SBML2BioPAX

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Conversion from SBML to BioPAX

Introduction

About SBML
SBML is a machine-readable format for representing models. It's 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's framework is suitable for representing models commonly found in research on a number of topics, including cell signaling pathways, metabolic pathways, biochemical reactions, gene regulation, and many others. If you want to know more, you can read the Basic Introduction on SBML
About BioPAX
The main objective of the BioPAX initiative is to develop a data exchange format for biological pathways that is flexible, extensible, optionally encapsulated and compatible with other standards and can be widely adopted in a timely manner.


Documentation

You can see a summary of the conversion applied for the SBML elements on the following schema:

SBML2BioPAX.png

You can see in the figure above the mapping that is done by the converter between SBML classes and BioPAX classes. We are using the MIRIAM annotations present in the SBML model to improve the BioPAX file generated. Using a configuration file that map a MIRIAM URI to a BioPAX class, we can assign a more precise class (protein, smallMolecule, complex, rna or dna) to an SBML species. The same apply for the SBML reaction or the model element.

The BioPAX file generated is compliant with BioPAX Level 2 version 1 or BioPAX Level 3 version 1.

Information lost in the conversion
  • the mathematical formula (kineticLaws, events, rules, constraints, InitialAssignments, functionDefinitions, unitDefinitions, parameters)
  • any SBML Level 3 packages
  • sboTerm
  • notes
  • non RDF annotation


Download

You can download SBML2BioPAX here: sbfc-1.3.7.zip.

End users

To run SBML2BioPAX 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 BioPAX 2 AND 3
    # The output file(s) will be in the same folder as the SBML file(s) with an extension .owl
    # To convert specifically to either BioPAX 2 OR BioPAX 3, you can use the scripts: sbml2biopax2.sh or sbml2biopax3.sh.
    ./sbml2biopax.sh [file.xml | folder]

Developers

To compile SBML2BioPAX 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 SBML2BioPAX 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] googlegroups.com.

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] googlegroups.com.

Other known converters