Open jpi-seb opened 10 months ago
This seems to be due to a change in the behaviour of the OWL API between 4.5.6 (used in Protégé 5.5) and 4.5.25 (used in Protégé 5.6).
I’ll have a closer look later, but my understanding (from OWL API tickets such as this one: https://github.com/owlcs/owlapi/issues/881) is that the behavourial change was intended and that the former behaviour was actually incorrect. I’ll check with the OWL API folks, but in the meantime I don’t think there is any possible workaround in Protégé itself.
We have just migrated from Protégé 5.5 to Protégé 5.6, and we detected a tricky bug in the serialization.
In our ontology, we have classes with
rdfs:subClassOf
axioms, which are annotated withrdfs:comment
using OWL 2 axiom annotations.With Protégé 5.5, no identifier was generated in this case, but now with Protégé 5.6 an identifier with the "genid" prefix is used in the serialization. See this example with the generated "genid1":
The problem we have is that when we add a new OWL 2 axiom annotations in our ontology, all the axiom annotations that follow the new one (in the order of the serialized file) are changed with a new "genid" (an offset in introduced for each genid).
See this example: result of the
git diff
command after introduction of a new axiom annotation (the previously generatedgenid1
is replaced bygenid3
):Our ontology is full of these annotations (hundreds of them), so at each new annotation introduced, git is polluted with a lot of these non-pertinent changes. Commits diff in git history become unreadeable, and merges between branches are now a lot more complex.
Is there a way to prevent this behaviour with Protégé 5.6 ?
You will find a full example in the ZIP file below :
tst0.rdf
is an small example ontology with OWL 2 axiom annotations, andtst1.rdf
is the same ontology with a new annotation added. Compare both files to see offsets in "genid". tst.zipThank you for your help !