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Conversion from BioPAX L1/L2 to L3


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.


This converter upgrades a BioPAX model from Level 1 or 2 to Level 3.


You can download the BioPAX2BioPAXL3 converter here:

End users

To run the BioPAX2BioPAXL3 converter you need java 1.6 or higher. After unpacking the zipped file, move to the folder that have been created and run:

    # Convert BioPAX L1/L2 (any *owl files if you put a folder) to BioPAX L3
    # The output file(s) will be in the same folder with extension .owl
    ./ BioPAXModel BioPAX2BioPAXL3 [file.owl | folder]


To compile BioPAX2BioPAXL3 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 SBFC 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]