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

Allyson Lister a.l.lister at newcastle.ac.uk
Wed Mar 11 03:49:27 PDT 2009


Hi Maria,

Thanks for your tips! Unfortunately, they didn't help me in this case.

Here's what I found when I followed them. Firstly, if I added my file path
to the rdf:about attribute of the owl:Ontology element, Protege gave a
loading error, so I left that at "#". Secondly, after I saved the ontology
in protege (after having manually modified the xmlns and xml:base as you
specified) examination of the owl file showed that while the xml:base value
stayed as the file:// path, the xmlns attribute went back to the original
http://biomodels.net/SBO/# .

Finally, when I tried to import this newly-modified OWL file into a brand
new Protege project, I am still getting the "The system cannot find the
ontology: http://biomodels.net/SBO/#" error message.

I even tried changing the http:// to file:// in the second ontology that
imports SBO - changing to absolute paths (with file://) within each of the
<owl:imports rdf:resource="http://biomodels.net/SBO/#"/>
xmlns:p1="http://biomodels.net/SBO/#"
<rdfs:Class rdf:about="http://biomodels.net/SBO/#SBO_0000000">

Thanks very much for your help. However, it doesn't seem to have solved the
problem for me.

I have figured out a solution, which I'll send as a separate post now.
However, I'm not sure *why* that solution works.

Thanks again,
Allyson

2009/3/11 Maria M. <maria.michou at gmail.com>

> Hello,
>
> One way that has worked for me is to replace the ontology with a valid
> namespace, because the url: http://biomodels.net/SBO/# is a broken link.
> A valid path would be the path you save the ontology, i.e.
> file:/C:/ontologies/yourOntology.owl
> Check that your file contains:
> -- xmlns="file:/C:/ontologies/yourOntology.owl"
> -- xml:base="file:/C:/ontologies/yourOntology.owl"
> -- <owl:Ontology rdf:about="file:/C:/ontologies/yourOntology.owl">
>
> Then, it will work, because the .owl is saved and loaded locally from your
> disk and not from an http uri that is not available.
>
> Maria
>
>
> On Wed, Mar 11, 2009 at 11:08 AM, Allyson Lister <
> a.l.lister at newcastle.ac.uk> wrote:
>
>> Hi all,
>>
>> I was just wondering if anyone could reproduce this error? I cannot figure
>> out why the import of the file attached in my last email simply doesn't
>> work, and I am starting to wonder if it is something to do with my system.
>> If someone could try to reproduce this problem or give me any idea of what
>> might be wrong with the OWL file, I would really appreciate it. It's an
>> automatic conversion from OBO, so there might be something that can be done
>> if it turns out there is a problem with the OWL.
>>
>> thanks very much,
>>
>> Allyson
>>
>> 2009/3/9 Allyson Lister <a.l.lister at newcastle.ac.uk>
>>
>>> 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.
>>>>> _______________________________________________
>>>>> 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
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>>
>>>> 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
>>>
>>
>>
>>
>> --
>>
>> Allyson Lister
>> http://lurena.vox.com
>>
>> CISBAN, http://www.cisban.ac.uk
>> Newcastle University
>>
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>>
>>
>
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-- 

Allyson Lister
http://lurena.vox.com

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