Abstract
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. SBGN comprises the three languages Entity Relationship, Activity Flow, and Process Description (PD) to cover biological and biochemical systems at distinct levels of detail. PD is closest to metabolic and regulatory pathways found in biological literature and textbooks. Its well-defined semantics offer a superior precision in expressing biological knowledge. PD represents mechanistic and temporal dependencies of biological interactions and transformations as a graph. Its different types of nodes include entity pools (e.g. metabolites, proteins, genes and complexes) and processes (e.g. reactions, associations and influences). The edges describe relationships between the nodes (e.g. consumption, production, stimulation and inhibition). This document details Level 1 Version 2.0 of the PD specification, including several improvements, in particular: 1) the addition of the equivalence operator, subunit, and annotation glyphs, 2) modification to the usage of submaps, and 3) updates to clarify the use of various glyphs (i.e. multimer, empty set, and state variable).
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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