Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

[protege-owl] Creating local repository for a project

Timothy Redmond tredmond at stanford.edu
Mon Aug 17 09:10:21 PDT 2009


I will give you a quick answer and try to look at this more later.   
The issue is that your ontology has a different xml base than its  
name.  The repository manager uses the xml base as a heuristic for  
finding the ontology with a given name and therefore does not find the  
desired ontology in the repository.  A workaround is to change the xml  
base but you will need to be a bit careful doing this (the obvious  
edit will also change the name of resources in the owl file).

This is an old Protege issue and it also exists in Protege 4.  (In  
Protege 4.1 it will go away because of changes to the OWL 2.0 imports  
specifications).  Fixing this is awkward.  Parsing the entire owl file  
to figure out the name will make the repositories very slow.   Some  
ontologies don't have an ontology declaration and some have several.   
Also in OWL 1.0, determining the name of an ontology by looking for  
the ontology declaration can be ambiguous and this has caused some to  
argue that the xml base is the real name of the ontology.

-TImothy


On Aug 14, 2009, at 3:57 AM, Marco Brandizi wrote:

> Hi all,
>
> I am working at an OWL file that imports (owl:imports) this:
>
>  http://swan.mindinformatics.org/ontologies/1.2/swan-alzheimer.owl
>
> and, transitively from the above, imports many other files from the  
> same
> URL (all located under 1.2/).
>
> Since I often work off line, I have downloaded all the .owl files  
> under
> the URL above into the swan/ directory and I am trying, during the
> project creation stage and after having disconnected my laptop, to  
> tell
> Protegé to use that directory as a local repository.
>
> Unfortunately it keeps telling me swan-alzheimer.owl is missing and it
> seems to completely ignore the repository selection part. I have tried
> many options: local directory repo, absolute dir repo, local/absolute
> file repo. It seems Protegé always looks at owl:imports and ignores
> everything else.
>
> Am I doing something wrong? Or is it a Protegé bug? It is being  
> quite a
> painful problem.
>
> -- 
>
> = 
> = 
> = 
> = 
> = 
> = 
> = 
> = 
> = 
> ======================================================================
> Marco Brandizi brandizi a-t ebi ac_uk>
>
> NET Project - Software Engineer
> http://www.ebi.ac.uk/net-project
>
> European Bioinformatics Institute
> Hinxton, CB10 1SD, United Kingdom
> Office A3141
>
> Tel.: +44 (0)1223 492 613
> Fax: +44 (0)1223 492 620
>
> http://www.ebi.ac.uk/~brandizi
>
> _______________________________________________
> protege-owl mailing list
> protege-owl at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/protege-owl
>
> Instructions for unsubscribing: http://protege.stanford.edu/doc/faq.html#01a.03




More information about the protege-owl mailing list