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Conversion between BioPAX and GPML


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.
About GPML
GPML (Graphical Pathway Markup Language) is simply an XML-based format. You can use it to define a pathway consisting of purely graphical elements (such as lines and shapes) or graphical elements with added biological information (such as genes, proteins and datanodes).


These converters aims to translate between BioPAX model and GPML, using the pathvisio-core library. For mode details about GPML, please refer to the documentation.


You can download the converters GPML2BioPAX and BioPAX2GPML and their jar dependencies here.

End users

These converters require java 1.6+. To run these converters, you have to copy all the jar files from the folder:

to the folder SBFC_core/lib.

To test the correct installation, you can type the scripts:

    # Print the list of available converters. GPML2BioPAX and BioPAX2GPML should be printed.
    # Print the list of available models. GPMLModel and BioPAXOldModel should be printed.

To run the converter, you can use the script with the usual syntax:

    # Convert a model from BioPAX to GPML
    ./ BioPAXOldModel BioPAX2GPML [file.owl | folder]
    # Convert a model from GPML to BioPAX
    ./ GPMLModel GPML2BioPAX [file.gpml | folder]

Please note that these converters use an old version of the BioPAX tools. The model for BioPAX is called BioPAXOldModel as it uses an old library, and it should not be confused with BioPAXModel, which is the default BioPAX model in SBFC_core.


To compile the package sbfc-pathvisio 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-pathvisio 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]