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[protege-owl] Loading the OWL version in protege 3.4 RC1

Allyson Lister a.l.lister at newcastle.ac.uk
Mon Mar 9 05:48:00 PDT 2009


Hi all,

Thanks for all your help so far. It's allowed me to make changes to the
attached file so that the correct default namespace is shown. (I replaced
the math elements with mathml:math elements.) However, whenever I try to
import the attached ontology, even into a brand new project, I get an error
message from Protege. Details follow.

When I look at the attached file in protege, the correct default namespace
is shown as "http://biomodels.net/SBO/#" . However, whenever I try to import
this file into another ontology, the following behavior occurs:


   1. Create brand-new Protege 3.4 RC1 Project in OWL/RDF.
   2. Import the attached SBO OWL file using the normal import button in the
   metadata tab
   3. save project and exit Protege
   4. open protege and load project
   5. *every* time I load the project at this stage, I get an error message:
   The system cannot find the ontology: http://biomodels.net/SBO/#
   6. If I try to add the file explicitly, even though it is already present
   in the new project's .repository file, it just brings up the same message
   again and again.

Can anyone spot the error, either in the OWL file attached or in Protege?
This is driving me crazy... :)

thanks very much!

2009/3/9 Allyson Lister <a.l.lister at newcastle.ac.uk>

> Hi Thomas,
>
> Thanks very much for your thoughts. Indeed, I am only wanting to import
> this file into another ontology, so I don't need to be doing any editing of
> the MathML sections.
>
> I've done a global search and replace of all "<math>" tags (opening and
> closing), replacing with mathml:math - and adding an xmlns:mathml to the
> header. This has meant that the default namespace is now being read
> correctly. However, I have what seems to be a related problem.
>
> When I try to import the ontology into another one, with my repository file
> as so:
>
> [Dublin Core DL Redirect]
> ./SBO_OWL-06-03-2009.owl?forceReadOnly=true
>
>
> then I get an error from Protege telling me that it cannot find the
> namespace http://biomodels.net/SBO/#. Even if I try to tell it that file
> explicitly, it still says it cannot find that namespace. Do you have any
> suggestions?
>
> Why would Protege give such an error when reading in this file for an
> import?
>
> Thanks very much!
>
> 2009/3/6 Thomas Russ <tar at isi.edu>
>
>
>> On Mar 6, 2009, at 10:09 AM, Allyson Lister wrote:
>>
>> > Hi all,
>> >
>> > I downloaded today's sbo OWL file (attached) and opened it in
>> > protege 3.4 RC1 on a machine running ubuntu intrepid 64 bit.
>> >
>> > As you can see from the attached screenshot, for some reason the
>> > default namespace is set to MathML - and this is with having the
>> > default namespace *actually* set to SBO, as the excerpt of the OWL
>> > file below prooves:
>> >
>> > <rdf:RDF
>> >     xmlns="http://biomodels.net/SBO/#"
>> >     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
>> >     xmlns:owl="http://www.w3.org/2002/07/owl#"
>> >     xmlns:daml="http://www.daml.org/2001/03/daml+oil#"
>> >     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
>> >   xml:base="http://biomodels.net/SBO/#">
>> >
>> > So, why is Protege doing this? Do you have any idea? I've sent to
>> > both protege owl and SBO. Perhaps somehow I've managed to set
>> > something incorrectly?
>>
>> I suspect that somehow the parsing is getting confused by encountering
>> the MathML markup tags, which look like
>>
>>  <math xmlns="http://www.w3.org/1998/Math/MathML">
>>
>> and introduce their own default namespace.  Now, according to the XML
>> parsing rules, that should be a local effect, valid only inside the
>> scope of the tag, but perhaps there is a bug in the parser or
>> namespace handler used by Protege that ends up keeping the last such
>> namespace encountered, instead of properly respecting the namespace
>> scoping rules.
>>
>> As a work-around, perhaps what you need to do is to introduce a math:
>> prefix and use that for the MathML parts.  Since they have structured
>> parts with their own sub-tags, this could get a bit tedious, although
>> it may be possible to do this using some sort of editor script.
>>
>> I'm not quite sure how Protege will handle the RDF literal parses of
>> the MathML objects, though.
>> _______________________________________________
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>> https://mailman.stanford.edu/mailman/listinfo/protege-owl
>>
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>>
>
>
>
> --
>
> Allyson Lister
> http://lurena.vox.com
>
> CISBAN, http://www.cisban.ac.uk
> Newcastle University
>



-- 

Allyson Lister
http://lurena.vox.com

CISBAN, http://www.cisban.ac.uk
Newcastle University
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