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[protege-discussion] Protege db schema conversion

Timothy Redmond tredmond at
Mon Dec 3 12:37:36 PST 2012

My first reaction was that I am not sure what is wrong but perhaps 
getting some clarification on parts of the message will help me figure 
out what is wrong.

On 11/28/12 3:17 PM, Todd Detwiler wrote:
> Through the life of Protege as a tool, the database schema has 
> undergone a few changes. As far as I know, the best approach for 
> upconverting the schema of a database ontology has always been to 
> first export it to clips (in an older Protege version) and then open 
> that clips file in a newer Protege version and then save it out to a 
> db. This has worked for us reasonably well in the past (we have an 
> ontology for which the developers still use an old Protege version). 
> But lately this isn't working well any more. I can still successfully 
> write out our ontology to clips files. Newer versions of Protege (i.e. 
> 3.4.7, 3.4.8, and 3.5beta) can open the clips file and things look OK. 

This makes it sound like you have successfully converted the database 
project to a clips project.  I am also assuming from this description 
that you are using Protege frames and not Protege OWL.

> But when I try and save it out to a db, things go wrong. The resultant 
> db, in the Protege UI, looks like all of our classes are untyped 
> (nothing in the right hand pane). 

It sounds like you have taken a valid clips backed Protege frames 
project, converted it to a Protege Database project (not a OWL/RDF 
Database) project.  After doing the conversion, it sounds like the 
database project does not look the same as the clips backed project.  If 
so, it sounds like this is where the problem occurred. Did you use one 
of the supported datablases (mysql or postgres)?  Is it possible to send 
us the ontology so that we can try it out?

> Also, lots of leaf classes appear to be missing in the tree. Now, if I 
> query the database, these classes exist and have types.

Are you talking about sql queries here?

> Further, if I open the new database ontology in Protege 3.4beta, it 
> looks fine. 

So the new database project looks fine in one version of Protege 
(3.4.*?) but not in another one (3.5?)?  I believe that the database 
backend format should be identical between the later 3.4 versions and 
the 3.5 version.


> What changes have occurred in the database backend, since 3.4beta, 
> that could be causing this?
> Thanks,
> Todd

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