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

Allyson Lister a.l.lister at
Wed Mar 11 02:08:40 PDT 2009

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,


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

> 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 "" . 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:
>    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>
> 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 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>
>>> 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=""
>>> >     xmlns:rdf=""
>>> >     xmlns:owl=""
>>> >     xmlns:daml=""
>>> >     xmlns:rdfs=""
>>> >   xml:base="">
>>> >
>>> > 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="">
>>> 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
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>> --
>> Allyson Lister
>> Newcastle University
> --
> Allyson Lister
> Newcastle University


Allyson Lister

Newcastle University
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