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[p4-feedback] Problems with OWL/XML files

Nick Drummond nick.drummond at cs.manchester.ac.uk
Wed Apr 29 09:04:03 PDT 2009


Should be working now (finally).

Nick

2009/4/29 Nick Drummond <nick.drummond at cs.manchester.ac.uk>

> 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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>>>>
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