Abstract
AbstractThe recently proposed Systems Biology Graphical Notation (SBGN) provides a standard for the visual representation of biochemical and cellular processes. SBGN helps to communicate biological knowledge more efficient and accurate between different research communities in the life sciences. However, to support SBGN, methods and tools for editing, validating, and translating of SBGN maps are necessary.We present methods for these tasks, the tool SBGN-ED, and an application example. SBGN-ED allows to create all three types of SBGN maps from scratch, to validate these maps for syntactical and semantical correctness, to translate maps from the KEGG and MetaCrop databases into SBGN, and to export SBGN maps into several file and image formats.
Highlights
The Systems Biology Graphical Notation (SBGN) Process Description notation shows the temporal courses of biochemical interactions in a network
The SBGN Process Description notation shows the temporal courses of biochemical interactions in a network
The SBGN Activity Flow notation shows the flow of information between biochemical entities in a network
Summary
The SBGN Process Description notation shows the temporal courses of biochemical interactions in a network. It can be used to illustrate all the molecular interactions taking place in a network of biochemical entities, with the same entity appearing multiple times in the same map. The SBGN Entity Relationship notation allows to see all relationships in which a given entity participates, regardless of temporal aspects.
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