Infinit Loop through Inconsistent Ontology Explanation

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Infinit Loop through Inconsistent Ontology Explanation

Stephan Opfer
Hi All,

I produced an inconsistent Ontology and I know why it is inconsistent. My problem is, that the reasoner does not terminate, when I want him to explain the inconsistency.

I use the Hermit Reasoner in its latest Version (1.3.6) and I produced a minimal example code, which produces this behaviour. It is based on the examples, which come with the Hermit download.

The interesting thing is, that protege 4.1 (with the Hermit plugin) has no problems to explain the inconsistency. Although it only identifies some hot spots, atleast it terminates.

So my question is: What is the difference between my code and the one in protege 4.1?

I was searching in the repository of protege, but I could not find the right lines of code.

In the attachment, you will find three ontologies. individual.owl is the inconsistent ontology and imports the other two ontologies. Furthermore, the minimal example is given in Explanations.java and AutoIRIMapperFixed.java. Just adapt the path to the ontologies in Explanations.java.

Best Regards,
  Stephan


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AutoIRIMapperFixed.java (10K) Download Attachment
Explanations.java (4K) Download Attachment
individuals.owl (109K) Download Attachment
alica-2.0.owl (103K) Download Attachment
robocupmsl.owl (30K) Download Attachment
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Re: Infinit Loop through Inconsistent Ontology Explanation

Lorenz Buehmann

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Hi,

as far as I know the explanation function in Protege was implemented by Matthew Horridge. And I'm pretty sure that he doesn't use the default BlackBoxExplanationGenerator from OWL API, but a new implementation maybe somehow optimized for inconsistent ontologies. You can see the code here http://smi-protege.stanford.edu/svn/protege4/plugins/org.protege.explanation/src/uk/ac/manchester/cs/owl/explanation/JustificationManager.java?revision=24772&view=markup, especially the method in line 191 is interesting.
On the other hand your code computes all explanations and there can be exponentially many justifications. In Protege the default limit is 2.
Anyway, we should wait for feedback from Matthew Horridge.

Regards,
Lorenz
On 19.08.2012 19:45, Stephan Opfer wrote:
> Hi All,
>
> I produced an inconsistent Ontology and I know why it is inconsistent. My problem is, that the reasoner does not terminate, when I want him to explain the inconsistency.
>
> I use the Hermit Reasoner in its latest Version (1.3.6) and I produced a minimal example code, which produces this behaviour. It is based on the examples, which come with the Hermit download.
>
> The interesting thing is, that protege 4.1 (with the Hermit plugin) has no problems to explain the inconsistency. Although it only identifies some hot spots, atleast it terminates.
>
> So my question is: What is the difference between my code and the one in protege 4.1?
>
> I was searching in the repository of protege, but I could not find the right lines of code.
>
> In the attachment, you will find three ontologies. individual.owl is the inconsistent ontology and imports the other two ontologies. Furthermore, the minimal example is given in Explanations.java and AutoIRIMapperFixed.java. Just adapt the path to the ontologies in Explanations.java.
>
> Best Regards,
> Stephan
>
>
>
> _______________________________________________
> p4-feedback mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/p4-feedback


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Re: Infinit Loop through Inconsistent Ontology Explanation

Stephan Opfer
Hi,

so where is this org.semanticweb.owl.explanation.impl.blackbox.checker.InconsistentOntologyExplanationGeneratorFactory ? Is it part of the owl-api? I cant find it in their java doc api.

I think, that this explanation plugin is not, what is used by the default protege 4.1. At least I cant find it in the plugin folder of my protege.

I will try to limit the number of explanations and give some feedback here...

Best Regards,
  Stephan
On 08/19/2012 09:02 PM, Lorenz Buehmann wrote:

>
> Hi,
>
> as far as I know the explanation function in Protege was implemented by Matthew Horridge. And I'm pretty sure that he doesn't use the default BlackBoxExplanationGenerator from OWL API, but a new implementation maybe somehow optimized for inconsistent ontologies. You can see the code here http://smi-protege.stanford.edu/svn/protege4/plugins/org.protege.explanation/src/uk/ac/manchester/cs/owl/explanation/JustificationManager.java?revision=24772&view=markup, especially the method in line 191 is interesting.
> On the other hand your code computes all explanations and there can be exponentially many justifications. In Protege the default limit is 2.
> Anyway, we should wait for feedback from Matthew Horridge.
>
> Regards,
> Lorenz
> On 19.08.2012 19:45, Stephan Opfer wrote:
>> Hi All,
>
>> I produced an inconsistent Ontology and I know why it is inconsistent. My problem is, that the reasoner does not terminate, when I want him to explain the inconsistency.
>
>> I use the Hermit Reasoner in its latest Version (1.3.6) and I produced a minimal example code, which produces this behaviour. It is based on the examples, which come with the Hermit download.
>
>> The interesting thing is, that protege 4.1 (with the Hermit plugin) has no problems to explain the inconsistency. Although it only identifies some hot spots, atleast it terminates.
>
>> So my question is: What is the difference between my code and the one in protege 4.1?
>
>> I was searching in the repository of protege, but I could not find the right lines of code.
>
>> In the attachment, you will find three ontologies. individual.owl is the inconsistent ontology and imports the other two ontologies. Furthermore, the minimal example is given in Explanations.java and AutoIRIMapperFixed.java. Just adapt the path to the ontologies in Explanations.java.
>
>> Best Regards,
>> Stephan
>
>
>
>> _______________________________________________
>> p4-feedback mailing list
>> [hidden email]
>> https://mailman.stanford.edu/mailman/listinfo/p4-feedback
>
>
>
>
> _______________________________________________
> p4-feedback mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/p4-feedback
>

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Re: Infinit Loop through Inconsistent Ontology Explanation

Stephan Opfer
Hi,

a limit for the number of explanation does not help. I also deleted some unnecessary lines form the example (see attachment).

