LibSBGN
The main goal of the LibSBGN project is to provide a standard electronic implementation for the Systems Biology Graphical Notation (SBGN). The project develops both:
- a standard exchange format: SBGN-ML and
- software libraries for reading SBGN-ML documents
On this page you will find information about:
- SBGN-ML files
- Software supporting SBGN-ML
SBGN-ML files
For SBGN-ML we decided on using a basic XML representation of glyphs and connecting arcs.
<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<sbgn xmlns="http://sbgn.org/libsbgn/0.2">
<map language="process description">
<glyph id="glyph9" class="macromolecule">
<label text="hexokinase"/>
<bbox y="40.0" x="170.0" h="60.0" w="120.0"/>
</glyph>
<glyph id="glyph0" class="simple chemical">
<label text="glucose"/>
<bbox y="140.0" x="90.0" h="60.0" w="60.0"/>
</glyph>
...
<arc target="glyph8" source="glyph9" class="catalysis">
<start y="100.0" x="230.0"/>
<end y="160.0" x="230.0"/>
</arc>
<arc target="glyph8.1" source="glyph0" class="consumption">
<start y="170.0" x="150.0"/>
<end y="170.0" x="210.0"/>
</arc>
</map>
</sbgn>
Example files are available on source forge:
http://libsbgn.svn.sourceforge.net/viewvc/libsbgn/trunk/example-files/
each file is stored with an accompanying image.
Software supporting SBGN-ML
Software support for SBGN-ML is steadily growing. The libSBGN project provides a Java and a C++ library based on code generation from the SBGN-ML schema. The Java library is used by:
 VANTED (SBGN-ED) http://vanted.ipk-gatersleben.de/addons/sbgn-ed/ |
Another implementation is available through SBMLLayout, and is available for use with the Systems Biology Workbench or online.
 Systems Biology Workbench http://sf.net/projects/sbw/files |
 Render Comparison http://sysbioapps.dyndns.org/RenderComparison |
More information
For further information see also the libSBGN development page at sourceforge: http://libsbgn.sf.net