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-discussion] DISPLAY_SLOT problem

Tania Tudorache tudorache at stanford.edu
Fri Mar 16 14:39:55 PDT 2007


Hi Bill,

Thanks a lot for the feedback. I will review the wiki page about hiding 
the identifiers with labels and update it.

Cheers,
Tania



William Bug wrote:
> 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>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------
>>>>>
>>>>> _______________________________________________
>>>>> protege-discussion mailing list
>>>>> 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 
>>>>
>>>> _______________________________________________
>>>> protege-discussion mailing list
>>>> 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>
>>>
>>>
>>>
>>>
>>
>
> 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>
>
>
>
>




More information about the protege-discussion mailing list