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[protege-owl] I can only see the Properties, but no Classes, in Protégé

Andrea Splendiani andrea.splendiani at univ-rennes1.fr
Mon May 19 09:23:16 PDT 2008


So... lot's of time I didn't see messages from you on the lists...
How are you doing ?

ciao,
Andrea

Il giorno 02/apr/08, alle ore 18:57, Ghazzaoui, Ramez (NIH/NLM/LHC)  
[C] ha scritto:

> Andrea, you have confirmed my conclusion. Thanks.
>
> Indeed, I am not even using RDFS.
>
> I suppose I can remap my data to OWL using things like subClassOf,  
> but since the goal of my exercise was to view the data as it is in  
> Protégé, the better course of action in my context would be to just  
> reach the conclusion that Protégé is the wrong tool for browsing or  
> visualizing this type of data.
>
> The data is not a taxonomy, although parts of it do look like one.   
> This is a set of lab test descriptions, such as blood or skin tests.  
> Each test has at least 6 attributes expressed in predicate form, and  
> tests are organized in classes which resemble taxonomies. For  
> example, red-blood-cell count is a type of blood test. Sugar test in  
> urine is a type of urine test, arterial blood is a type of blood,  
> and so on.
>
> Your help today has allowed me to reach a final conclusion, and I am  
> fully satisfied.
>
> Thank you so so much!
>
> -Ramez
>
>
> From: Andrea Splendiani [mailto:andrea.splendiani at univ-rennes1.fr]
> Sent: Wednesday, April 02, 2008 12:40 PM
> To: User support for the Protege-OWL editor
> Subject: Re: [protege-owl] I can only see the Properties, but no  
> Classes, in Protégé
>
> Hi Ramez,
>
> it's difficult to five a definitive answers without knowing the  
> background of what you are doing.
>
> Looks like you have exported the content of a "information resource"  
> in RDF. This information resources seems to have a notion of classes  
> and inheritance, but this is not expressed in OWL. So at least the  
> most common settings for Protégé won't help. I don't know whether  
> under some setting you can use Protégé (or part of it) to browse a  
> RDF graph. If I remember well, you don't even use RDFS (but I may be  
> wrong on this).
>
> So, the questions are two:
>
> first: can you make a mapping in OWL of your information ? What is  
> it ? Looks like a taxonomy.. at least expressivity should be  
> sufficient (different thing is if you can map your is_A to  
> subclassOf).
>
> second: otherwise you have an RDF graph. As store you would probably  
> go for a tripleStore (Sesame, Virtuoso...Jena... just a few of them,  
> depends on you tests and necessities). As a viewer there are a few,  
> most notably browsers and graph visualizers.
>
> ciao,
> Andrea
>
>
>
> Il giorno 02/apr/08, alle ore 17:41, Ghazzaoui, Ramez (NIH/NLM/LHC)  
> [C] ha scritto:
>
>
> Thank you Andrea, Samson and Nick.
>
> So I can’t see my classes because they are not OWL classes.  This  
> takes me back to step 1 of my project, and leads me to conclude that  
> my data is not meant for viewing / browsing / querying through an  
> OWL editor such as Protégé.
>
> I started out with a set of triples meant for an RDF graph. I was  
> asked by my boss to load it into Protégé so we can visualize and  
> browse it.
>
> With help from Tania (of this forum), I learned that I need to use  
> Jena to convert my triples to RDF/XML in order to be able to load  
> them into Protégé. Then with help from Csongor (of this forum) I  
> learned how to load the RDF/XML file into Protégé. That was two  
> steps forward, and I was pretty happy with it.
>
> Now I learn from Andrea that for a class to be seen in Protégé, it  
> needs to be an OWL class and not just any node on an RDF graph. I  
> tend to refer to RDF graph nodes as “Classes” and to RDF predicates  
> as “Properties”.  Maybe I am wrong to confuse the two. In any case,  
> it sounds like as long as my original set of triples does not define  
> true OWL classes (using the OWL namespace), I won’t be able to see  
> any classes in Protégé. What I should use is an RDF store /  
