OWL API, adding the URI and Name between <!-- --> without adding URI to other sections

Question

I am having an issue with the OWL API when trying to display the URI + Name between < !-- -- > without it also adding the URI+Name to other sections.

For instance, I am using the pizza ontology as my source and the ontology file shows the below set of code for individuals.

<!-- Individual: http://www.co-ode.org/ontologies/pizza/pizza.owl#America -->

<owl:Thing rdf:about="#America">
    <rdf:type rdf:resource="#Country"/>
</owl:Thing>

Using the code below I get pretty much the same thing but the URI is still missing from between the <-- #America-->, I can just add the iri+name to the getOWLClass method but that will end up giving me the URI+Name between the < !-- -- > and also on the namedIndividual i.e. rdf:about = http://www.co-ode.org/ontologies/pizza/pizza.owl#America instead of just #America.

 OWLClass tClass = dataFactory.getOWLClass(IRI.create("#Country"));
 OWLNamedIndividual tIndividual = dataFactory.getOWLNamedIndividual(IRI.create("#America"));
 OWLClassAssertionAxiom classAssertion = dataFactory.getOWLClassAssertionAxiom(tClass, tIndividual);
 manager.addAxiom(ontology, classAssertion);

Output:

<!-- #America -->

<owl:NamedIndividual rdf:about="#America">
    <rdf:type rdf:resource="#Country"/>
</owl:NamedIndividual>

What it is supposed to be:

<!-- http://www.co-ode.org/ontologies/pizza/pizza.owl#America -->

<owl:NamedIndividual rdf:about="#America">
    <rdf:type rdf:resource="#Country"/>
</owl:NamedIndividual>

What am I missing and how do I get it to look like the correct way like in the pizza ontology? I am using OWL API 4.0.

EDIT:

Based on Ignazio's suggestion I made a change with no success, here is the code. Again I am using the OWL API 4, the URI is still not being added to the comment < ! -- #America -- >.

 OWLClass tClass = dataFactory.getOWLClass(IRI.create("#Country"));
 OWLNamedIndividual tIndividual = dataFactory.getOWLNamedIndividual(IRI.create("#America"));
 OWLClassAssertionAxiom classAssertion = dataFactory.getOWLClassAssertionAxiom(tClass, tIndividual);
 XMLWriterPreferences.getInstance().setUseNamespaceEntities(true);
 OWLDocumentFormat format = m.getOntologyFormat(ontology);

 format.asPrefixOWLOntologyFormat()
    .setPrefix("ns:",
               "http://www.co-ode.org/ontologies/pizza/pizza.owl#");

 try
 {
     m.addAxiom(ontology, classAssertion);
     m.saveOntology(ontology, format, new SystemOutDocumentTarget());
 } catch (OWLOntologyStorageException e)
 {
     e.printStackTrace();
     System.exit(0);
 }

I am still pretty new to this, sorry if I am being redundant.

Output Still Without URI + #America in < ! -- #America -- >:

 <!-- #America-->

 <owl:NamedIndividual rdf:about="#America">
     <rdf:type rdf:resource="#Country"/>
 </owl:NamedIndividual>

Answer 1

You're trying to output relative IRIs in the RDF/XML. OWL API does not support that (except by actually creating entities with relative IRIs as you do in your code. However, the resulting ontology violates OWL 2 profiles).

You can get a similar result with entities:

XMLWriterPreferences.getInstance().setUseNamespaceEntities(true);
ontology.getFormat()
            .asPrefixOWLOntologyFormat()
            .setPrefix("ns:",
                    "http://www.co-ode.org/ontologies/pizza/pizza.owl#");

And save ontology at that point.