jUDDI is designed to allow different persistence (datastore) implementations to be "plugged-in". jUDDI's default DataStore implementation attempts to support as many of the mainstream DBMS's as possible (Oracle, DB2, Sybase, MySQL - even HSQLdb). If you're interested in using something other than JDBC or if you want to take advantages of proprietary features of your RDBMS (i.e. using stored procedures to improve performance) then you will need to develop your own datastore implementation.
juddi.datastore = org.apache.juddi.datastore.jdbc.JDBCDataStore
To create your own DataStore you'll need to create a new implementation of the DataStore interfaces which you'll find in the org.apache.juddi.datastore package and make a change to the jUDDI properties file to use your new DataStore implementation (i.e. the judd.dataStore property) instead of the one supplied.
The jUDDI properties file is located in the WEB-INF/classes directory. In the example above you'll need to replace org.apache.juddi.datastore.JDBCDataStore with the fully qualified name of your DataStore implementation. Remember to restart the jUDDI web application for this change to take effect. Take a look at the the JDBCDataStore class in the org.apache.juddi.datastore.jdbc package for an example.