feng zhong | 1 Apr 07:17 2005
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some questions about the OWL plugin install

Dear professor:

Sorry for troubling you. Recently, with the guidance of my supervisor, I began to focus on the academic area of Ontology. And I find that the research field is very interesting, I was eager to do further study on the subject. Since I was a green hander and was not familiar with it. So I want to practice on my computer.

 

However, when I download the protégé owl plugin and unzip it to the folder of “F:\Protege_3.0\plugins” , and the folder of “F:\Protege_3.0\” is the destination where I installed the my protégé software. As you stated in the plugin instruction, I can now see the entries "OWL Files" and "OWL Database" in the listing of project formats at Protege's startup screen.  But when I choose the owl files and click the button of “new” , the console windows displays some incorrect messages showing that some class was missed.(the message are attached in this mail and represent in the form of pictures)

 

Would you please help me to troubleshoot this problem?

 

Thank you very much. And looking forward to your timely reply



Best Regards

Feng Zhong
P.O.Box 209
Tianjin University Post Office
Tianjin 300072,P.R.China
TEL:(8622)87401113


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Re: some questions about the OWL plugin install

i think you should use Protege 3.1 if you use the OWL plugin 2.0 (build 246)

De : protege-owl-bounce <at> crg-gw.Stanford.EDU [mailto:protege-owl-bounce <at> crg-gw.Stanford.EDU] De la part de feng zhong
Envoyé : vendredi 1 avril 2005 07:18
À : protege-owl <at> SMI.Stanford.EDU
Objet : [protege-owl] some questions about the OWL plugin install

Dear professor:

Sorry for troubling you. Recently, with the guidance of my supervisor, I began to focus on the academic area of Ontology. And I find that the research field is very interesting, I was eager to do further study on the subject. Since I was a green hander and was not familiar with it. So I want to practice on my computer.

 

However, when I download the protégé owl plugin and unzip it to the folder of “F:\Protege_3.0\plugins” , and the folder of “F:\Protege_3.0\” is the destination where I installed the my protégé software. As you stated in the plugin instruction, I can now see the entries "OWL Files" and "OWL Database" in the listing of project formats at Protege's startup screen.  But when I choose the owl files and click the button of “new” , the console windows displays some incorrect messages showing that some class was missed.(the message are attached in this mail and represent in the form of pictures)

 

Would you please help me to troubleshoot this problem?

 

Thank you very much. And looking forward to your timely reply



Best Regards

Feng Zhong
P.O.Box 209
Tianjin University Post Office
Tianjin 300072,P.R.China
TEL:(8622)87401113


Do You Yahoo!?
150万曲MP3疯狂搜,带您闯入音乐殿堂
美女明星应有尽有,搜遍美图、艳图和酷图
1G就是1000兆,雅虎电邮自助扩容!
Matt Williams | 1 Apr 10:33 2005
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Re: SWRL ?inference support

Dear Rand,

I was very interested (and impressed) by your email to the protege
mailing list - very impressive!

I'm in the process of downloading all the bits and getting them to work,
but I was wondering why you didn't either:

Write the rules directly in Jess, using the JessTab Protege plugin or

Pass the SWRL -> Jess converted files through a text parser to tidy them
up. 

Clearly, I'm sure you had good reasons for this, but I was just
wondering what they were. Also, converting the ontology to RuleML seems
to loose a whole load of advantages, mainly in that I don't think you
can now use the DL reasoners to classify individuals.

I'd be interested to know what you think,

Matt
--

-- 
Dr. M. Williams MRCP(UK)
Clinical Research Fellow
Cancer Research UK
+44 (0)207 269 2953
+44 (0)7384 899570

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rand | 1 Apr 15:15 2005
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Re: SWRL ?inference support

Dear Matt

You were quite right when you said I had very good reasons for (1) not 
writing the rules directly in Jess to start with and (2) not running the 
SWRL --> Jess file through some cleanup program of my own.   They all 
had to do with the fact that I was building a demonstration system where 
there was a requirement to demonstrate that standarded formatted files 
(in this case OWL and RuleML)  could be used with existing tools and 
made to work in an application without further intervention.  Part of 
the idea is that the application is designed to be modular in that the 
reasoning system (which is the back-end part of the application) could 
be changed without any required alteration to the rest of the 
application.  The user can have no idea that it is Jess or anything else 
sitting inside.  The user must be able to start with these standard 
files and the application, through a logic engine independent interface 
to the reasoning engine must be able to send those files and request 
whatever processing is necessary.  So building Jess files directly is 
out of the question.