Best Regards,
  Stephan

On 08/19/2012 10:58 PM, Stephan Opfer wrote:

> Hi,
>
> so where is this org.semanticweb.owl.explanation.impl.blackbox.checker.InconsistentOntologyExplanationGeneratorFactory ? Is it part of the owl-api? I cant find it in their java doc api.
>
> I think, that this explanation plugin is not, what is used by the default protege 4.1. At least I cant find it in the plugin folder of my protege.
>
> I will try to limit the number of explanations and give some feedback here...
>
> Best Regards,
>   Stephan
> On 08/19/2012 09:02 PM, Lorenz Buehmann wrote:
>>
>> Hi,
>>
>> as far as I know the explanation function in Protege was implemented by Matthew Horridge. And I'm pretty sure that he doesn't use the default BlackBoxExplanationGenerator from OWL API, but a new implementation maybe somehow optimized for inconsistent ontologies. You can see the code here http://smi-protege.stanford.edu/svn/protege4/plugins/org.protege.explanation/src/uk/ac/manchester/cs/owl/explanation/JustificationManager.java?revision=24772&view=markup, especially the method in line 191 is interesting.
>> On the other hand your code computes all explanations and there can be exponentially many justifications. In Protege the default limit is 2.
>> Anyway, we should wait for feedback from Matthew Horridge.
>>
>> Regards,
>> Lorenz
>> On 19.08.2012 19:45, Stephan Opfer wrote:
>>> Hi All,
>>
>>> I produced an inconsistent Ontology and I know why it is inconsistent. My problem is, that the reasoner does not terminate, when I want him to explain the inconsistency.
>>
>>> I use the Hermit Reasoner in its latest Version (1.3.6) and I produced a minimal example code, which produces this behaviour. It is based on the examples, which come with the Hermit download.
>>
>>> The interesting thing is, that protege 4.1 (with the Hermit plugin) has no problems to explain the inconsistency. Although it only identifies some hot spots, atleast it terminates.
>>
>>> So my question is: What is the difference between my code and the one in protege 4.1?
>>
>>> I was searching in the repository of protege, but I could not find the right lines of code.
>>
>>> In the attachment, you will find three ontologies. individual.owl is the inconsistent ontology and imports the other two ontologies. Furthermore, the minimal example is given in Explanations.java and AutoIRIMapperFixed.java. Just adapt the path to the ontologies in Explanations.java.
>>
>>> Best Regards,
>>> Stephan
>>
>>
>>
>>> _______________________________________________
>>> p4-feedback mailing list
>>> [hidden email]
>>> https://mailman.stanford.edu/mailman/listinfo/p4-feedback
>>
>>
>>
>>
>> _______________________________________________
>> p4-feedback mailing list
>> [hidden email]
>> https://mailman.stanford.edu/mailman/listinfo/p4-feedback
>>
>
> _______________________________________________
> p4-feedback mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/p4-feedback
>

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Re: Infinit Loop through Inconsistent Ontology Explanation

Lorenz Buehmann

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This is not part of OWL API, you can find a jar file in the lib folder of the plugin in the svn:http://smi-protege.stanford.edu/repos/protege/protege4/plugins/org.protege.explanation/lib/
But I'm not sure if this plugin is already used in Protege 4.1 or if there is another implementation for the explanation workbench.
On 19.08.2012 23:38, Stephan Opfer wrote:
> Hi,
>
> a limit for the number of explanation does not help. I also deleted some unnecessary lines form the example (see attachment).
>
> Best Regards,
> Stephan
>
> On 08/19/2012 10:58 PM, Stephan Opfer wrote:
>> Hi,
>>
>> so where is this org.semanticweb.owl.explanation.impl.blackbox.checker.InconsistentOntologyExplanationGeneratorFactory ? Is it part of the owl-api? I cant find it in their java doc api.
>>
>> I think, that this explanation plugin is not, what is used by the default protege 4.1. At least I cant find it in the plugin folder of my protege.
>>
>> I will try to limit the number of explanations and give some feedback here...
>>
>> Best Regards,
>> Stephan
>> On 08/19/2012 09:02 PM, Lorenz Buehmann wrote:
>>>
>>> Hi,
>>>
>>> as far as I know the explanation function in Protege was implemented by Matthew Horridge. And I'm pretty sure that he doesn't use the default BlackBoxExplanationGenerator from OWL API, but a new implementation maybe somehow optimized for inconsistent ontologies. You can see the code here http://smi-protege.stanford.edu/svn/protege4/plugins/org.protege.explanation/src/uk/ac/manchester/cs/owl/explanation/JustificationManager.java?revision=24772&view=markup, especially the method in line 191 is interesting.
>>> On the other hand your code computes all explanations and there can be exponentially many justifications. In Protege the default limit is 2.
>>> Anyway, we should wait for feedback from Matthew Horridge.
>>>
>>> Regards,
>>> Lorenz
>>> On 19.08.2012 19:45, Stephan Opfer wrote:
>>>> Hi All,
>>>
>>>> I produced an inconsistent Ontology and I know why it is inconsistent. My problem is, that the reasoner does not terminate, when I want him to explain the inconsistency.
>>>
>>>> I use the Hermit Reasoner in its latest Version (1.3.6) and I produced a minimal example code, which produces this behaviour. It is based on the examples, which come with the Hermit download.
>>>
>>>> The interesting thing is, that protege 4.1 (with the Hermit plugin) has no problems to explain the inconsistency. Although it only identifies some hot spots, atleast it terminates.
>>>
>>>> So my question is: What is the difference between my code and the one in protege 4.1?
>>>
>>>> I was searching in the repository of protege, but I could not find the right lines of code.
>>>
>>>> In the attachment, you will find three ontologies. individual.owl is the inconsistent ontology and imports the other two ontologies. Furthermore, the minimal example is given in Explanations.java and AutoIRIMapperFixed.java. Just adapt the path to the ontologies in Explanations.java.
>>>
>>>> Best Regards,
>>>> Stephan
>>>
>>>
>>>
>>>> _______________________________________________
>>>> p4-feedback mailing list
>>>> [hidden email]
>>>> https://mailman.stanford.edu/mailman/listinfo/p4-feedback
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> p4-feedback mailing list
>>> [hidden email]
>>> https://mailman.stanford.edu/mailman/listinfo/p4-feedback
>>>
>>
>> _______________________________________________
>> p4-feedback mailing list
>> [hidden email]
>> https://mailman.stanford.edu/mailman/listinfo/p4-feedback
>>
>
>
>
> _______________________________________________
> p4-feedback mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/p4-feedback


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Re: Infinit Loop through Inconsistent Ontology Explanation

Stephan Opfer
Ok, but unfortunately no source code is available.

