Abstract
AbstractStandard graphical representations have played a crucial role in science and engineering throughout the last century. Without electrical symbolism, it is very likely that our industrial society would not have evolved at the same pace. Similarly, specialised notations such as the Feynmann notation or the process flow diagrams did a lot for the adoption of concepts in their own fields. With the advent of Systems Biology, and more recently of Synthetic Biology, the need for precise and unambiguous descriptions of biochemical interactions has become more pressing. While some ideas have been advanced over the last decade, with a few detailed proposals, no actual community standard has emerged. The Systems Biology Graphical Notation (SBGN) is a graphical representation crafted over several years by a community of biochemists, modellers and computer scientists. Three orthogonal and complementary languages have been created, the Process Diagrams, the Entity Relationship Diagrams and the Activity Flow Diagrams. Using these three idioms a scientist can represent any network of biochemical interactions, which can then be interpreted in an unambiguous way. The set of symbols used is limited, and the grammar quite simple, to allow its usage in textbooks and its teaching directly in high schools. The first level of the SBGN Process Diagram has been publicly released. Software support for SBGN Process Diagram was developed concurrently with its specification in order to speed-up public adoption. Shared by the communities of biochemists, genomicians, theoreticians and computational biologists, SBGN languages will foster efficient storage, exchange and reuse of information on signalling pathways, metabolic networks and gene regulatory maps.
Highlights
The goal of the Systems Biology Graphical Notation (SBGN) is to standardize the graphical/visual representation of biochemical and cellular processes
In the rest of this section, we describe the controlled vocabularies (CVs) used in SBGN Process Description Level 1
For certain predefined types of information having controlled vocabularies associated with them, SBGN defines specific prefixes that must be included in the label to indicate the type of information in question
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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