And that leads to your second questions about not being able to use DL 
reasoners on the ontology.  As I have explained it above, you can see 
that the application takes a ready made ontology and automatically does 
the translating and merging at run time (it will also save a compiled 
version of the combined file to be used later if the user wishes - that 
is why I talked in my message about calling all of the Sweetrules 
functions programatically through the Sweetrules API).  In other words, 
the ontology is translated only when it is complete.  I still build and 
update the ontology using Protege and use the DL reasoner there while 
building it.  So no advantage is lost whatsoever.  You as an ontology 
builder never even see the translation or have anything to do with it 
(as it should be - unless of course something has gone wrong and you 
need to do some debugging!!).

Hope that helps.

Regards,

Rand

Matt Williams wrote:

>Dear Rand,
>
>I was very interested (and impressed) by your email to the protege
>mailing list - very impressive!
>
>I'm in the process of downloading all the bits and getting them to work,
>but I was wondering why you didn't either:
>
>Write the rules directly in Jess, using the JessTab Protege plugin or
>
>Pass the SWRL -> Jess converted files through a text parser to tidy them
>up. 
>
>Clearly, I'm sure you had good reasons for this, but I was just
>wondering what they were. Also, converting the ontology to RuleML seems
>to loose a whole load of advantages, mainly in that I don't think you
>can now use the DL reasoners to classify individuals.
>
>I'd be interested to know what you think,
>
>Matt
>  
>

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K Cahalan | 1 Apr 16:04 2005

OWL Reasoning API - Missing Files

Can someone tell me which jar file contains the classes OWLNamedClass and 
ProtegeOWL?  Apparently these two files are needed in order to use the Protege-
OWL Reasoning API.  I am attempting to follow directions at 
http://protege.stanford.edu/plugins/owl/api/ReasonerAPIExamples.html, which 
states "you need to make sure that the jar files in the Protege application 
folder and the the jar files in the OWL plugin folder are in your classpath".  
But there are so many jar files in those two folders that it does not seem 
practical to add all of them to the project, and I cannot find these two 
classes in any of the jar files.  Please forgive me if the answer turns out to 
be obvious, or if this message gets posted more than once by accident.  Thanks 
in advance.

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Lemaster, Timothy E. | 1 Apr 16:36 2005
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Problem deleting instance

I'll rephrase my question from March 30th with more details. I'm calling
delete() on a OWLIndividual over a remote server. When I do I get an
exception. Also after that calls to getInstances on its OWLNamedClass
also throw an exception. The delete code looks like this:

oModel.beginTransaction("deleteInstance: " + instance.getName());
instance.delete();
oModel.endTransaction();

Its throws the same exception with or with out the begin/end Transaction
stuff. If I close the remote project and reopen it works fine and the
instance has been deleted.

