You can build a web service server using Tomcat. Using Tomcat you can write applications able to manage your ontology writing java code (and so, exploiting the existing java libraries to interface your ontology).

I hope I have answered your question

You can provide access by exposing your ontology through a end-point. End points are typically urls. And in return when accessing this ontology we write that end-point in namespce. Search for "how to expose ontology or rdf using protege"

I agree with Dario: using a Tomcat server enables you to expose different aspects of the ontology in a seamlessly way as most of the APIs and reasoners usually used to handle ontologies are developed in Java.

Thank you all for your helpful suggestions. I found ARC 2 - An Easy RDF and SPARQL for LAMP systems to expose the endpoints.

(https://github.com/semsol/arc2/wiki )

As the rest of our system was build using LAMP, PHP and MqSQL getting ARC2 working with the rest of the system was very easy. You can try our end point at

f.using.net/arc2

This is an agriculture knowledgebase for farmers.

Our Agriculture Ontology was developed using protege. We find it takes a very long time to populate it with NamedIndividual.

Does anyone know a better method to add large number of NamedIndividuals to an ontology developed with protege ?

Depending on the objective of the ontology in your system, I wouldn't recommend you to include all the instances in the ontology, but the most needed ones. Take into account that after including them all, you may also have to state that they are all different individuals (Protegé allows to do it automatically) due to the Open World Assumption. This includes a lot of axioms to the reasoning process, leading to a much more expensive procedure (as a general rule, reasoning with A-Boxes is usually more expensive than just with T-Boxes).

@Athula

FYI also Fuseki (http://jena.apache.org/documentation/serving_data/), which is part of the Apache Jena project, can give you a hand in this.