BioPAX2BioPAXL3

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Conversion from BioPAX L1/L2 to L3

Introduction

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


Download

You can download the BioPAX2BioPAXL3 converter here: sbfc-1.3.7.zip.

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
    ./sbfConverter.sh BioPAXModel BioPAX2BioPAXL3 [file.owl | folder]

Developers

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] 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.