Changing "ends with" prefix to # doesn't stick unless you also manually set prefix in Active Ontology tab about protege

[matthewhorridge]

Reproduced this. The problem seems to be specific to saving and reloading an ontology in Turtle format. I'm not sure whether this is a Protege bug or an OWL API bug. A work around is to use a different format, for example RDF/XML for saving the ontology.

[matthewhorridge]

Another workaround is to make sure the ontology IRI is not a prefix for entity IRIs. So, if the ontology is named http://foo.com make sure entity IRIs do not have the http://foo.com prefix, e.g. http://bar.com won't exhibit this problem. Less than ideal but it's a work around.

[matthewhorridge]

Pasting in this from a user called Hyacinth,

This is one of the many bugs and malfunctions of OWLAPI pertaining to the default : prefix.

The reason why the problem emerges in your file is that the default : prefix is not defined by the # but by the / character:

Once you set the IRI of the new entities to be followed by the # character, every new entity will have a full IRI containing the # character. In this case, if there exists any prefix that abbreviates the ontology IRI followed by a # character, then the new entities will be saved by prefixed name using that specific prefix. But in the case of your file, there is no such prefix (The default : prefix is the ontology IRI followed by / and not #). The logical behaviour in this case is for OWLAPI to save the new entities by full IRI and not by prefixed name. However, OWLAPI incorrectly saves the new entities by prefixed name using the default : prefix which in fact defines the IRI by / character and not the # character. This is the reason why all of the entities will contain / instead of # in their IRIs when you open the ontology next time.

A quick fix is to change the default : prefix to end with # instead of the / character: