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[p4-feedback] Problems with OWL/XML files

Nick Drummond nick.drummond at cs.manchester.ac.uk
Wed Apr 29 06:19:13 PDT 2009


Alright, I can reproduce this.

Will fix.

Nick

2009/4/28 S Essaid <sielists at gmail.com>

> 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
>>>>>>
>>>>>
>>>>>
>>>>
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