providing a standardized description of sets of symbols to use. SBGN comprises three distinct but complementary languages: Process Description (PD), Entity Relationship (ER), and Activity Flow (AF). SBGN captures distinct levels of details. SBGN PD is well-suited for representing detailed sequential biochemical mechanisms, such as metabolic pathways. SBGN AF shows cascades of influences between the activities carried out by biomolecular entities (e.g., stimulation and inhibition) in signaling pathways and regulatory networks. SBGN ER represents independent interactions between features of biological entities, thereby avoiding the complexity of represented biological states and interactions. SBGN has become a well-established standard in systems biology and systems medicine. Numerous visualization tools support SBGN, which is increasingly used in many popular biological databases as well as in scientific publications. This article aims at providing an overview of SBGN and its current applications in the field of biomedicine.