SBML2BioPax Outdated XSL

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Conversion from SBML to BioPax

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

This converter is not maintained any more, last updates are from 2007. The recommended converter to use is the new java version.

However, this converter should work on simple SBML L2V1 models.

SBML2BioPAX xsl.png

You can see in the figure above the mapping that is done by the converter between SBML classes and BioPax classes. This converter version was a bit basic and we could use the annotations to add more information to the biopax file, that is why we developed the java version.


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


Quick Setup

   To generate a BioPax file from an SBML model, run:

      Xalan MyModel_sbml.xml sbml2biopax.xsl > MyModel.owl

   You can download the XSL stylesheet in the section below.

Download


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