Hi, @jesus_barrasa ! Thanks for the reply.
We seek to provide an ontology both as a graph and as an OWL file keeping compatibility. Domain experts maintain the ontology in Protege, then we add changes to the graph.
And here is where the blank node problem stands. After the blank nodes obtain URIs Protege starts showing them in the class hierarchy window, which is not very handy.
Actually, I solved this problem by adding to my exporting script a functions that replaces strings like "bnode://generated_name" with "_:generated_name", and it works well.
Sorry for the late answer. My google mailbox dumped the notification to the spam folder for some reason.
And sorry for my English too :)