SBML2BioPAX

= 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:



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: .

End users
To run SBML2BioPAX you need.

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

Other known converters

 * Out-of-date SBML to BioPax XSL converter