Yes. When you insert a sequence you must be prepared that when inserting its ontology term or tag/value annotation the term may already be present because another bioentry uses it too.
Ok, the proper way is to catch the SQLException in BIOSQLFeature, test if it is a Dublicate key entry, get the identifier of the term (would that be the BioSQLfeatureId ?) and insert it in the term_relationship table? And there is no nice BioJava method for this, I have to do it "manually", like conn.prepareStatement(..) and stuff? BioJava spoiled me so!
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