On 08/20/2012 02:20 AM, Lorenz Buehmann wrote:

>
> This is not part of OWL API, you can find a jar file in the lib folder of the plugin in the svn:http://smi-protege.stanford.edu/repos/protege/protege4/plugins/org.protege.explanation/lib/
> But I'm not sure if this plugin is already used in Protege 4.1 or if there is another implementation for the explanation workbench.
> On 19.08.2012 23:38, Stephan Opfer wrote:
>> Hi,
>
>> a limit for the number of explanation does not help. I also deleted some unnecessary lines form the example (see attachment).
>
>> Best Regards,
>> Stephan
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Re: Infinit Loop through Inconsistent Ontology Explanation

Lorenz Buehmann
Why do you need the source code?
On 20.08.2012 08:20, Stephan Opfer wrote:

> Ok, but unfortunately no source code is available.
>
> On 08/20/2012 02:20 AM, Lorenz Buehmann wrote:
>> This is not part of OWL API, you can find a jar file in the lib folder of the plugin in the svn:http://smi-protege.stanford.edu/repos/protege/protege4/plugins/org.protege.explanation/lib/
>> But I'm not sure if this plugin is already used in Protege 4.1 or if there is another implementation for the explanation workbench.
>> On 19.08.2012 23:38, Stephan Opfer wrote:
>>> Hi,
>>> a limit for the number of explanation does not help. I also deleted some unnecessary lines form the example (see attachment).
>>> Best Regards,
>>> Stephan
> _______________________________________________
> p4-feedback mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/p4-feedback
>

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Re: Infinit Loop through Inconsistent Ontology Explanation

Timothy Redmond
In reply to this post by Lorenz Buehmann

I haven't looked at this yet but I can verify some of this reply.

On 08/19/2012 12:02 PM, Lorenz Buehmann wrote:

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Hi,

as far as I know the explanation function in Protege was implemented by Matthew Horridge. And I'm pretty sure that he doesn't use the default BlackBoxExplanationGenerator from OWL API, but a new implementation maybe somehow optimized for inconsistent ontologies.

This is exactly right.  The source code for this new explanation code is not yet available.

-Timothy


You can see the code here http://smi-protege.stanford.edu/svn/protege4/plugins/org.protege.explanation/src/uk/ac/manchester/cs/owl/explanation/JustificationManager.java?revision=24772&view=markup, especially the method in line 191 is interesting.
On the other hand your code computes all explanations and there can be exponentially many justifications. In Protege the default limit is 2.
Anyway, we should wait for feedback from Matthew Horridge.

Regards,
Lorenz
On 19.08.2012 19:45, Stephan Opfer wrote:
> Hi All,
>
> I produced an inconsistent Ontology and I know why it is inconsistent. My problem is, that the reasoner does not terminate, when I want him to explain the inconsistency.
>
> I use the Hermit Reasoner in its latest Version (1.3.6) and I produced a minimal example code, which produces this behaviour. It is based on the examples, which come with the Hermit download.
>
> The interesting thing is, that protege 4.1 (with the Hermit plugin) has no problems to explain the inconsistency. Although it only identifies some hot spots, atleast it terminates.
>
> So my question is: What is the difference between my code and the one in protege 4.1?
>
> I was searching in the repository of protege, but I could not find the right lines of code.
>
> In the attachment, you will find three ontologies. individual.owl is the inconsistent ontology and imports the other two ontologies. Furthermore, the minimal example is given in Explanations.java and AutoIRIMapperFixed.java. Just adapt the path to the ontologies in Explanations.java.
>
> Best Regards,
> Stephan
>
>
>
> _______________________________________________
> p4-feedback mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/p4-feedback


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Re: Infinit Loop through Inconsistent Ontology Explanation

Stephan Opfer
In reply to this post by Lorenz Buehmann
It would be nice to integrate it into my application. At the moment my app with Hermit is just reasoning forever (I gave it 10-15 minutes and canceled afterwards).

On 08/20/2012 08:59 AM, Lorenz Bühmann wrote:

> Why do you need the source code?
> On 20.08.2012 08:20, Stephan Opfer wrote:
>> Ok, but unfortunately no source code is available.
>>
>> On 08/20/2012 02:20 AM, Lorenz Buehmann wrote:
>>> This is not part of OWL API, you can find a jar file in the lib folder of the plugin in the svn:http://smi-protege.stanford.edu/repos/protege/protege4/plugins/org.protege.explanation/lib/
>>> But I'm not sure if this plugin is already used in Protege 4.1 or if there is another implementation for the explanation workbench.
>>> On 19.08.2012 23:38, Stephan Opfer wrote:
>>>> Hi,
>>>> a limit for the number of explanation does not help. I also deleted some unnecessary lines form the example (see attachment).
>>>> Best Regards,
>>>> Stephan
>> _______________________________________________
>> p4-feedback mailing list
>> [hidden email]
>> https://mailman.stanford.edu/mailman/listinfo/p4-feedback
>>
>
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> https://mailman.stanford.edu/mailman/listinfo/p4-feedback
>

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Re: Infinit Loop through Inconsistent Ontology Explanation

Timothy Redmond
On 08/20/2012 06:46 AM, Stephan Opfer wrote:
> It would be nice to integrate it into my application. At the moment my app with Hermit is just reasoning forever (I gave it 10-15 minutes and canceled afterwards).

