You can use SPARQL query language to query directly the ontology.

yes that i already had done..but need to save in database for communication with some user interface..

is it possible to attach some how any ui which can communicate with protege in SPARQL?

Use Jena+Java.

Using Jena OWL API (http://jena.apache.org/documentation/ontology/) you can read the OWL file and parse it. After that, use Java to insert the values to any database you want. I have done the same approach before and it worked!

The ontology can be saved on the disk or memory.  Then, you have to use what we call a triplestore.  The later is a database management system for RDF triples.  After that, you can query the database which is composed of Ontology + instances.  A triplestore contains also a set of reasoning systems.   The list of available triplestore can be found in :

http://www.w3.org/wiki/LargeTripleStores

check the link if it could be of any use to you

http://protegewiki.stanford.edu/wiki/Working_with_the_Database_Backend_in_OWL

Thanks everybody i will try each approach..

i tried with protege 3.4 where it is mentioned in interface itself save file in database format but not working some "jdbc classpath name doesnot exist" error is occuring