Could you tell me what are the main differences between JENA and OWL-API?
From the Apache Jena Website:
Apache Jena (or Jena in short) is a free and open source Java framework for building semantic web and Linked Data applications. The framework is composed of different APIs interacting together to process RDF data.
From OWL API Github:
The OWL API is a Java API for creating, manipulating and serialising OWL Ontologies.
Hence, Jena deals with RDF, while the OWL API deals with OWL.
What does this mean?
The short answer: Roughly you can see this as Jena dealing with data and the OWL API as dealing with structure. The parallel with relational databases is that the OWL API defines the schema and RDF the records.
The longer answer: For good explanations of the differences between OWL and RDF have a look at the answers of this SO question.