I will need to verify this but I believe that the OWL api version of the
explanation tool does not explain inconsistent ontologies.  I thought it
only handled unsatisfiable classes or class expressions. If I am wrong
about this then I wasted some effort because I tried to write a tool
that explained inconsistent ontologies some time back.

I don't actually know of an open source tool that will explain
inconsistent ontologies.  I suspect that Clark-Parsia has something like
this but their code will probably come with restrictions.  You could try
to use Matthews library.  It doesn't come with source but it is very
good and you might be able to figure it out by looking at how it is used
[1].

I will try to verify my assertions later today.

-Timothy


[1] https://smi-protege.stanford.edu/repos/protege/protege4/plugins/org.protege.explanation

>
> On 08/20/2012 08:59 AM, Lorenz Bühmann wrote:
>> Why do you need the source code?
>> On 20.08.2012 08:20, Stephan Opfer wrote:
>>> Ok, but unfortunately no source code is available.
>>>
>>> On 08/20/2012 02:20 AM, Lorenz Buehmann wrote:
>>>> This is not part of OWL API, you can find a jar file in the lib folder of the plugin in the svn:http://smi-protege.stanford.edu/repos/protege/protege4/plugins/org.protege.explanation/lib/
>>>> But I'm not sure if this plugin is already used in Protege 4.1 or if there is another implementation for the explanation workbench.
>>>> On 19.08.2012 23:38, Stephan Opfer wrote:
>>>>> Hi,
>>>>> a limit for the number of explanation does not help. I also deleted some unnecessary lines form the example (see attachment).
>>>>> Best Regards,
>>>>> Stephan
>>> _______________________________________________
>>> p4-feedback mailing list
>>> [hidden email]
>>> https://mailman.stanford.edu/mailman/listinfo/p4-feedback
>>>
>> _______________________________________________
>> p4-feedback mailing list
>> [hidden email]
>> https://mailman.stanford.edu/mailman/listinfo/p4-feedback
>>
> _______________________________________________
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Re: Infinit Loop through Inconsistent Ontology Explanation

Thomas Schneider-2
According to my (perhaps not up-to-date) knowledge, Matthew's implementation in Protégé and OWL API indeed explain inferences of consistent ontologies "only". The Pellet reasoner can compute explanations of inconsistencies, but only on the command line AFAIK. Try calling "pellet help explain". I don't know about the availability of their source code.

Thomas

On 20.08.2012, at 16:32, Timothy Redmond wrote:

> On 08/20/2012 06:46 AM, Stephan Opfer wrote:
>> It would be nice to integrate it into my application. At the moment my app with Hermit is just reasoning forever (I gave it 10-15 minutes and canceled afterwards).
>
> I will need to verify this but I believe that the OWL api version of the explanation tool does not explain inconsistent ontologies.  I thought it only handled unsatisfiable classes or class expressions. If I am wrong about this then I wasted some effort because I tried to write a tool that explained inconsistent ontologies some time back.
>
> I don't actually know of an open source tool that will explain inconsistent ontologies.  I suspect that Clark-Parsia has something like this but their code will probably come with restrictions.  You could try to use Matthews library.  It doesn't come with source but it is very good and you might be able to figure it out by looking at how it is used [1].
>
> I will try to verify my assertions later today.
>
> -Timothy
>
>
> [1] https://smi-protege.stanford.edu/repos/protege/protege4/plugins/org.protege.explanation
>
>>
>> On 08/20/2012 08:59 AM, Lorenz Bühmann wrote:
>>> Why do you need the source code?
>>> On 20.08.2012 08:20, Stephan Opfer wrote:
>>>> Ok, but unfortunately no source code is available.
>>>>
>>>> On 08/20/2012 02:20 AM, Lorenz Buehmann wrote:
>>>>> This is not part of OWL API, you can find a jar file in the lib folder of the plugin in the svn:http://smi-protege.stanford.edu/repos/protege/protege4/plugins/org.protege.explanation/lib/
>>>>> But I'm not sure if this plugin is already used in Protege 4.1 or if there is another implementation for the explanation workbench.
>>>>> On 19.08.2012 23:38, Stephan Opfer wrote:
>>>>>> Hi,
>>>>>> a limit for the number of explanation does not help. I also deleted some unnecessary lines form the example (see attachment).
>>>>>> Best Regards,
>>>>>> Stephan
>>>> _______________________________________________
>>>> p4-feedback mailing list
>>>> [hidden email]
>>>> https://mailman.stanford.edu/mailman/listinfo/p4-feedback
>>>>
>>> _______________________________________________
>>> p4-feedback mailing list
>>> [hidden email]
>>> https://mailman.stanford.edu/mailman/listinfo/p4-feedback
>>>
>> _______________________________________________
>> p4-feedback mailing list
>> [hidden email]
>> https://mailman.stanford.edu/mailman/listinfo/p4-feedback
>
> _______________________________________________
> p4-feedback mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/p4-feedback

----------------------------------------------------------------------
Dr. Thomas Schneider
Universität Bremen, FB 03
Postfach 330440
28334 Bremen
Germany
+49 421 218-64432
http://www.informatik.uni-bremen.de/~ts/
For visits: Cartesium, Room 2.56
----------------------------------------------------------------------

Dorchester (n.)
Someone else's throaty cough which obscures the crucial part of the rather amusing remark you've just made.

Douglas Adams, John Lloyd: The Deeper Meaning of Liff

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Re: Infinit Loop through Inconsistent Ontology Explanation

Lorenz Buehmann

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

As far as I know the latest lib from Matthew also explains why
ontologies are inconsistent. That's what the thread creator mentioned,
that it works in Protege, but not in his own implementation.

