Is it also possible to build an ontology with Jena API for example by Java coding in Eclipse? if yes what is the difference between making an ontology in Protege with making an ontology by Jena API in Eclipse?I am really confused about differences as I am not good in java programming. Lots of thanks
It depends on what you actually want to do. Are you trying to build a new ontology from scratch? Do you have an existing ontology that you want to extend by adding some data. Are you generating lots of triples using pre-existing classes and properties, based on some data you're already processing in Java?
Protege offers a GUI that allows you to create the ontology more quickly. It also gives you a graphical overview of the ontology in creation. It's sometimes hard to get the big picture even with all this help. It's a powerful tool for overall ontology authoring. Writing an entire ontology by scribbling Java code line-by line seems a gruelling task to me.
Writing plain Java code to create an onthology would be very difficult and inefficient. On top of the complexity of RDF itself, you'd need to understand the Jena API. IMO, it only makes sense if you have a well-defined ontology and you're really sure what kind of triples you want to add. In such case, using Java code to interface with some data source could save you a lot of time. Provided that you know Java itself to do it efficiently.
In your case, sticking with Protege seems the most reasonable option.