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[p4-feedback] Protege 4.1 import URI resolution

Samson Tu swt at
Mon Apr 19 16:57:20 PDT 2010

Yes, I use Dropbox, an internet-based software for synchronizing files 
across multiple machines. After deleting the catalog.xml file as you 
suggested, I was able to open the ontologies in Protege 4.1. Now I can 
report that the problem I have with the class depth displayed by OWLviz 
occurs in Protege 4.1 as well.

Thank you.

With best regards,

On 4/19/2010 2:43 PM, Timothy Redmond wrote:
> On 04/19/2010 12:56 PM, Samson Tu wrote:
>> Hi,
>> I have a collection of OWL ontologies that load without any problem 
>> in Protege 4.0x, but when I tried to load it with Protege 4.1, I got 
>> "file not found error."
>> I see that the file of an imported ontology study_examples has been 
>> resolved to "file:/Users/tu/Dropbox/OCRE/trunk/study_examples.owl" 
>> which is the correct file path for my Mac at home. However, I am 
>> using a Windows workstation. Where is Protege 4.1 getting the path 
>> information, and why does Protege 4.0 behaves correctly but Protege 
>> 4.1 doesn't?
> This is a bug that has been fixed in the latest svn but perhaps not in 
> the latest update.  I need to send another update in soon anyway 
> because there have been several improvements.  (Actually I think that 
> I will push for a new build when Jennifer gets back.)
> I believe that the invalid path information is coming from a 
> catalog.xml file (which is like the old .repository files except it is 
> a standard).   My guess is that you are synchronizing the two machines 
> using some kind of synchronization software?  Unfortunately I was 
> putting absolute addresses in the catalog.xml file when I didn't need 
> to and I was not checking for files that had been deleted.  I will try 
> to push an update soon but deleting  the calalog.xml will probably fix 
> the problem.  I will have to think about whether there are other 
> problems with synchronization that I will have to solve.
> This is new to Protege 4.1 because it is an attempt to deal with the 
> change from import by name to import  by location change in OWL 2.0.  
> XML catalogs are an industry standard way of redirecting references 
> made by an xml catalog to external resources.
> -Timothy

Samson Tu                                   email: swt at
Senior Research Scientist                   web:
Center for Biomedical Informatics Research  phone: 1-650-725-3391
Stanford University                         fax: 1-650-725-7944

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