Systems biology graphical notation : entity relationship language Level 1 Version 2

Abstract

The Systems Biological Graphical Notation (SBGN) is an international community effortfor standardized graphical representations of biological pathways and networks. The goalof SBGN is to provide unambiguous pathway and network maps for readers with differentscientific backgrounds as well as to support efficient and accurate exchange of biologicalknowledge between different research communities, industry, and other players in systemsbiology. Three SBGN languages, Process Description (PD), Entity Relationship (ER) andActivity Flow (AF), allow for the representation of different aspects of biological and bio-chemical systems at different levels of detail.The SBGN Entity Relationship language (ER) represents biological entities and their inter-actions and relationships within a network. SBGN ER focuses on all potential relationshipsbetween entities without considering temporal aspects. The nodes (elements) describe bio-logical entities, such as proteins and complexes. The edges (connections) provide descrip-tions of interactions and relationships (or influences), e.g., complex formation, stimulationand inhibition. Among all three languages of SBGN, ER is the closest to protein interac-tion networks in biological literature and textbooks, but its well-defined semantics offer asuperior precision in expressing biological knowledge.