The stack trace

java.lang.ArrayIndexOutOfBoundsException: 0
	at
edu.stanford.smi.protegex.owl.model.factory.OWLJavaFactory.createSimpleI
nstance(OWLJavaFactory.java:237)
	at
edu.stanford.smi.protegex.owl.model.framestore.OWLFrameFactoryInvocation
Handler.convertInstance(OWLFrameFactoryInvocationHandler.java:164)
	at
edu.stanford.smi.protegex.owl.model.framestore.OWLFrameFactoryInvocation
Handler.convert(OWLFrameFactoryInvocationHandler.java:56)
	at
edu.stanford.smi.protegex.owl.model.framestore.OWLFrameFactoryInvocation
Handler.convertEvent(OWLFrameFactoryInvocationHandler.java:114)
	at
edu.stanford.smi.protegex.owl.model.framestore.OWLFrameFactoryInvocation
Handler.convert(OWLFrameFactoryInvocationHandler.java:62)
	at
edu.stanford.smi.protegex.owl.model.framestore.OWLFrameFactoryInvocation
Handler.convertCollection(OWLFrameFactoryInvocationHandler.java:81)
	at
edu.stanford.smi.protegex.owl.model.framestore.OWLFrameFactoryInvocation
Handler.convert(OWLFrameFactoryInvocationHandler.java:53)
	at
edu.stanford.smi.protegex.owl.model.framestore.OWLFrameFactoryInvocation
Handler.handleInvoke(OWLFrameFactoryInvocationHandler.java:180)
	at
edu.stanford.smi.protege.model.framestore.AbstractFrameStoreInvocationHa
ndler.invoke(Unknown Source)
	at $Proxy1.getEvents(Unknown Source)
	at sun.reflect.GeneratedMethodAccessor71.invoke(Unknown Source)
	at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
Impl.java:25)
	at java.lang.reflect.Method.invoke(Method.java:585)
	at
edu.stanford.smi.protege.model.framestore.AbstractFrameStoreInvocationHa
ndler.invoke(Unknown Source)
	at
edu.stanford.smi.protege.model.framestore.AbstractFrameStoreInvocationHa
ndler.invoke(Unknown Source)
	at
edu.stanford.smi.protege.model.framestore.ArgumentCheckingFrameStoreHand
ler.handleInvoke(Unknown Source)
	at
edu.stanford.smi.protege.model.framestore.AbstractFrameStoreInvocationHa
ndler.invoke(Unknown Source)
	at $Proxy0.getEvents(Unknown Source)
	at sun.reflect.GeneratedMethodAccessor71.invoke(Unknown Source)
	at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
Impl.java:25)
	at java.lang.reflect.Method.invoke(Method.java:585)
	at
edu.stanford.smi.protege.model.framestore.AbstractFrameStoreInvocationHa
ndler.invoke(Unknown Source)
	at
edu.stanford.smi.protege.model.framestore.AbstractFrameStoreInvocationHa
ndler.invoke(Unknown Source)
	at
edu.stanford.smi.protege.model.framestore.ChangeMonitorFrameStoreHandler
.handleInvoke(Unknown Source)
	at
edu.stanford.smi.protege.model.framestore.AbstractFrameStoreInvocationHa
ndler.invoke(Unknown Source)
	at $Proxy0.getEvents(Unknown Source)
	at
edu.stanford.smi.protege.model.framestore.FrameStoreAdapter.getEvents(Un
known Source)
	at
edu.stanford.smi.protege.model.framestore.FrameStoreAdapter.getEvents(Un
known Source)
	at
edu.stanford.smi.protege.model.framestore.FrameStoreAdapter.getEvents(Un
known Source)
	at sun.reflect.GeneratedMethodAccessor71.invoke(Unknown Source)
	at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
Impl.java:25)
	at java.lang.reflect.Method.invoke(Method.java:585)
	at
edu.stanford.smi.protege.model.framestore.AbstractFrameStoreInvocationHa
ndler.invoke(Unknown Source)
	at
edu.stanford.smi.protege.model.framestore.AbstractFrameStoreInvocationHa
ndler.invoke(Unknown Source)
	at
edu.stanford.smi.protege.server.LocalizeFrameStoreHandler.handleInvoke(U
nknown Source)
	at
edu.stanford.smi.protege.model.framestore.AbstractFrameStoreInvocationHa
ndler.invoke(Unknown Source)
	at $Proxy0.getEvents(Unknown Source)
	at
edu.stanford.smi.protege.server.ServerFrameStore.getEvents(Unknown
Source)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.jav
a:39)
	at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
Impl.java:25)
	at java.lang.reflect.Method.invoke(Method.java:585)
	at
sun.rmi.server.UnicastServerRef.dispatch(UnicastServerRef.java:294)
	at sun.rmi.transport.Transport$1.run(Transport.java:153)
	at java.security.AccessController.doPrivileged(Native Method)
	at sun.rmi.transport.Transport.serviceCall(Transport.java:149)
	at
sun.rmi.transport.tcp.TCPTransport.handleMessages(TCPTransport.java:460)
	at
sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run(TCPTransport.ja
va:701)
	at java.lang.Thread.run(Thread.java:595)
	at
sun.rmi.transport.StreamRemoteCall.exceptionReceivedFromServer(StreamRem
oteCall.java:263)
	at
sun.rmi.transport.StreamRemoteCall.executeCall(StreamRemoteCall.java:239
)
	at sun.rmi.server.UnicastRef.invoke(UnicastRef.java:148)
