Abstract
Summary The Systems Biological Graphical Notation (SBGN) is an international community effort for standardized graphical representations of biological pathways and networks. The goal of SBGN is to provide unambiguous pathway and network maps for readers with different scientific backgrounds as well as to support efficient and accurate exchange of biological knowledge between different research communities, industry, and other players in systems biology. Three SBGN languages, Process Description (PD), Entity Relationship (ER) and Activity Flow (AF), allow for the representation of different aspects of biological and biochemical systems at different levels of detail.The SBGN Process Description language represents biological entities and processes between these entities within a network. SBGN PD focuses on the mechanistic description and temporal dependencies of biological interactions and transformations. The nodes (elements) are split into entity nodes describing, e.g., metabolites, proteins, genes and complexes, and process nodes describing, e.g., reactions and associations. The edges (connections) provide descriptions of relationships (or influences) between the nodes, such as consumption, production, stimulation and inhibition. Among all three languages of SBGN, PD is the closest to metabolic and regulatory pathways in biological literature and textbooks, but its well-defined semantics offer a superior precision in expressing biological knowledge.
Highlights
With the rise of systems and synthetic biology, the use of graphical representations of pathways and networks to describe biological systems has become pervasive
The Systems Biology Graphical Notation (SBGN) is an international community effort that aims to standardise the visualisation of pathways and networks for readers with diverse scientific backgrounds as well as to support an efficient and accurate exchange of biological knowledge between disparate research communities, industry, and other players in systems biology
A level of one of the SBGN languages represents a set of features deemed to fit together cohesively, constituting a useful set of functionality that the user community agrees sufficient for a reasonable set of tasks and goals
Summary
The previous chapters describe the appearance and meaning of SBGN Process Description Level 1 components. The components of a Process Description have to be placed in a meaningful way – a random distribution with spaghetti-like connections will most likely hide the information encoded in the underlying model, whereas an elegant placement of the objects, giving a congenial appearance of the maps, may reveal new insights. We provide rules for the layout of process description maps, divided into two categories: 1. We provide a list of additional suggestions which may help in producing aesthetically more pleasant layouts, possibly easier to understand. Those layout rules are independent of the method used to produce the map, and apply to both manually drawn maps as well as maps produced by an automatic layout algorithm. The meaning of a graph should be conserved upon scaling as far as possible
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