Use concise form for physical entity composites OMEX metadata files

[maxneal]

If there's a physical entity composite that uses a reference ontology term at the end of the composite physical entity, SemGen should use that entity's reference term URI in the final triple, not an instantiated local entity that bqbiol:is the URI.

[maxneal]

Addressed in several commits, including 0e7996b2c60f5fd61fd63e7847687779bef10ae4