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

Thomas Russ tar at ISI.EDU
Fri Mar 6 13:54:08 PST 2009


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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