SBGN-ML Import Export Plug-In

The SBGN-ML Import/Export Plug-In allows to import and export files in the Systems Biology Graphical Notation format SBGN-ML.

After installation, the plug-in functionality is available in opening files as well as when importing or exporting the network model. The corresponding file dialogs allow to select Systems Biology Graphical Notation files (file name suffix *.sbgn).

The SBGN notation provides different diagram types. The plug-in is only capable to load process diagrams. Therefore, the SBGN files map tag must provide the attribute "language" that must be "process description":

<map language="process description">

The map tag contains glyph tags and arc tags representing entities and connections. Both tags provide the attribute "class" that describes the meaning of the glyph.
Glyphs of class "simple chemical", "simple chemical multimer" as well as "source and sink" are interpreted as metabolite in Omix.
Glyphs of class "process", "omitted process" and "uncertain process" are interpreted as reactions.
A Glyph of class "compartment" leads to an Omix compartment.
Glyphs of all other classes are represented as graphics node in the Omix diagram.

The arc classes "consumption" and "production" are interpreted as flux edges. All other arcs are represented as graphics edge in the Omix diagram.