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[protege-owl] Transforming an OWL file

Timothy Redmond tredmond at stanford.edu
Mon Jan 28 11:04:14 PST 2008


There are some directions at http://protege.cim3.net/cgi-bin/wiki.pl?HidingIdentifiersWithLabelsInOWLPlugin 
.  In addition if you are not trying to make the ontology multi- 
lingual you can ignore the directions about importing the Protege meta- 
ontology and setting the defaultLanguage attribute.

The short version of the directions is

1. make owl:Class and rdf:Class visible by using the OWL Menu ->  
Preferences -> Visibility.

2. Go to the forms tab and change the display slot for owl:Class (and  
possibly rdfs:Class) to rdfs:label.

You can do the same for owl:Property if needed.

-Timothy



On Jan 28, 2008, at 10:07 AM, Ghajar, Anoosh wrote:

> Hi,
> Thank you for your reply.
> I am new to protégé. Would you be kind enough to provide me with the  
> details
> Of how to configure protégé to display the rdf:label when viewing  
> Ontologies?
>
> Thank you.
>
> -----Original Message-----
> From: protege-owl-bounces at lists.stanford.edu [mailto:protege-owl-bounces at lists.stanford.edu 
> ] On Behalf Of Timothy Redmond
> Sent: Monday, January 28, 2008 12:46 PM
> To: User support for the Protege-OWL editor
> Subject: Re: [protege-owl] Transforming an OWL file
>
>
>> I am thinking of using java and XSLT(are there better options?) for
>> the transformation but my problem is with the <rdf:SubClassOf> node
>> that reports another class name of the format 'PRO_XXXX' which has
>> its details(I mean <rdfs:label> further down in the .owl file). Any
>> idea of how to implement this transformation will be greatly
>> appreciated.
>
> I would recommend avoiding things like XSLT to work with OWL.  It may
> work with your particular problem but the solution will be fragile and
> hacky.  (Of course fragile and hacky might be fine for a single use.)
> There are several distinct XML ways to say the identical thing in RDF
> and OWL and there have been other discussions of this issue on this
> mailing list (not sure how easy they would be to find though).  So for
> example your XSLT would work with a declaration like
>
> 	<owl:Class rdf:ID="PRO_00019440">
>
> but would it be equally happy with the equivalent (modulo rdf syntax
> errors) line:
>
>        <rdf:Description rdf:ID="PRO_00019440">
> 	   <rdf:type="owl:Class">
>
> 	?
> There are also several subtleties in the OWL specifications and a
> couple of issues that are unspecified.
>
> A much better approach would be to use some OWL api to read and write
> the owl file.  At the top of my recommendations would be the OWL api
> (owlapi.sourceforge.net) and Jena (jena.sourceforge.net).
>
>> I have an owl file that needs to be modified to properly reflect the
>> class names. The existing class names in <owl:Class> tags are in the
>> format 'PRO_XXXXX" where XXXX is a sequence of numbers and I would
>> like the class names to be changed to the textual content of the
>> first child node <rdfs:label> .
>
> So my other question is whether you are sure this is what you want.
> There is a common recommendation that the uri for class be a
> unchanging meaningless identifier and that the real name of the class
> live in the rdf:label (there is an Alan Rector paper about this
> somewhere).  Part of the point is that this insulates you against
> change.  The class can be referred to in a consistent manner (by uri)
> even when the name of the class changes.  Also, many tools (e.g.
> Protege) allow you to view ontologies by displaying the rdf:label.
>
> -Timothy
>
>
> On Jan 28, 2008, at 8:20 AM, Ghajar, Anoosh wrote:
>
>> Hi,
>> I have an owl file that needs to be modified to properly reflect the
>> class names. The existing class names in <owl:Class> tags are in the
>> format 'PRO_XXXXX" where XXXX is a sequence of numbers and I would
>> like the class names to be changed to the textual content of the
>> first child node <rdfs:label> .
>> I am thinking of using java and XSLT(are there better options?) for
>> the transformation but my problem is with the <rdf:SubClassOf> node
>> that reports another class name of the format 'PRO_XXXX' which has
>> its details(I mean <rdfs:label> further down in the .owl file). Any
>> idea of how to implement this transformation will be greatly
>> appreciated.
>> Thank You.
>> Here is a section of my .owl file:
>> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>> ++++++
>> <owl:Class rdf:ID="PRO_00019440">
>>    <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>>> Smad2 sequence 1 phosphorylated and ubiquitinated form</
>> rdfs:label>
>>    <oboInOwl:hasDbXref>
>>      <oboInOwl:DbXref rdf:nodeID="A0">
>>        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string
>> "
>>> MOD:00696 has_modification - phosphorylated residue</
>> rdfs:label>
>>      </oboInOwl:DbXref>
>>    </oboInOwl:hasDbXref>
>>    <oboInOwl:hasDbXref>
>>      <oboInOwl:DbXref rdf:nodeID="A1">
>>        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string
>> "
>>> MOD:00688 has_modification - isopeptide crosslinked
>> residues</rdfs:label>
>>      </oboInOwl:DbXref>
>>    </oboInOwl:hasDbXref>
>>    <rdfs:subClassOf>
>>      <owl:Restriction>
>>        <owl:someValuesFrom>
>>          <owl:Class rdf:ID="PRO_00000011"/>
>>        </owl:someValuesFrom>
>>        <owl:onProperty>
>>          <owl:TransitiveProperty rdf:ID="UNDEFINED_derives_from"/>
>>        </owl:onProperty>
>>      </owl:Restriction>
>>    </rdfs:subClassOf>
>>    <rdfs:subClassOf rdf:resource="http://www.w3.org/2002/07/
>> owl#Thing"/>
>>  </owl:Class>
>>
>>
>>
>>
>>
>>
>>
>>
>>
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