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[p4-feedback] Problems with OWL/XML files

S Essaid sielists at gmail.com
Tue Apr 28 09:08:34 PDT 2009


I still have the same issue as before.

- Create new OWL/XML ontology, save and close.
- Open and add class A, save and close.

This is the OWL/XML file:

<?xml version="1.0"?>
<Ontology xmlns="http://www.w3.org/2006/12/owl2-xml#"
     xml:base="http://www.w3.org/2006/12/owl2-xml#"
     xmlns:owl2xml="http://www.w3.org/2006/12/owl2-xml#"
     xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
     xmlns:owlxmlns="http://test/owlxmlns#"
     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
     xmlns:owl="http://www.w3.org/2002/07/owl#"
     xmlns:="http://www.w3.org/2006/12/owl2-xml#"        <---  same problem
     URI="http://test/owlxmlns">
    <EntityAnnotation>
        <Class URI="http://test/owlxmlns#A"/>
        <Annotation annotationURI="
http://www.w3.org/2000/01/rdf-schema#label">
            <Constant>A</Constant>
        </Annotation>
    </EntityAnnotation>
</Ontology>

<!-- Generated by the OWL API (version 2.2.1.1101)
http://owlapi.sourceforge.net -->



I am using the 111 build with the included JVM on XP. Here is my
information:

cwd: C:\P\P4b111_jvm
cmd: "C:\P\P4b111_jvm\jre\bin\java.exe" -Xms209715200 -Xmx209715200
-classpath "C:\P\P4b111_jvm\org.eclipse.osgi.jar;C:\P\P4b111_jvm\lax.jar;"
com.zerog.lax.LAX "C:/P/P4b111_jvm/Protege.lax" "C:/Docum
ents and Settings/sam/Local Settings/Temp/lax15D.tmp"
Starting Protege 4 OWL Editor (Version 4.0.111)
Platform:
    Java: JVM 1.5.0_11-b03 Memory: 208M
    Language: en, Country: US
    Framework: Eclipse (1.4.0)
    OS: WindowsXP (5.1)
    Processor: x86
Installed plugin Pellet Reasoner Plug-in
Installed plugin Cardinality View
Installed plugin Change
Installed plugin Cloud Views
Installed plugin DL Query Tab
Installed plugin Existential Tree
Installed plugin Matrix Views
Installed plugin Browser View (OWLDoc)
Installed plugin Owlviz Plug-in
Installed plugin Annotation Search
Installed plugin owleditor
Installed plugin The OWL API
Installed plugin Pellet Reasoner
Installed plugin Factplusplus Plug-in
Using OWL API version 2.2.1.1101


Thanks,
Shahim



On Tue, Apr 28, 2009 at 5:15 AM, Nick Drummond <
nick.drummond at cs.manchester.ac.uk> wrote:

