Extract a fraction of an ontology that is expressed by OWL-Full

I have an ontology expressed in OWL-Full, however, I need a subset of this ontology in the OWL-QL profile. In other words, I want to remove all axioms that violate the OWL-QL. I wonder if there is a tool for that.

You can use the org.semanticweb.owlapi.profiles.Profiles enumeration to choose the profile you wish your ontology to conform to.

OWLProfileReport report = Profiles.OWL2_QL.checkOntology(ontology)

This will return an OWLProfileReport. It contains all the violations found. For each violation, you can either remove the axiom it references from the ontology:

for (OWLProfileViolation v : report.getViolations()) {
    if (v.getAxiom() != null) {
        // OWLAPI 5 for this
        ontology.removeAxiom(v.getAxiom());
        // OWLAPI 4 for this
        ontology.getOWLOntologyManager().removeAxiom(ontology, v.getAxiom());
    }
}

or collect the repair changes from the violations (a list of changes to apply to the ontology to fix the violation) and then apply the changes.