	at
edu.stanford.smi.protege.server.ServerFrameStore_Stub.getEvents(Unknown
Source)
	at
edu.stanford.smi.protege.server.RemoteClientFrameStore.getEvents(Unknown
Source)
	at sun.reflect.GeneratedMethodAccessor65.invoke(Unknown Source)
	at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
Impl.java(Compiled Code))
	at java.lang.reflect.Method.invoke(Method.java(Compiled Code))
	at
edu.stanford.smi.protege.model.framestore.AbstractFrameStoreInvocationHa
ndler.invoke(Unknown Source)
	at
edu.stanford.smi.protege.model.framestore.AbstractFrameStoreInvocationHa
ndler.invoke(Unknown Source)
	at
edu.stanford.smi.protege.model.framestore.CallCachingFrameStore.handleIn
voke(Unknown Source)
	at
edu.stanford.smi.protege.model.framestore.AbstractFrameStoreInvocationHa
ndler.invoke(Unknown Source)
	at $Proxy0.getEvents(Unknown Source)
	at
edu.stanford.smi.protege.model.framestore.FrameStoreAdapter.getEvents(Un
known Source)
	at sun.reflect.GeneratedMethodAccessor65.invoke(Unknown Source)
	at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
Impl.java(Compiled Code))
	at java.lang.reflect.Method.invoke(Method.java(Compiled Code))
	at
edu.stanford.smi.protege.model.framestore.AbstractFrameStoreInvocationHa
ndler.invoke(Unknown Source)
	at
edu.stanford.smi.protege.model.framestore.AbstractFrameStoreInvocationHa
ndler.invoke(Unknown Source)
	at
edu.stanford.smi.protegex.owl.model.framestore.OWLFrameFactoryInvocation
Handler.handleInvoke(OWLFrameFactoryInvocationHandler.java(Compiled
Code))
	at
edu.stanford.smi.protege.model.framestore.AbstractFrameStoreInvocationHa
ndler.invoke(Unknown Source)
	at $Proxy0.getEvents(Unknown Source)
	at
edu.stanford.smi.protege.model.framestore.EventDispatchFrameStore.dispat
chEvents(Unknown Source)
	at
edu.stanford.smi.protege.model.framestore.EventDispatchFrameStore.dispat
chEvents(Unknown Source)
	at
edu.stanford.smi.protege.model.framestore.EventDispatchFrameStore.delete
SimpleInstance(Unknown Source)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.jav
a:79)
	at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
Impl.java(Compiled Code))
	at java.lang.reflect.Method.invoke(Method.java(Compiled Code))
	at
edu.stanford.smi.protege.model.framestore.AbstractFrameStoreInvocationHa
ndler.invoke(Unknown Source)
	at
edu.stanford.smi.protege.model.framestore.AbstractFrameStoreInvocationHa
ndler.invoke(Unknown Source)
	at
edu.stanford.smi.protege.model.framestore.ArgumentCheckingFrameStoreHand
ler.handleInvoke(Unknown Source)
	at
edu.stanford.smi.protege.model.framestore.AbstractFrameStoreInvocationHa
ndler.invoke(Unknown Source)
	at $Proxy0.deleteSimpleInstance(Unknown Source)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.jav
a:79)
	at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
Impl.java(Compiled Code))
	at java.lang.reflect.Method.invoke(Method.java(Compiled Code))
	at
edu.stanford.smi.protege.model.framestore.AbstractFrameStoreInvocationHa
ndler.invoke(Unknown Source)
	at
edu.stanford.smi.protege.model.framestore.AbstractFrameStoreInvocationHa
ndler.invoke(Unknown Source)
	at
edu.stanford.smi.protege.model.framestore.ChangeMonitorFrameStoreHandler
.handleInvoke(Unknown Source)
	at
edu.stanford.smi.protege.model.framestore.AbstractFrameStoreInvocationHa
ndler.invoke(Unknown Source)
	at $Proxy0.deleteSimpleInstance(Unknown Source)
	at
edu.stanford.smi.protege.model.framestore.FrameStoreAdapter.deleteSimple
Instance(Unknown Source)
	at
edu.stanford.smi.protege.model.framestore.DeleteSimplificationFrameStore
.deleteFrame(Unknown Source)
	at
edu.stanford.smi.protege.model.framestore.DeleteSimplificationFrameStore
.internalDeleteFrame(Unknown Source)
	at
edu.stanford.smi.protege.model.framestore.DeleteSimplificationFrameStore
.internalDeleteInstance(Unknown Source)
	at
edu.stanford.smi.protege.model.framestore.DeleteSimplificationFrameStore
.internalDeleteSimpleInstance(Unknown Source)
	at
edu.stanford.smi.protege.model.framestore.DeleteSimplificationFrameStore
.deleteSimpleInstance(Unknown Source)
	at
edu.stanford.smi.protege.model.framestore.FrameStoreAdapter.deleteSimple
Instance(Unknown Source)
	at
edu.stanford.smi.protegex.owl.model.framestore.OWLFrameStore.deleteSimpl
eInstance(OWLFrameStore.java:477)
	at
edu.stanford.smi.protege.model.DefaultKnowledgeBase.deleteSimpleInstance
(Unknown Source)
	at
edu.stanford.smi.protege.model.DefaultKnowledgeBase.deleteFrame(Unknown
Source)
	at edu.stanford.smi.protege.model.DefaultFrame.delete(Unknown
Source)

