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: sbfc-1.3.7.zip.
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]
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.