Lorenz
On 20.08.2012 17:02, Thomas Schneider wrote:
> According to my (perhaps not up-to-date) knowledge, Matthew's implementation in Protégé and OWL API
indeed explain inferences of consistent ontologies "only". The Pellet
reasoner can compute explanations of inconsistencies, but only on the
command line AFAIK. Try calling "pellet help explain". I don't know
about the availability of their source code.
>
> Thomas
>
> On 20.08.2012, at 16:32, Timothy Redmond wrote:
>
>> On 08/20/2012 06:46 AM, Stephan Opfer wrote:
>>> It would be nice to integrate it into my application. At the moment
my app with Hermit is just reasoning forever (I gave it 10-15 minutes
and canceled afterwards).
>>
>> I will need to verify this but I believe that the OWL api version of
the explanation tool does not explain inconsistent ontologies. I thought
it only handled unsatisfiable classes or class expressions. If I am
wrong about this then I wasted some effort because I tried to write a
tool that explained inconsistent ontologies some time back.
>>
>> I don't actually know of an open source tool that will explain
inconsistent ontologies. I suspect that Clark-Parsia has something like
this but their code will probably come with restrictions. You could try
to use Matthews library. It doesn't come with source but it is very good
and you might be able to figure it out by looking at how it is used [1].
>>
>> I will try to verify my assertions later today.
>>
>> -Timothy
>>
>>
>> [1]
https://smi-protege.stanford.edu/repos/protege/protege4/plugins/org.protege.explanation
>>
>>>
>>> On 08/20/2012 08:59 AM, Lorenz Bühmann wrote:
>>>> Why do you need the source code?
>>>> On 20.08.2012 08:20, Stephan Opfer wrote:
>>>>> Ok, but unfortunately no source code is available.
>>>>>
>>>>> On 08/20/2012 02:20 AM, Lorenz Buehmann wrote:
>>>>>> This is not part of OWL API, you can find a jar file in the lib
folder of the plugin in the
svn:http://smi-protege.stanford.edu/repos/protege/protege4/plugins/org.protege.explanation/lib/
>>>>>> But I'm not sure if this plugin is already used in Protege 4.1 or
if there is another implementation for the explanation workbench.
>>>>>> On 19.08.2012 23:38, Stephan Opfer wrote:
>>>>>>> Hi,
>>>>>>> a limit for the number of explanation does not help. I also
deleted some unnecessary lines form the example (see attachment).

>>>>>>> Best Regards,
>>>>>>> Stephan
>>>>> _______________________________________________
>>>>> p4-feedback mailing list
>>>>> [hidden email]
>>>>> https://mailman.stanford.edu/mailman/listinfo/p4-feedback
>>>>>
>>>> _______________________________________________
>>>> p4-feedback mailing list
>>>> [hidden email]
>>>> https://mailman.stanford.edu/mailman/listinfo/p4-feedback
>>>>
>>> _______________________________________________
>>> p4-feedback mailing list
>>> [hidden email]
>>> https://mailman.stanford.edu/mailman/listinfo/p4-feedback
>>
>> _______________________________________________
>> p4-feedback mailing list
>> [hidden email]
>> https://mailman.stanford.edu/mailman/listinfo/p4-feedback
>
> ----------------------------------------------------------------------
> Dr. Thomas Schneider
> Universität Bremen, FB 03
> Postfach 330440
> 28334 Bremen
> Germany
> +49 421 218-64432
> http://www.informatik.uni-bremen.de/~ts/
> For visits: Cartesium, Room 2.56
> ----------------------------------------------------------------------
>
> Dorchester (n.)
> Someone else's throaty cough which obscures the crucial part of the
rather amusing remark you've just made.
>
> Douglas Adams, John Lloyd: The Deeper Meaning of Liff
>
> _______________________________________________
> p4-feedback mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/p4-feedback
>

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Re: Infinit Loop through Inconsistent Ontology Explanation

Timothy Redmond
In reply to this post by Thomas Schneider-2
On 8/20/12 8:02 AM, Thomas Schneider wrote:
> According to my (perhaps not up-to-date) knowledge, Matthew's implementation in Protégé and OWL API indeed explain inferences of consistent ontologies "only".

In the latest Protege 4.2, Matthew's implementation will also explain
inconsistent ontologies.  This is a major move forwards in my opinion (I
always used to use "pellet explain").  The explanation library is freely
available but is not open source as of yet.

-Timothy


> The Pellet reasoner can compute explanations of inconsistencies, but only on the command line AFAIK. Try calling "pellet help explain". I don't know about the availability of their source code.
>
> Thomas
>
> On 20.08.2012, at 16:32, Timothy Redmond wrote:
>
>> On 08/20/2012 06:46 AM, Stephan Opfer wrote:
>>> It would be nice to integrate it into my application. At the moment my app with Hermit is just reasoning forever (I gave it 10-15 minutes and canceled afterwards).
>> I will need to verify this but I believe that the OWL api version of the explanation tool does not explain inconsistent ontologies.  I thought it only handled unsatisfiable classes or class expressions. If I am wrong about this then I wasted some effort because I tried to write a tool that explained inconsistent ontologies some time back.
>>
>> I don't actually know of an open source tool that will explain inconsistent ontologies.  I suspect that Clark-Parsia has something like this but their code will probably come with restrictions.  You could try to use Matthews library.  It doesn't come with source but it is very good and you might be able to figure it out by looking at how it is used [1].
>>
>> I will try to verify my assertions later today.
>>
>> -Timothy
>>
>>
>> [1] https://smi-protege.stanford.edu/repos/protege/protege4/plugins/org.protege.explanation
>>
>>> On 08/20/2012 08:59 AM, Lorenz Bühmann wrote:
>>>> Why do you need the source code?
>>>> On 20.08.2012 08:20, Stephan Opfer wrote:
>>>>> Ok, but unfortunately no source code is available.
>>>>>
>>>>> On 08/20/2012 02:20 AM, Lorenz Buehmann wrote:
>>>>>> This is not part of OWL API, you can find a jar file in the lib folder of the plugin in the svn:http://smi-protege.stanford.edu/repos/protege/protege4/plugins/org.protege.explanation/lib/
>>>>>> But I'm not sure if this plugin is already used in Protege 4.1 or if there is another implementation for the explanation workbench.
>>>>>> On 19.08.2012 23:38, Stephan Opfer wrote:
>>>>>>> Hi,
>>>>>>> a limit for the number of explanation does not help. I also deleted some unnecessary lines form the example (see attachment).
>>>>>>> Best Regards,
>>>>>>> Stephan
>>>>> _______________________________________________
>>>>> p4-feedback mailing list
>>>>> [hidden email]
>>>>> https://mailman.stanford.edu/mailman/listinfo/p4-feedback
>>>>>
>>>> _______________________________________________
>>>> p4-feedback mailing list
>>>> [hidden email]
>>>> https://mailman.stanford.edu/mailman/listinfo/p4-feedback
>>>>
>>> _______________________________________________
>>> p4-feedback mailing list
>>> [hidden email]
>>> https://mailman.stanford.edu/mailman/listinfo/p4-feedback
>> _______________________________________________
>> p4-feedback mailing list
>> [hidden email]
>> https://mailman.stanford.edu/mailman/listinfo/p4-feedback
> ----------------------------------------------------------------------
> Dr. Thomas Schneider
> Universität Bremen, FB 03
> Postfach 330440
> 28334 Bremen
> Germany
> +49 421 218-64432
> http://www.informatik.uni-bremen.de/~ts/
> For visits: Cartesium, Room 2.56
> ----------------------------------------------------------------------
>
> Dorchester (n.)
> Someone else's throaty cough which obscures the crucial part of the rather amusing remark you've just made.
>
> Douglas Adams, John Lloyd: The Deeper Meaning of Liff
>
> _______________________________________________
> p4-feedback mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/p4-feedback