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Suzanne Gormley | 1 Apr 16:43 2005
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[protege OWL] Abox is incoherent

Hi,

Sorry for bothering everyone again, but i'm getting an error when I
run racer.  I've posted about this before and I was explained why the
error happens but I cannot understand why it is happening with my
ontology.  The error is ABox http://dl.kr.org/dig/kb--36375 is
incoherent.
I was told that this occurs because my individuals don't match up with
my classes and axioms, but I think they do!  I attached the file if
anyone had a chance to look at it, I would be eternally grateful!
Thanks very much!
Suzanne
Attachment (chess.owl): application/octet-stream, 24 KiB
Volker Haarslev | 1 Apr 17:59 2005
Picon
Picon

Re: Abox is incoherent

On 1-Apr-05, at 9:43, Suzanne Gormley wrote:

> Hi,
>
> Sorry for bothering everyone again, but i'm getting an error when I
> run racer.  I've posted about this before and I was explained why the
> error happens but I cannot understand why it is happening with my
> ontology.  The error is ABox http://dl.kr.org/dig/kb--36375 is
> incoherent.
> I was told that this occurs because my individuals don't match up with
> my classes and axioms, but I think they do!  I attached the file if
> anyone had a chance to look at it, I would be eternally grateful!

Hi,

I checked it with version 1.7.24 and it recognizes the Abox as 
inconsistent. Unfortunately, this is a bug in 1.7.24, which is not 
maintained anymore. The new version 1.8 recognizes your Abox as 
consistent. It will be available rsn.

Cheers, Volker

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Olivier Dameron | 1 Apr 18:01 2005
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Re: OWL Reasoning API - Missing Files

On Fri, 1 Apr 2005 14:04:08 +0000 (UTC), K Cahalan
<kathy.cahalan <at> convergys.com> wrote:
> Can someone tell me which jar file contains the classes OWLNamedClass
> and  ProtegeOWL?  

They are in protege-owl.jar

Good luck
Olivier
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Suzanne Gormley | 1 Apr 18:06 2005
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Re: Abox is incoherent

Thats good to hear,
Thanks Volker

On Apr 1, 2005 4:59 PM, Volker Haarslev <haarslev <at> cse.concordia.ca> wrote:
> On 1-Apr-05, at 9:43, Suzanne Gormley wrote:
> 
> > Hi,
> >
> > Sorry for bothering everyone again, but i'm getting an error when I
> > run racer.  I've posted about this before and I was explained why the
> > error happens but I cannot understand why it is happening with my
> > ontology.  The error is ABox http://dl.kr.org/dig/kb--36375 is
> > incoherent.
> > I was told that this occurs because my individuals don't match up with
> > my classes and axioms, but I think they do!  I attached the file if
> > anyone had a chance to look at it, I would be eternally grateful!
> 
> Hi,
> 
> I checked it with version 1.7.24 and it recognizes the Abox as
> inconsistent. Unfortunately, this is a bug in 1.7.24, which is not
> maintained anymore. The new version 1.8 recognizes your Abox as
> consistent. It will be available rsn.
> 
> Cheers, Volker
> 
>
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