From Protege Wiki
The XML back-end is still under development. Feedback on the Schema is strongly solicited. The schema should not be considered fixed at this point and users should not rely on this back-end functioning correctly or upon the schema remaining fixed from build to build. We do encourage you to try it out and report any problems that you see. Thanks!!
The XML back-end maintains the entire Protege knowledge base into an XML file. All information in the knowledge base is treated as "instances". There is a single XML Schema file that describes the format of these "instances". This file is available at: http://protege.stanford.edu/xml/schema/protege.xsd.
This back-end cannot be used to generate XML Schema files. It does not turn Protege classes into XML Schema complex types, for example. An export mechanism that does this will be developed separately.
The format of the "instances" in the XML file is designed to be simple, readable, and easily processable by XSLT in straightforward ways.