I am trying to develop a semantic web application using:
like in this article but I think this will only work with "select" statements. is there anyway to develop a semantic web application can offer full CRUD operations on my ontology? should I use some triple store to host the ontology instead of working with Jena?
It's hard to answer your question with specific details since it is so general, but basically, ontologies are graphs just like any other graph.
So if your application supports SPARQL Update queries, there should be no problem in updating your ontology through your application directly.
A quick word of warning though. The ontology is the closest thing to a "model" that semantic applications use. If you plan to change your ontology on-the-go, you have to make sure that the rest of your knowledge base stays consistent with your changes.
For instance, if you delete a class from the ontology, then you have to make sure that you have no instances of that class in the knowledge base. Otherwise, your knowledge base will contain triples referring to classes or predicates that might not exist anymore.