Parse one OWL API axiom in context of an existing OWLOntology

I'm not familiar with the OWL API, but from a quick scan of the JavaDoc for OWLOntology, it seems that the interface is "immutable". There is only getters, no set or add methods. In this case, you'll need to do some form of concatenation to a third object (whether serialising and deserialising is the best way to concatenate, I'm not sure).

However, there is a subinterface OWLMutableOntology which adds methods to change an ontology. In that case, you have two applyChange* methods that will take OWLAxiomChange objects. In other words, if your objects implement that subinterface, you can modify the ontology directly.

You'll probably have to set up an instance of OWLFunctionalSyntaxParser and use it to parse the string. Feed it with a StringReader. See OWLFunctionalSyntaxOWLParser (note slightly different name!) for how to invoke and run it.

(I haven't tried this, but have created parsers myself with JavaCC, the library used here to generate the parser code.)