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Re: Infinit Loop through Inconsistent Ontology Explanation

Stephan Opfer
Ok, but Hermit can explain inconsistent ontologies, as it is stated in the examples, which you can download with the Hermit files.
What they do, is stop throwing InconsistentOntologyException and ask why Thing is unsatisfiable. Whether you would denote the results as a real explanation, is another question, I think. Nevertheless, I created a minimal ontology, which reproduces the behaviour I encountered with protege 4.1. (see attachment)

But there are some problems, if you say that:
1. Case: Thing isOneOf {InconsistentNode, NormalNode1, NormalNode2, trans1to2, trans2to1} -> starting Hermit creates a ConcurrentModificationException
2. Case: See InconsistentRepaired.owl -> it offers a lot of explanations, for the inconsistency, although I would say, that it is not inconsistent.

What I want, is to classify loosely coupled nodes - those nodes which does not have an incoming transition.

I hope you have some ideas about that strange behaviour.

Best Regards,
  Stephan

On 08/20/2012 07:17 PM, Timothy Redmond wrote:

> On 8/20/12 8:02 AM, Thomas Schneider wrote:
>> According to my (perhaps not up-to-date) knowledge, Matthew's implementation in Protégé and OWL API indeed explain inferences of consistent ontologies "only".
>
> In the latest Protege 4.2, Matthew's implementation will also explain inconsistent ontologies.  This is a major move forwards in my opinion (I always used to use "pellet explain").  The explanation library is freely available but is not open source as of yet.
>
> -Timothy
>
>
>> The Pellet reasoner can compute explanations of inconsistencies, but only on the command line AFAIK. Try calling "pellet help explain". I don't know about the availability of their source code.
>>
>> Thomas
>>
>> On 20.08.2012, at 16:32, Timothy Redmond wrote:
>>
>>> On 08/20/2012 06:46 AM, Stephan Opfer wrote:
>>>> It would be nice to integrate it into my application. At the moment my app with Hermit is just reasoning forever (I gave it 10-15 minutes and canceled afterwards).
>>> I will need to verify this but I believe that the OWL api version of the explanation tool does not explain inconsistent ontologies.  I thought it only handled unsatisfiable classes or class expressions. If I am wrong about this then I wasted some effort because I tried to write a tool that explained inconsistent ontologies some time back.
>>>
>>> I don't actually know of an open source tool that will explain inconsistent ontologies.  I suspect that Clark-Parsia has something like this but their code will probably come with restrictions.  You could try to use Matthews library.  It doesn't come with source but it is very good and you might be able to figure it out by looking at how it is used [1].
>>>
>>> I will try to verify my assertions later today.
>>>
>>> -Timothy
>>>
>>>
>>> [1] https://smi-protege.stanford.edu/repos/protege/protege4/plugins/org.protege.explanation
>>>
>>>> On 08/20/2012 08:59 AM, Lorenz Bühmann wrote:
>>>>> Why do you need the source code?
>>>>> On 20.08.2012 08:20, Stephan Opfer wrote:
>>>>>> Ok, but unfortunately no source code is available.
>>>>>>
>>>>>> On 08/20/2012 02:20 AM, Lorenz Buehmann wrote:
>>>>>>> This is not part of OWL API, you can find a jar file in the lib folder of the plugin in the svn:http://smi-protege.stanford.edu/repos/protege/protege4/plugins/org.protege.explanation/lib/
>>>>>>> But I'm not sure if this plugin is already used in Protege 4.1 or if there is another implementation for the explanation workbench.
>>>>>>> On 19.08.2012 23:38, Stephan Opfer wrote:
>>>>>>>> Hi,
>>>>>>>> a limit for the number of explanation does not help. I also deleted some unnecessary lines form the example (see attachment).
>>>>>>>> Best Regards,
>>>>>>>> Stephan
>>>>>> _______________________________________________
>>>>>> p4-feedback mailing list
>>>>>> [hidden email]
>>>>>> https://mailman.stanford.edu/mailman/listinfo/p4-feedback
>>>>>>
>>>>> _______________________________________________
>>>>> p4-feedback mailing list
>>>>> [hidden email]
>>>>> https://mailman.stanford.edu/mailman/listinfo/p4-feedback
>>>>>
>>>> _______________________________________________
>>>> p4-feedback mailing list
>>>> [hidden email]
>>>> https://mailman.stanford.edu/mailman/listinfo/p4-feedback
>>> _______________________________________________
>>> p4-feedback mailing list
>>> [hidden email]
>>> https://mailman.stanford.edu/mailman/listinfo/p4-feedback
>> ----------------------------------------------------------------------
>> Dr. Thomas Schneider
>> Universität Bremen, FB 03
>> Postfach 330440
>> 28334 Bremen
>> Germany
>> +49 421 218-64432
>> http://www.informatik.uni-bremen.de/~ts/
>> For visits: Cartesium, Room 2.56
>> ----------------------------------------------------------------------
>>
>> Dorchester (n.)
>> Someone else's throaty cough which obscures the crucial part of the rather amusing remark you've just made.
>>
>> Douglas Adams, John Lloyd: The Deeper Meaning of Liff
>>
>> _______________________________________________
>> p4-feedback mailing list
>> [hidden email]
>> https://mailman.stanford.edu/mailman/listinfo/p4-feedback
>
> _______________________________________________
> p4-feedback mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/p4-feedback
>

