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[p4-feedback] Problems with OWL/XML files

Adam Wyner adam at
Sun Apr 12 04:09:46 PDT 2009

Hi Nick,

I have the same problem as Rord and someone else with build 109 with any
ontology I create,
save, then try to reload.  owl2xml gets deleted *every time* I save and
the owl files.  I'm using Protege 4 in Ubuntu.  This is a problem in the

Furthermore, in the Ontology definition section (after DOCTYPE), I have a
related problem.  The line:


is frequently truncated after saving and reloading to:


And an additional line is added later:


Either of these give rise to errors.

When I manually edit the files to correct for these mistakes, the files load
and run fine.


Nick Drummond wrote:
> Hi Rörd,
> 1) I've just tried in build 109 this and it appears to be rendering this
> xml
> entity and namespace correctly
> <!ENTITY owl2xml "" >
>      xml:base=""
> 2) Again, this is working for me for an arbitrary case. This will depend
> on
> your setup.
> It sounds like the ontology URI in the file you are trying to import is
> not
> correct - ie doesn't match what p4 believes it to be.
> What happens if you load it directly? What format is it?
> Have you got an example of both? Can you send me the files?
> Nick
> 2009/4/5 Rörd Hinrichsen <roerd.hinrichsen at>
>> Hello,
>> I'm using Protégé 4 (build 109) with files in the OWL/XML format.
>> I've encountered the following problems and I'd like to know if these
>> are (known?) bugs in Protégé or what might otherwise be the problem:
>> 1) Corrupted files:
>> Protégé saves corrupted XML files. Inside the doctype declaration, this
>> line:
>>     <!ENTITY owl2xml "" >
>> is missing the name ("owl2xml") and inside this namespace attribute,
>> the name ("base") is also missing:
>>      xml:base=""
>> 2) Problems with importing another ontology:
>> If I try to import the other ontology by the option "Import an
>> ontology that is contained in one of the ontology libraries." and
>> choose its URI, it works. But if I choose the option "Import am
>> ontology contained in a specific file.", it doesn't work (it's
>> displaying "(Not loaded)"), and the displayed URI of the file isn't
>> its own, it's "" instead.
>> Thanks in advance
>> Rörd
>> _______________________________________________
>> p4-feedback mailing list
>> p4-feedback at
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