Systems Biology Graphical Notation (original) (raw)

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Welcome to the global portal for documentation, news, and other information about the Systems Biology Graphical Notation (SBGN) project, an effort to standardise the graphical notation used in maps of biological processes.

Cool visualisation

Exact meaning of all symbols

Below, the same biological system (Le Novère, 2015, doi:10.1038/nrg3885) is shown in different languages of SBGN: Activity Flow (AF), Process Description (PD) and Entity Relationship (ER).

Representations

Exchange and storage format SBGN-ML and software library

Various tools can export an import SBGN visualization in the XML-based file format SBGN-ML. SBGN-ML can be processed and generated by the standard library LibSBGNOne can compare the rendering of SBGN-ML by different software packages on the LibSBGN Render Comparison site.

Databases visualizing pathways as SBGN: Reactome*, PANTHER Pathway*, BioModels database,Pathway Commons*, Atlas of Cancer Signalling Networks*, Path2Models*, and more (*exporting SBGN-ML).

Modeling software that draw PD diagrams: CellDesigner, BioUML.

Editors that draw SBGN diagrams and export/import SBGN-ML: KrayonForSbgn (PD), Newt Editor (PD, AF), Vanted/SBGN-ED (PD, AF, ER), PathVisio (PD, AF, ER), yEd/ & ySBGN (PD, AF), and more.

Tools that convert different formats to SBGN: ChiBE (BioPAX → SBGN),KEGGtranslator (KEGG-ML → SBGN), CySBGN (SBML → SBGN), SBGNTikZ (LaTex → SBGN), and more.

Tools that visualize PD diagrams: BIOCHAM, COPASI, JWS Onlineand more.

SBGN is the work of many people. It would not have been possible without the generous support of multiple organizations over the years, for which we are very thankful.