I wanted to know if there is a way to take xml files from KEGG and be able to add proteins in a pre-existing group in the pathway, then save that in a new xml file that retains the existing xml information with the new changes. I've been running into trouble with being able to save the xml files using KEGGscape or CytoKegg apps in Cytoscape. I end up with missing information, such as group id.
I'm trying to work with some xml files in KEGG to make changes that incorporate information (i.e. specific proteins) that isn't included in the pathway, but might be useful for my own needs. I want to analyze and compare the differences later on using the original xml files as a base of comparison.