For accessing ontology data, you can use Jena, OWL API... Not sure if this is the tools you are looking for

No, I do not ... I do not mean that. Those are API for working with ontologies, I refer to those known as OBDA Framework (data access based on ontology). I need to use one of them to manipulate an ontology with a lot of instances. The API you mention become ineffective to the extent that grow the number of instances in the ontology, what is recommended is to store the instances in a database and let the taxonomy and the rest of the components in the ontology.

Greetings.

OK. I am facing the same problem. I am trying to use graph database for this purpose. You might want to explore tools like Sesame, Neo4j, and InfiniteGraph and query ontologies using SPARQL.

Would love to discuss with you more.

Cheers

Ontop 

"-ontop- is a platform to query databases as Virtual RDF Graphs using SPARQL. It's extremely fast and is packed with features."

http://ontop.inf.unibz.it

I created a SPARQL endpoint using ARC2 and query the ontology.

Jena ontology api

https://jena.apache.org/documentation/ontology/

TaKe a look!

http://d2rq.org/d2r-server