Hi Benjamin,
I don't know whether the behavior has been changed recently, but it at least used to be that blank node structures could be deleted normally through VIVO's RDFService (that is, any deletion being done through VIVO rather than directly against the triple store). The RDFService should convert the blank node labels into corresponding variables in query patterns whose matching triples are then removed.
If you're using the Harvester directly against the triple store, you won't get this extra fuctionality. That said, I can't think of any reason why the academicDegree.rdf file should have any blank nodes. (Usually they occur -- by necessity -- only in ontology files that include things like restrictions and other anonymous classes.)
Brian
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