==== Explanation ====

This is the worse case because EquivalentClasses is one of the kinds
of axioms where annotations have to be repeated for each triple
generated, and because we have an annotation on an annotation, which
always triggers reification of the second level annotation. To
compare, first is the ontology and expansion without annotations, then
ontology with annotations and expansion.

References:
http://www.w3.org/2007/OWL/wiki/Syntax
http://www.w3.org/2007/OWL/wiki/Mapping_to_RDF_Graphs

Code:
http://svn.mumble.net:8080/svn/lsw/trunk/owl/owl2/
(princ (t-rdf (parse-functional-syntax <string>)))

Caveat: I've made some effort to verify that the translations are
correct but there's always the possibility I've got something
wrong. Let me know: alanruttenberg@gmail.com

==== Ontology without annotations ====

Prefix (ex:=<http://example.com/>)
Prefix (rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
Ontology(ex:foo 
EquivalentClasses( ex:bar  ex:baz ObjectComplementOf(ex:quux))
        )

<rdf:RDF
    xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
    xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
    xmlns:owl="http://www.w3.org/2002/07/owl#"
    xmlns:ex="http://example.com/">
  <owl:Ontology rdf:about="http://example.com/foo"/>
  <rdf:Description rdf:about="http://example.com/bar">
    <owl:equivalentClass>
      <rdf:Description rdf:about="http://example.com/baz">
        <owl:equivalentClass>
          <owl:Class>
            <owl:complementOf rdf:resource="http://example.com/quux"/>
          </owl:Class>
        </owl:equivalentClass>
      </rdf:Description>
    </owl:equivalentClass>
  </rdf:Description>
</rdf:RDF>

==== Ontology with annotations ====

Prefix (ex:=<http://example.com/>)
Prefix (rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
Ontology(ex:foo 
EquivalentClasses( Annotation( Annotation(rdfs:comment "something about labeling as foo") rdfs:label "foo") 
                   ex:bar  ex:baz ObjectComplementOf(ex:quux))
        )

<rdf:RDF
    xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
    xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
    xmlns:owl="http://www.w3.org/2002/07/owl#"
    xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
    xmlns:ex="http://example.com/">
  <owl:Ontology rdf:about="http://example.com/foo"/>
  <owl:Class rdf:nodeID="A0">
    <owl:complementOf rdf:resource="http://example.com/quux"/>
  </owl:Class>
  <owl:Annotation>
    <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
    >something about labeling as foo</rdfs:comment>
    <owl:object rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
    >foo</owl:object>
    <owl:predicate rdf:resource="http://www.w3.org/2000/01/rdf-schema#label"/>
    <owl:subject>
      <owl:axiom>
        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
        >foo</rdfs:label>
        <owl:object rdf:nodeID="A0"/>
        <owl:predicate rdf:resource="http://www.w3.org/2002/07/owl#equivalentClass"/>
        <owl:subject>
          <rdf:Description rdf:about="http://example.com/baz">
            <owl:equivalentClass rdf:nodeID="A0"/>
          </rdf:Description>
        </owl:subject>
      </owl:axiom>
    </owl:subject>
  </owl:Annotation>
  <owl:Annotation>
    <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
    >something about labeling as foo</rdfs:comment>
    <owl:object rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
    >foo</owl:object>
    <owl:predicate rdf:resource="http://www.w3.org/2000/01/rdf-schema#label"/>
    <owl:subject>
      <owl:axiom>
        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
        >foo</rdfs:label>
        <owl:object rdf:resource="http://example.com/baz"/>
        <owl:predicate rdf:resource="http://www.w3.org/2002/07/owl#equivalentClass"/>
        <owl:subject>
          <rdf:Description rdf:about="http://example.com/bar">
            <owl:equivalentClass rdf:resource="http://example.com/baz"/>
          </rdf:Description>
        </owl:subject>
      </owl:axiom>
    </owl:subject>
  </owl:Annotation>
</rdf:RDF>