> Just looked at this again and its working for OWL/XML. Are you still having
> problems?
>
> Nick
>
> <?xml version="1.0"?>
>
>
> <!DOCTYPE Ontology [
>     <!ENTITY owl2xml2 "http://test/owl2xml#" >
>     <!ENTITY owl "http://www.w3.org/2002/07/owl#" >
>     <!ENTITY xsd "http://www.w3.org/2001/XMLSchema#" >
>     <!ENTITY owl2xml "http://www.w3.org/2006/12/owl2-xml#" >
>     <!ENTITY rdfs "http://www.w3.org/2000/01/rdf-schema#" >
>     <!ENTITY rdf "http://www.w3.org/1999/02/22-rdf-syntax-ns#" >
>     <!ENTITY pizza "http://www.co-ode.org/ontologies/pizza/pizza.owl#" >
> ]>
>
>
> <Ontology xmlns="http://www.w3.org/2006/12/owl2-xml#"
>      xml:base="http://www.w3.org/2006/12/owl2-xml#"
>      xmlns:owl2xml="http://www.w3.org/2006/12/owl2-xml#"
>      xmlns:pizza="http://www.co-ode.org/ontologies/pizza/pizza.owl#"
>      xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
>      xmlns:owl2xml2="http://test/owl2xml#"
>      xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
>      xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
>      xmlns:owl="http://www.w3.org/2002/07/owl#"
>      URI="http://test/owl2xml">
> ...
> </Ontology>
>
>
>
> <!-- Generated by the OWL API (version 2.2.1.1101)
> http://owlapi.sourceforge.net -->
>
>
>
>
>
> 2009/4/23 S Essaid <sielists at gmail.com>
>
> Nick,
>>
>> I tried svn revision 13891 (the one that has the bug fix) and it still has
>> the same problem. Is the fix still not checked in?
>>
>> <?xml version="1.0"?>
>> <Ontology xmlns="http://www.w3.org/2006/12/owl2-xml#"
>>      xml:base="http://www.w3.org/2006/12/owl2-xml#"
>>      xmlns:="http://www.w3.org/2006/12/owl2-xml#"
>>      xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
>>      xmlns:owl2xml="http://www.w3.org/2006/12/owl2-xml#"
>>       xmlns:test="http://trunk/test#"
>>      xmlns:owl="http://www.w3.org/2002/07/owl#"
>>      xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
>>      xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
>>      URI="http://trunk/test">
>>     <EntityAnnotation>
>>         <Class URI="http://trunk/test#a"/>
>>         <Annotation annotationURI="
>> http://www.w3.org/2000/01/rdf-schema#label">
>>             <Constant>a</Constant>
>>         </Annotation>
>>     </EntityAnnotation>
>> </Ontology>
>>
>>
>>
>> <!-- Generated by the OWL API (version 2.2.1.1101)
>> http://owlapi.sourceforge.net -->
>>
>>
>>
>> Thanks,
>> Shahim
>>
>>
>>
>> On Wed, Apr 22, 2009 at 6:29 AM, Nick Drummond <
>> nick.drummond at cs.manchester.ac.uk> wrote:
>>
>>> Fixed in the next release.
>>>
>>> Nick
>>>
>>> 2009/4/22 Nick Drummond <nick.drummond at cs.manchester.ac.uk>
>>>
>>> Right, I can reproduce now.
>>>> As you say its when you re-save that the problem arises - weird.
>>>> Anyway, I can now look into it.
>>>>
>>>> Cheers
>>>>
>>>> Nick
>>>>
>>>> 2009/4/19 S Essaid <sielists at gmail.com>
>>>>
>>>> I am also having the problem described here:
>>>>>
>>>>>
>>>>> https://mailman.stanford.edu/pipermail/p4-feedback/2009-April/001887.html
>>>>>
>>>>> The initial XML file that is created with a new ontology has no
>>>>> problems. Any subsequent edits of the ontology will rerecreate the two
>>>>> following problems:
>>>>>
>>>>> <!ENTITY  "http://www.w3.org/2006/12/owl2-xml#" >
>>>>> and
>>>>>     xmlns:="http://www.w3.org/2006/12/owl2-xml#"
>>>>>
>>>>> My info:
>>>>>
>>>>> cwd: C:\P\P4b110_jvm_bare
>>>>> cmd: "C:\P\P4b110_jvm_bare\jre\bin\java.exe" -Xms209715200
>>>>> -Xmx209715200
>>>>> -classpath
>>>>>
>>>>> "C:\P\P4b110_jvm_bare\org.eclipse.osgi.jar;C:\P\P4b110_jvm_bare\lax.jar;"
>>>>> com.zerog.lax.LAX "C:/P/P4b110_jvm_bare/Pr
>>>>> otege.lax" "C:/Documents and Settings/sam/Local
>>>>> Settings/Temp/lax12.tmp"
>>>>> Starting Protege 4 OWL Editor (Version 4.0.110)
>>>>> Platform:
>>>>>    Java: JVM 1.5.0_11-b03 Memory: 208M
>>>>>    Language: en, Country: US
>>>>>    Framework: Eclipse (1.4.0)
>>>>>    OS: WindowsXP (5.1)
>>>>>    Processor: x86
>>>>>
>>>>> No prefix mappings for owl2xm and no empty mappings.
>>>>>
>>>>> The full OWL file is below.
>>>>>
>>>>> Thanks,
>>>>> Shahim
>>>>>
>>>>>
>>>>> <?xml version="1.0"?>
>>>>>
>>>>>
>>>>> <!DOCTYPE Ontology [
>>>>>    <!ENTITY owl2xml2 "http://test/owl2xml#" >
>>>>>    <!ENTITY owl "http://www.w3.org/2002/07/owl#" >
>>>>>    <!ENTITY xsd "http://www.w3.org/2001/XMLSchema#" >
>>>>>    <!ENTITY  "http://www.w3.org/2006/12/owl2-xml#" >
>>>>>    <!ENTITY rdfs "http://www.w3.org/2000/01/rdf-schema#" >
>>>>>    <!ENTITY rdf "http://www.w3.org/1999/02/22-rdf-syntax-ns#" >
>>>>> ]>
>>>>>
>>>>>
>>>>> <Ontology xmlns="http://www.w3.org/2006/12/owl2-xml#"
>>>>>     xml:base="http://www.w3.org/2006/12/owl2-xml#"
>>>>>     xmlns:owl2xml="http://www.w3.org/2006/12/owl2-xml#"
>>>>>     xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
>>>>>     xmlns:owl2xml2="http://test/owl2xml#"
>>>>>     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
>>>>>     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
>>>>>     xmlns:owl="http://www.w3.org/2002/07/owl#"
>>>>>     xmlns:="http://www.w3.org/2006/12/owl2-xml#"
>>>>>     URI="http://test/owl2xml">
>>>>>    <EntityAnnotation>
>>>>>        <Class URI="&owl2xml2;Owl2xmlTest"/>
>>>>>        <Annotation annotationURI="&rdfs;label">
>>>>>            <Constant>Owl2xmlTest</Constant>
>>>>>        </Annotation>
>>>>>    </EntityAnnotation>
>>>>>    <EntityAnnotation>
>>>>>        <Class URI="&owl2xml2;Test"/>
>>>>>        <Annotation annotationURI="&rdfs;label">
>>>>>            <Constant>Test</Constant>
>>>>>        </Annotation>
>>>>>    </EntityAnnotation>
>>>>> </Ontology>
>>>>>
>>>>>
>>>>>
>>>>> <!-- Generated by the OWL API (version 2.2.1.1090)
>>>>> http://owlapi.sourceforge.net -->
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> p4-feedback mailing list
>>>>> p4-feedback at lists.stanford.edu
>>>>> https://mailman.stanford.edu/mailman/listinfo/p4-feedback
>>>>>
>>>>
>>>>
>>>
>>> _______________________________________________
>>> p4-feedback mailing list
>>> p4-feedback at lists.stanford.edu
>>> https://mailman.stanford.edu/mailman/listinfo/p4-feedback
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>>>
>>
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