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[protege-discussion] DISPLAY_SLOT problem

William Bug William.Bug at DrexelMed.edu
Fri Mar 16 00:33:12 PDT 2007


Thanks for the feedback, Tania.

Please see comments inline below.

Cheers,
Bill

On Mar 14, 2007, at 7:48 PM, Tania Tudorache wrote:

> Hi William,
>
> William Bug wrote:
>> Just to clarify the issue for the curious on this list who may  
>> have read it, I do believe I understand what the outcome of  
>> setting any AnnotationProperty to the DISPLAY_SLOT should be  
>> across several Protege-OWL features. My problem comes down to the  
>> behavior being different when I set the "LANG" attribute for that  
>> AnnotationProperty as opposed to when the LANG attribute is left  
>> unset.  When unset, the behavior of several Protege-OWL features  
>> to setting an AnnotationProperty other than :NAME or rdfs:label to  
>> the DISPLAY_SLOT is as it should be according to my  
>> understanding.  When the LANG attribute is set for a given class -  
>> to any value, as far as I can tell from my ad hoc testing - then  
>> the value of that AnnotationProperty for that class is not as  
>> advertised.
>
> It would help if you could give me an example from the ontologies  
> that you have sent in your previous post. If there is a bug in the  
> display text of classes when the language is set on the browser  
> slot, we should fix it.
>
>
>>
>> Regarding the protege:defaultLanguage ontology meta-data  
>> AnnotationProperty - thanks for pointing out the inconsistency  
>> across our ontology files (the BIRNLex ontology is modularized  
>> into a collection of OWL files imported according to a specified  
>> hierarchy).  This property turned out to be causing a few problems  
>> with various aspects of the integration of the modules.  I tried  
>> to fix those problems by including this property in each of the  
>> OWL files and setting it to the same value (either 'en' or the  
>> more proper according to DC specs 'us-EN').  Neither worked.  If I  
>> removed this property from ALL the OWL files, then the import- 
>> related problems did go away.
>>
>
> I forgot to mention that you should set the protege:default  
> language only on the top level ontology, so on the ontology that  
> imports the others. Otherwise, the display text may not work  
> correctly. I think this is also documented on the wiki.
>
> And another thing that I have not tested before is setting the  
> language to "us-EN" rather than just "en". I am not sure that this  
> works in Protege. You should try first to set the default language  
> to "en" and see if it works that way.

Yes - this was at the root of the problem.  I figured it out about a  
week ago with help from Trish Whetzel on the OBI project.  Once I set  
the protege:defaultLanguage for the root ontology to "en", then the  
DISPLAY_SLOT assignment worked just fine.

The only thing I'd add is the Wiki writeup (http://protege.cim3.net/ 
cgi-bin/wiki.pl?HidingIdentifiersWithLabelsInOWLPlugin - which I'd  
seen before but had forgotten about), has one issue that could use to  
be cleared up for future users directed to it.  The behavior as  
described on that page is not quite correct.  Item 4.3.2 is not the  
way things work.  4.3.1 and 4.3.3 are working as advertised, but not  
4.3.2.  It's possible if all the classes in all the ontologies  
imported via BIRNLex-Main had the LANG attribute for their rdfs:label  
property set to 'en', then things would work as described in 4.3.2.   
But this isn't true for some of the external ontologies we import  
(e.g., OBI), so it's not really possible to test that right now.  If  
having all the LANG attributes of the selected DISPLAY_SLOT  
AnntotationProperty set to a single language value IS a requirement,  
this should probably be stated on the page.

Thanks again for passing on these valuable pointers.

By the way, the current root BIRNLex OWL file is available at:
	http://www.nbirn.net/birnlex/1.2/BIRNLex-Main.owl

If you create a dummy Protege-OWL project, import that BIRNLex- 
Main.owl file using that URL, then set the DISPLAY_SLOT to rdfs:label  
as described on that Wiki page (protege:defaultLanguage is now set to  
'en' in BIRNLex-Main.owl, so you don't have to do that), then you can  
see all the classes in BIRNLex-Main and the several OWL files it  
imports assigned the rdfs:label in the Class Browser.