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Inconsistent.owl (11K) Download Attachment
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Re: Infinit Loop through Inconsistent Ontology Explanation

Lorenz Buehmann

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For this you should ask the HermiT developers, especially Birte Glimm. I'm sure they will help you and they are also fast in answering questions.
On 20.08.2012 20:24, Stephan Opfer wrote:
> Ok, but Hermit can explain inconsistent ontologies, as it is stated in the examples, which you can download with the Hermit files.
> What they do, is stop throwing InconsistentOntologyException and ask why Thing is unsatisfiable. Whether you would denote the results as a real explanation, is another question, I think. Nevertheless, I created a minimal ontology, which reproduces the behaviour I encountered with protege 4.1. (see attachment)
>
> But there are some problems, if you say that:
> 1. Case: Thing isOneOf {InconsistentNode, NormalNode1, NormalNode2, trans1to2, trans2to1} -> starting Hermit creates a ConcurrentModificationException
> 2. Case: See InconsistentRepaired.owl -> it offers a lot of explanations, for the inconsistency, although I would say, that it is not inconsistent.
>
> What I want, is to classify loosely coupled nodes - those nodes which does not have an incoming transition.
>
> I hope you have some ideas about that strange behaviour.
>
> Best Regards,
> Stephan
>
> On 08/20/2012 07:17 PM, Timothy Redmond wrote:
>> On 8/20/12 8:02 AM, Thomas Schneider wrote:
>>> According to my (perhaps not up-to-date) knowledge, Matthew's implementation in Protégé and OWL API indeed explain inferences of consistent ontologies "only".
>>
>> In the latest Protege 4.2, Matthew's implementation will also explain inconsistent ontologies. This is a major move forwards in my opinion (I always used to use "pellet explain"). The explanation library is freely available but is not open source as of yet.
>>
>> -Timothy
>>
>>
>>> The Pellet reasoner can compute explanations of inconsistencies, but only on the command line AFAIK. Try calling "pellet help explain". I don't know about the availability of their source code.
>>>
>>> Thomas
>>>
>>> On 20.08.2012, at 16:32, Timothy Redmond wrote:
>>>
>>>> On 08/20/2012 06:46 AM, Stephan Opfer wrote:
>>>>> It would be nice to integrate it into my application. At the moment my app with Hermit is just reasoning forever (I gave it 10-15 minutes and canceled afterwards).
>>>> I will need to verify this but I believe that the OWL api version of the explanation tool does not explain inconsistent ontologies. I thought it only handled unsatisfiable classes or class expressions. If I am wrong about this then I wasted some effort because I tried to write a tool that explained inconsistent ontologies some time back.
>>>>
>>>> I don't actually know of an open source tool that will explain inconsistent ontologies. I suspect that Clark-Parsia has something like this but their code will probably come with restrictions. You could try to use Matthews library. It doesn't come with source but it is very good and you might be able to figure it out by looking at how it is used [1].
>>>>
>>>> I will try to verify my assertions later today.
>>>>
>>>> -Timothy
>>>>
>>>>
>>>> [1] https://smi-protege.stanford.edu/repos/protege/protege4/plugins/org.protege.explanation
>>>>
>>>>> On 08/20/2012 08:59 AM, Lorenz Bühmann wrote:
>>>>>> Why do you need the source code?
>>>>>> On 20.08.2012 08:20, Stephan Opfer wrote:
>>>>>>> Ok, but unfortunately no source code is available.
>>>>>>>
>>>>>>> On 08/20/2012 02:20 AM, Lorenz Buehmann wrote:
>>>>>>>> This is not part of OWL API, you can find a jar file in the lib folder of the plugin in the svn:http://smi-protege.stanford.edu/repos/protege/protege4/plugins/org.protege.explanation/lib/
>>>>>>>> But I'm not sure if this plugin is already used in Protege 4.1 or if there is another implementation for the explanation workbench.
>>>>>>>> On 19.08.2012 23:38, Stephan Opfer wrote:
>>>>>>>>> Hi,
>>>>>>>>> a limit for the number of explanation does not help. I also deleted some unnecessary lines form the example (see attachment).
>>>>>>>>> Best Regards,
>>>>>>>>> Stephan
>>>>>>> _______________________________________________
>>>>>>> p4-feedback mailing list
>>>>>>> [hidden email]
>>>>>>> https://mailman.stanford.edu/mailman/listinfo/p4-feedback
>>>>>>>
>>>>>> _______________________________________________
>>>>>> p4-feedback mailing list
>>>>>> [hidden email]
>>>>>> https://mailman.stanford.edu/mailman/listinfo/p4-feedback
>>>>>>
>>>>> _______________________________________________
>>>>> p4-feedback mailing list
>>>>> [hidden email]
>>>>> https://mailman.stanford.edu/mailman/listinfo/p4-feedback
>>>> _______________________________________________
>>>> p4-feedback mailing list
>>>> [hidden email]
>>>> https://mailman.stanford.edu/mailman/listinfo/p4-feedback
>>> ----------------------------------------------------------------------
>>> Dr. Thomas Schneider
>>> Universität Bremen, FB 03
>>> Postfach 330440
>>> 28334 Bremen
>>> Germany
>>> +49 421 218-64432
>>> http://www.informatik.uni-bremen.de/~ts/
>>> For visits: Cartesium, Room 2.56
>>> ----------------------------------------------------------------------
>>>
>>> Dorchester (n.)
>>> Someone else's throaty cough which obscures the crucial part of the rather amusing remark you've just made.
>>>
>>> Douglas Adams, John Lloyd: The Deeper Meaning of Liff
>>>
>>> _______________________________________________
>>> p4-feedback mailing list
>>> [hidden email]
>>> https://mailman.stanford.edu/mailman/listinfo/p4-feedback
>>
>> _______________________________________________
>> p4-feedback mailing list
>> [hidden email]
>> https://mailman.stanford.edu/mailman/listinfo/p4-feedback
>>
>
>
>
> _______________________________________________
> p4-feedback mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/p4-feedback