> visualizer, not an Ontology editor / visualizer such as Protégé.
>
> Can anyone confirm that my conclusion is true?
>
> Thanks much!
>
> -Ramez
>
>
> PS to Samson:  Yes, “isa_CLASS is something that is defined in my  
> own namespace.
>
>
> From: Andrea Splendiani [mailto:andrea.splendiani at univ-rennes1.fr]
> Sent: Tuesday, April 01, 2008 6:58 PM
> To: User support for the Protege-OWL editor
> Subject: Re: [protege-owl] I can only see the Properties, but no  
> Classes, in Protégé
>
> Again,
>
> looks like you don't have OWL classes inside your file. You have  
> just a declaration isa_CLASS in your own namespace, nothing OWL  
> interpretable.
>
> ciao,
> Andrea
>
> Il giorno 01/apr/08, alle ore 23:08, Ghazzaoui, Ramez (NIH/NLM/LHC)  
> [C] ha scritto:
>
>
>
> Nothing shows up in the Results panel, but the query repeats in a  
> panel at the top as the “Value” for a Property named  
> “assert:notEmpty”.
>
> -Ramez
>
>
> From: Pitonyak, Andrew D [mailto:PitonyakA at BATTELLE.ORG]
> Sent: Tuesday, April 01, 2008 3:44 PM
> To: User support for the Protege-OWL editor
> Subject: [protege-owl] RE: I can only see the Properties, but no  
> Classes, in Protégé
>
> What do you see if you do the following:
>
> Use Reasoning > Open SPARQL Query Panel
>
> Execute the following query:
>
> SELECT *
> WHERE { ?x a owl:Class} order by ?x
>
> Is anything displayed?
> How about for this?
>
> SELECT *
> WHERE {  ?x rdfs:subClassOf ?y }
>
> Is anything displayed?
>
>
> From: protege-owl-bounces at lists.stanford.edu [mailto:protege-owl-bounces at lists.stanford.edu 
> ] On Behalf Of Ghazzaoui, Ramez (NIH/NLM/LHC) [C]
> Sent: Tuesday, April 01, 2008 2:49 PM
> To: protege-owl at lists.stanford.edu
> Subject: [protege-owl] I can only see the Properties, but no  
> Classes, in Protégé
>
> Hi,
>
> With help from Tania and much help from Csongor, I managed last week  
> to load an RDF/XML file into an OWL/RDF project in Protégé without  
> seeing any error messages. (This was quite an achievement, and I am  
> happy with it)
>
>
> Now my problem is:
>
> Although I can see my 38 or so Properties under the “Properties”  
> tab’s “All” sub-tab, which is correct, I cannot see any of my  
> Classes anywhere, not even under the “OWLClasses” tab. Where are  
> those Classes supposed to be listed?  How can I see them? (I know  
> they are in the RDF/XML file because I can see them there)
>
>
> Sorry for asking such a basic question but I am a first-time Protégé  
> user having a hard time navigating the program. If you prefer to  
> just point me to the proper documentation to answer my question then  
> I will gladly download and read it.
>
> -Ramez
>
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> -----------
> Andrea Splendiani
> post-doc, bootstrep project (www.bootstrep.eu)
>
> UPRES-EA 3888 - Laboratoire d'Informatique Médicale
> CHU de Pontchaillou
> 2, rue Henri Le Guilloux
> 35033 Rennes - France
> Tel : +33 2 99 28 92 45 / +33 2 99 28 42 15 (secr.)
> Fax : +33 2 99 28 41 60
>
> 48° 07.275N
> 1° 41.643W
>
>
>
>
>
>
>
>
> _______________________________________________
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> protege-owl at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/protege-owl
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>
> -----------
> Andrea Splendiani
> post-doc, bootstrep project (www.bootstrep.eu)
>
> UPRES-EA 3888 - Laboratoire d'Informatique Médicale
> CHU de Pontchaillou
> 2, rue Henri Le Guilloux
> 35033 Rennes - France
> Tel : +33 2 99 28 92 45 / +33 2 99 28 42 15 (secr.)
> Fax : +33 2 99 28 41 60
>
> 48° 07.275N
> 1° 41.643W
>
>
>
>
>
>
>
> _______________________________________________
> 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

-----------
Andrea Splendiani
post-doc, bootstrep project (www.bootstrep.eu)

UPRES-EA 3888 - Laboratoire d'Informatique Médicale
CHU de Pontchaillou
2, rue Henri Le Guilloux
35033 Rennes - France
Tel : +33 2 99 28 92 45 / +33 2 99 28 42 15 (secr.)
Fax : +33 2 99 28 41 60

48° 07.275N
1° 41.643W






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