>
>
> Tania
>
>> Thanks for redirecting me to the proper list.
>>
>> Cheers,
>> Bill
>>
>> On Mar 9, 2007, at 11:26 AM, Tania Tudorache wrote:
>>
>>> William,
>>>
>>> The browser slot is working fine in the OWL ontologies that you  
>>> have given as example. What version of Protege did you use? We  
>>> recommend that you use the latest release 3.2.1.
>>>
>>> If you set the browser slot to another slot than the name or  
>>> rdfs:label, for example, core:pref-label, then the same rules for  
>>> computing the browser text apply as the ones for rdfs:label and  
>>> name. I just tested that and it works in Protege 3.2.1.
>>>
>>> One thing that I've observed in your ontologies, was the the  
>>> protege:defaultLanguage was set to "en-US" instead of just "en".  
>>> Maybe that was the problem.
>>>
>>> Please ask in future OWL related questions on the OWL mailing list.
>>>
>>> Thanks,
>>> Tania
>>>
>>>
>>>
>>> William Bug wrote:
>>>> Sorry to be posting this a second time, but I'm in the midst of  
>>>> a meeting, where it would be really good to be able to display  
>>>> the "preferred labels" for all the classes in our OWL files.
>>>>
>>>> Am I getting something wrong here?  Can other folks pick a class  
>>>> annotation property as the DISPLAY_SLOT and get it to display in  
>>>> the class browser as the class name regardless of whether the  
>>>> LANG attribute is set to 'en' for that property or not?
>>>>
>>>> Many thanks ahead of time for any assistance others can provide  
>>>> in solving this problem.
>>>>
>>>> Cheers,
>>>> Bill
>>>>
>>>>
>>>>
>>>> On Mar 8, 2007, at 1:22 AM, William Bug wrote:
>>>>
>>>>> Dear Protege Support folks,
>>>>>
>>>>> We have been having difficulty using the rdfs:label field as a  
>>>>> DISPLAY_SLOT, when the language attribute is set to "en".  For  
>>>>> classes where language is left blank, that field value is used  
>>>>> as the display name.
>>>>>
>>>>> Is this the expected behavior, when setting the DISPLAY_SLOT to  
>>>>> a field other than the class :NAME?  I don't know whether this  
>>>>> matters, but this for an imported ontology, but I see the same  
>>>>> behavior for classes that exist within the OWL file itself.
>>>>>
>>>>> If you would likely to examine this directly both of these  
>>>>> ontologies are available online:
>>>>> main ontology file:  http://www.nbirn.net/birnlex/1.2/BIRNLex- 
>>>>> Investigation.owl
>>>>> imported file: http://obi.sourceforge.net/ontology/OBI.owl
>>>>>
>>>>> I've attached two screen shots below demonstrating what I  
>>>>> mean.  These are illustrative examples, but this behavior is  
>>>>> observed across the entire ontology.
>>>>>
>>>>> Many thanks for your help with this issue.
>>>>>
>>>>> Cheers,
>>>>> Bill
>>>>>
>>>>> <Picture 15.png>
>>>>> <Picture 16.png>
>>>>>
>>>>>
>>>>>
>>>>> Bill Bug
>>>>> Senior Research Analyst/Ontological Engineer
>>>>>
>>>>> Laboratory for Bioimaging  & Anatomical Informatics
>>>>> www.neuroterrain.org
>>>>> Department of Neurobiology & Anatomy
>>>>> Drexel University College of Medicine
>>>>> 2900 Queen Lane
>>>>> Philadelphia, PA    19129
>>>>> 215 991 8430 (ph)
>>>>> 610 457 0443 (mobile)
>>>>> 215 843 9367 (fax)
>>>>>
>>>>>
>>>>> Please Note: I now have a new email - William.Bug at DrexelMed.edu  
>>>>> <mailto:William.Bug at DrexelMed.edu>  
>>>>> <mailto:William.Bug at DrexelMed.edu>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> <Picture 15.png>
>>>>> <Picture 16.png>
>>>>> _______________________________________________
>>>>> protege-discussion mailing list
>>>>> protege-discussion at lists.stanford.edu <mailto:protege- 
>>>>> discussion at lists.stanford.edu> <mailto:protege- 
>>>>> discussion at lists.stanford.edu>
>>>>> https://mailman.stanford.edu/mailman/listinfo/protege-discussion
>>>>>
>>>>> Instructions for unsubscribing: http://protege.stanford.edu/doc/ 
>>>>> faq.html#01a.03
>>>>
>>>>
>>>>
>>>> Bill Bug
>>>> Senior Research Analyst/Ontological Engineer
>>>>
>>>> Laboratory for Bioimaging  & Anatomical Informatics
>>>> www.neuroterrain.org
>>>> Department of Neurobiology & Anatomy
>>>> Drexel University College of Medicine
>>>> 2900 Queen Lane
>>>> Philadelphia, PA    19129
>>>> 215 991 8430 (ph)
>>>> 610 457 0443 (mobile)
>>>> 215 843 9367 (fax)
>>>>
>>>>
>>>> Please Note: I now have a new email - William.Bug at DrexelMed.edu  
>>>> <mailto:William.Bug at DrexelMed.edu>  
>>>> <mailto:William.Bug at DrexelMed.edu>
>>>>
>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------- 
>>>> -----
>>>>
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>>>
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>>
>>
>>
>>
>> Bill Bug
>> Senior Research Analyst/Ontological Engineer
>>
>> Laboratory for Bioimaging  & Anatomical Informatics
>> www.neuroterrain.org
>> Department of Neurobiology & Anatomy
>> Drexel University College of Medicine
>> 2900 Queen Lane
>> Philadelphia, PA    19129
>> 215 991 8430 (ph)
>> 610 457 0443 (mobile)
>> 215 843 9367 (fax)
>>
>>
>> Please Note: I now have a new email - William.Bug at DrexelMed.edu  
>> <mailto:William.Bug at DrexelMed.edu>
>>
>>
>>
>>
>

Bill Bug
Senior Research Analyst/Ontological Engineer

Laboratory for Bioimaging  & Anatomical Informatics
www.neuroterrain.org
Department of Neurobiology & Anatomy
Drexel University College of Medicine
2900 Queen Lane
Philadelphia, PA    19129
215 991 8430 (ph)
610 457 0443 (mobile)
215 843 9367 (fax)


Please Note: I now have a new email - William.Bug at DrexelMed.edu




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