To convert many concept maps made in yEd to another format, I made some java bindings following these steps:
The ygraphml-specific part of the xsd files I used almost surely come from:
Am I allowed to also publish the code I have in a public repository? Under which terms can these xsd files be used?
Yes, you are allowed to publish the code in a public repository.
For further legal questions, please contact yWorks through the contact form on the yWorks website.