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Re: Infinit Loop through Inconsistent Ontology Explanation

Stephan Opfer
Hm, but Birte Glimm is listed as former member of the research group.

On 08/20/2012 09:48 PM, Lorenz Buehmann wrote:
> For this you should ask the HermiT developers, especially Birte Glimm. I'm sure they will help you and they are also fast in answering questions.

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Re: Infinit Loop through Inconsistent Ontology Explanation

Lorenz Buehmann

-----BEGIN PGP SIGNED MESSAGE-----
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I know she is in Ulm(Germany) now, but I'm sure she is still a HermiT developer. Anyway, to get support please aks here: http://hermit-reasoner.com/support.html
Anybody will definitely help you.
<http://hermit-reasoner.com/support.html>

On 21.08.2012 15:40, Stephan Opfer wrote:
> Hm, but Birte Glimm is listed as former member of the research group.
>
> On 08/20/2012 09:48 PM, Lorenz Buehmann wrote:
>> For this you should ask the HermiT developers, especially Birte Glimm. I'm sure they will help you and they are also fast in answering questions.
>
> _______________________________________________
> p4-feedback mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/p4-feedback
>


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Re: Infinit Loop through Inconsistent Ontology Explanation

Stephan Opfer
As far as I understand the problem now, I never had a problem with Hermit. I was a little bit confused, by a ontology modelling mistake of me and that you denied that protege 4.1 can explain inconsistent ontologies.

On the one hand I found the mistake, which prevent me from repairing the inconsistency of my ontology and on the other hand I found some remark about the capabilities of Protege 4.1 in the release notes of Protege 4.2. The remark states that Protege 4.1 could explain inconsistent ontologies in an ad-hoc fashion, but sometimes it did not find an explanation.

What I learned from this, is that an inconsistent ontology is nothing you want to use, in order to explain the user, that he/she created something forbidden. At least not without some nice explanation tool, as it is introduced in Protege 4.2. Therefore, it would be nice to have that explanation tool downloadable as simple jar-lib, so that it could be integrated like the OWL-API and its explanation interface.

Ciao,
  Stephan


On 08/21/2012 06:08 PM, Lorenz Buehmann wrote:

>
> I know she is in Ulm(Germany) now, but I'm sure she is still a HermiT developer. Anyway, to get support please aks here: http://hermit-reasoner.com/support.html
> Anybody will definitely help you.
> <http://hermit-reasoner.com/support.html>
>
> On 21.08.2012 15:40, Stephan Opfer wrote:
>> Hm, but Birte Glimm is listed as former member of the research group.
>
>> On 08/20/2012 09:48 PM, Lorenz Buehmann wrote:
>>> For this you should ask the HermiT developers, especially Birte Glimm. I'm sure they will help you and they are also fast in answering questions.

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Re: Infinit Loop through Inconsistent Ontology Explanation

Timothy Redmond
On 08/22/2012 08:40 AM, Stephan Opfer wrote:
> As far as I understand the problem now, I never had a problem with Hermit. I was a little bit confused, by a ontology modelling mistake of me and that you denied that protege 4.1 can explain inconsistent ontologies.

Yes - I did write a tool of this sort and it found its way into some
Protege versions.  It was ad-hoc and though it often gave the right
answers, Matthew's principled tool that came later with Protege 4.2 is
much, much better.

>
> On the one hand I found the mistake, which prevent me from repairing the inconsistency of my ontology and on the other hand I found some remark about the capabilities of Protege 4.1 in the release notes of Protege 4.2. The remark states that Protege 4.1 could explain inconsistent ontologies in an ad-hoc fashion, but sometimes it did not find an explanation.

I was always somewhat unhappy with that tool.  It only existed at the
time because there was no other alternative (other than going to the
command line and using tools such as pellet).

>
> What I learned from this, is that an inconsistent ontology is nothing you want to use, in order to explain the user, that he/she created something forbidden. At least not without some nice explanation tool, as it is introduced in Protege 4.2. Therefore, it would be nice to have that explanation tool downloadable as simple jar-lib, so that it could be integrated like the OWL-API and its explanation interface.

Yes that would be nice.

-Timothy


>
> Ciao,
>    Stephan
>
>
> On 08/21/2012 06:08 PM, Lorenz Buehmann wrote:
>> I know she is in Ulm(Germany) now, but I'm sure she is still a HermiT developer. Anyway, to get support please aks here: http://hermit-reasoner.com/support.html
>> Anybody will definitely help you.
>> <http://hermit-reasoner.com/support.html>
>>
>> On 21.08.2012 15:40, Stephan Opfer wrote:
>>> Hm, but Birte Glimm is listed as former member of the research group.
>>> On 08/20/2012 09:48 PM, Lorenz Buehmann wrote:
>>>> For this you should ask the HermiT developers, especially Birte Glimm. I'm sure they will help you and they are also fast in answering questions.
> _______________________________________________
> p4-feedback mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/p4-feedback

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