Tagged values from the UML model are not forwarded 
correctly into the MOF model. This is because, for 
example, Poseidon generates something like:

<UML:TaggedValue xmi.id = 'a53'
    isSpecification = 'false'
    dataValue = 'edu.stanford.smi.protegex.xmi'>
    <UML:TaggedValue.type>
        <UML:TagDefinition xmi.idref = 'a54'/>
    </UML:TaggedValue.type>
</UML:TaggedValue>

<UML:TagDefinition xmi.id = 'a54' 
    isSpecification = 'false' 
    tagType = 'javax.jmi.packagePrefix'>
      <UML:TagDefinition.multiplicity>
        <UML:Multiplicity xmi.id = 'a244'>
          <UML:Multiplicity.range>
            <UML:MultiplicityRange xmi.id = 'a245' 
                lower = '1' upper = '1'/>
          </UML:Multiplicity.range>
        </UML:Multiplicity>
      </UML:TagDefinition.multiplicity>
    </UML:TagDefinition>

which is not handled by the mapTags method in Transformer 
(which expects every tag to have a name). Apparently, MOF 
either allows taggedValues to have a name or a type.

If have attached a new version of Transformer.java, where 
I modified the mapTags method (including a new helper 
method), that works well for my system. Now I get the 
packagePrefix and other tags correctly in the MOF.