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[protege-discussion] protege-discussion Digest, Vol 90, Issue 18

Timothy Redmond tredmond at stanford.edu
Thu Jan 30 21:29:54 PST 2014


Ok - there is a disconnect here that somewhat invalidates my initial 
response.  We would better understand your issue if we have a look at 
your ontology.

> > that does not exist in my ontology (it is not shown in Proteg?'s
> > Indivuduals tab) but exists according to the reasoner (FACT++).
>
> By what means did FaCT++ tell you that the individual exists.  Did you
> run FaCT++ from the command line or otherwise?  This may not be
> important if my guess about your ontology is correct.
>
> I run FACT++ from the GUI.  The message shown is:
>
> ReasonerInternalException. Unsupported datatype 
> 'http://www.w3.org/2002/07/owl#real' 
> <http://www.w3.org/2002/07/owl#real%27>

This error message does not indicate that an individual exists. It 
indicates that the owl:real datatype exists but it says nothing about 
any individuals.  (In the OWL language, the entities in the language 
come in six flavours - class, object property, data property, annotation 
property, datatype and individual.)  While owl:real is a datatype that 
is included with the OWL 2 language, this error indicates that FaCT++ 
does not handle this datatype.

This error does not indicate that you have any problem in your 
ontology.  In particular it does not mean that there is any individual 
in your ontology with the name owl:real.

> > that does not exist in my ontology (it is not shown in Proteg?'s
> > Indivuduals tab) but exists according to the reasoner (FACT++).

If your ontology is well formed there will be no individual with the 
name owl:real.  But if you go to the entities tab in Protege and click 
on the datatypes tab (down on the lower left) you will see the owl:real 
datatype regardless of whether it is mentioned in your ontology.  If you 
then click on the usage tab (upper right) you will see whether and how 
your ontology uses the owl:real datatype.





> What is the full name of this individual?  If for example, you meant
> that the name is owl:real so that the full name is
>
>      http://www.w3.org/2002/07/owl#real
>
> In order to solve this issue I deleted the individual however the 
> error still shows up. How so? Would there be a "hidden" individual 
> somewhere as cleverly show below?

There are a couple of issues here.  First of all, by the error still 
shows up, I am guessing that you mean that the FaCT++ reasoner is still 
generating the exact same error.  If you changed real to Real then I am 
not sure what would happen - I would have to try it.  You might be 
having trouble because you are using the reserved vocabulary (the owl: 
namespace) or you might have trouble because you didn't declare a 
user-defined datatype.  I would have to look at the specifications and 
experiment with FaCT++.  In any case this is not the right thing to do 
and might turn a perfectly good OWL 2 ontology into OWL Full.

Secondly, editing an RDF/XML file with a text editor is not recommended 
for the faint of heart.  It is very hard serialization of RDF or OWL to 
read, understand and modify.  It is quite possible that in editing the 
RDF/XML you had an unexpected consequence.

In summary, it is possible that your ontology is fine.  Some options 
that you have are

  * to remove all references to owl:real in your ontology.  This is very
    easy in Protege (though it is done in a slightly unexpected way
    perhaps) and I can show you what to do.
  * to use a reasoner other than FaCT++.

I also recommend that you use the latest Protege.

-Timothy



On 01/30/2014 12:32 PM, André Luiz Tietböhl Ramos wrote:
> Dear Timothy,
>
> Thanks for the very good explanation. Read below please.
>
>
> On Ter, 2014-01-28 at 12:05 -0800, 
> protege-discussion-request at lists.stanford.edu wrote:
>
>> Message: 2
>> Date: Mon, 27 Jan 2014 13:12:12 -0800
>> From: Timothy Redmond <tredmond at stanford.edu  <mailto:tredmond at stanford.edu>>
>> To:protege-discussion at lists.stanford.edu  <mailto:protege-discussion at lists.stanford.edu>
>> Hello,
>>
>> My guess is that with a little more detail we will be able to quickly
>> figure this out.  First, if possible it would be nice to see the ontology.
>>
>> > I do have an Individual (own#real)
>>
>> What is the full name of this individual?  If for example, you meant
>> that the name is owl:real so that the full name is
>>
>>      http://www.w3.org/2002/07/owl#real
>
> In order to solve this issue I deleted the individual however the 
> error still shows up. How so? Would there be a "hidden" individual 
> somewhere as cleverly show below?
>
>> then this is probably the source of your problem.  Using reserved names
>> (such as the names of datatypes) for your own use can lead to ambiguous
>> parsing by different owl parsers.  It is possible that the parser used
>> by FaCT++ generated a different in memory version of your ontology than
>> the Protege parser did.  It may be a bit tricky to tell by looking at
>> the rdf what the full name of the resource is.
>>
>> > that does not exist in my ontology (it is not shown in Proteg?'s
>> > Indivuduals tab) but exists according to the reasoner (FACT++).
>>
>> By what means did FaCT++ tell you that the individual exists.  Did you
>> run FaCT++ from the command line or otherwise?  This may not be
>> important if my guess about your ontology is correct.
>
> I run FACT++ from the GUI.  The message shown is:
>
> ReasonerInternalException. Unsupported datatype 
> 'http://www.w3.org/2002/07/owl#real' 
> <http://www.w3.org/2002/07/owl#real%27>
>
>> You would want to only change those that occur as the individual.  You
>> should also at some point (maybe after getting this ontology to parse in
>> Protege as you expect it) change the namespace of these individuals so
>> that they are not in the owl: namespace.
>
> Ok, thanks! I will when I'm good enough using Protege for I still 
> don't know how to accomplish it effectively.
>
>> > Version: 4.1
>>
>> If by this you mean Protege 4.1, I would recommend that you upgrade to
>> Protege 4.2 if you can.
>
> Yes, it is Protege version 4.1. Using 4.2b or 4.3 doesn't help much 
> either.
>
> Sincerely,
>
> Andre Luiz
>
>
>
>
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