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Conversion from SBML to SBGN ML


About SBML
SBML is a machine-readable format for representing models. It is oriented towards describing systems where biological entities are involved in, and modified by, processes that occur over time. An example of this is a network of biochemical reactions. SBML framework is suitable for representing models commonly found in research on a number of topics, including cell signalling pathways, metabolic pathways, biochemical reactions, gene regulation, and many others. If you want to know more, you can read the Basic Introduction on SBML.
SBGN ML offers a standard graphical language for representing biological processes and interactions. To know more, you can read the SBGN-About page.


The converter is based on JSBML, so support all the levels and versions of SBML until SBML level 3 version 1 core. When present the RDF annotations or the SBO terms are used to determine which SBGN glyph to use in the graph.

[[File:]] For notes, please visit GitHub Wiki

[[File:]] For notes, please visit GitHub Wiki

Information lost in the conversion
  • Most of the mathematical parts of the SBML model are ignored, only the reaction network is exported.
  • FunctionDefinition,UnitDefinition,Parameters,InitialAssignment,Rule,Constraint,Event
  • Attributes of Species, Reaction, Compartment, SpeciesReference, and ModifierSpeciesReference


You can download SBML2SBGNML by downloading on sourceforge.

End users

To run SBML2SBGNML you need java 1.6 or higher.

After unpacking the zipped file, move to the folder that have been created and run:

    # Convert SBML (any *.xml files if you put a folder) to SBGN-ML
    # The output file(s) will be in the same folder as the SBML file(s) with an extension .xml
    ./ [file.xml | folder]


To compile SBML2SBGNML from source, you also need Apache Ant 1.6.5 or higher.

After editing the source code you can build the jar file by just typing in the SBML2SBGNML folder:

    # Generate the jar file
    ant jar

    # Generate the java documentation
    ant javadoc

Getting Help and Support

In case you discover a bug within SBFC or request new features, please let us know. There are two dedicated trackers:

For general discussions about SBFC, please use the forum:

sbfc-forum [at]

If you need further support or you wish to develop new modules in SBFC you can contact the team using the following e-mail address:

sbfc-devel [at]

Conversion from SBGN ML to SBML


Information lost in the conversion
  • The source and target reference of an Arc