1) Not generating valid OWL for annotations - i've seen it for DbXref, Synonym, Definition
<rdfs:label xml:lang="en">xylem mother cell</rdfs:label>
i see that you're asserting
but you'll have to name the individuals unless you make explicit class expressions, although i've never tried to build something with annotations, and not having looked into it, i don't know if it will work.
2) Do not include "Obsolete Class"/"Obsolete Property" in the OWL ontology. If you think it is necessary - then use the proper OWL class assertions
Assistant Professor of Bioinformatics