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Tutorial for Protege 5.0

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Tutorial for Protege 5.0

ecos
I've found some tutorials for Protege 4.x, but not for 5.0, can you please refer me some tutorials where I can learn the basics including how to create associations between entities in a ontology? for example, hasTopping(Hawaiian Pizza, Pineapple)

Thanks.
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Re: Tutorial for Protege 5.0

Tania Tudorache
The tutorials for Protege 4 also apply for Protege 5, which is only an
incremental upgrade to version 4. Maybe some of the screenshots will be
outdated, but the actual content will still apply. There is no Protege 5
specific tutorial.

We also have some references to different tutorials and resources for
learning OWL on our wiki:
http://protegewiki.stanford.edu/wiki/Protege4UserDocs#Getting_started_.2F_tutorials

Cheers,
Tania

On 02/24/2015 01:21 PM, ecos wrote:

> I've found some tutorials for Protege 4.x, but not for 5.0, can you please
> refer me some tutorials where I can learn the basics including how to create
> associations between entities in a ontology? for example,
> hasTopping(Hawaiian Pizza, Pineapple)
>
> Thanks.
>
>
>
> --
> View this message in context: http://protege-project.136.n4.nabble.com/Tutorial-for-Protege-5-0-tp4662396.html
> Sent from the Protege User mailing list archive at Nabble.com.
> _______________________________________________
> protege-user mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-user


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Re: Tutorial for Protege 5.0

hazevedo
The A Practical Guide to Building OWL Ontologies tutorial, version V1.3 works properly with Protege 5.0 up to the 4.11 Automated Classification item. Of course the figures and the nomenclature are are slightly different.

Unfortunately,  in the item 4.11 of the  Protege tutorial it was created the owl: Nothing class highlighting inconsistencies in the Pizza ontology. Of course, I should try to fix it, but I'm starting ontology and using the tool. How should I proceed:
1. Start to use previous version of Protege or
2. Get  a location to download a compatable pizza.owl file with Protege 5.0
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Re: Tutorial for Protege 5.0

Matthew Horridge-2
Administrator
Hi,

If you’re talking about the ProbeInconsistentTopping class then you should just be able to delete this class.  Is that what you mean?

Cheers,

Matthew


> On 9 May 2017, at 12:58, hazevedo <[hidden email]> wrote:
>
> The /A Practical Guide to Building OWL Ontologies/ tutorial, version V1.3
> works properly with Protege 5.0 up to the /4.11 Automated Classification/
> item. Of course the figures and the nomenclature are are slightly different.
>
> Unfortunately,  in the item 4.11 of the  Protege tutorial it was created the
> /owl: Nothing/ class highlighting inconsistencies in the Pizza ontology. Of
> course, I should try to fix it, but I'm starting ontology and using the
> tool. How should I proceed:
> 1. Start to use previous version of Protege or
> 2. Get  a location to download a compatable pizza.owl file with Protege 5.0
>
>
>
> --
> View this message in context: http://protege-project.136.n4.nabble.com/Tutorial-for-Protege-5-0-tp4662396p4668431.html
> Sent from the Protege User mailing list archive at Nabble.com.
> _______________________________________________
> protege-user mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-user

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Re: Tutorial for Protege 5.0

hazevedo
Hi Matthew

Thanks for your answer.

You're right. I deleted ProbeInconsistentTopping and got to advance in the Tutorial ...

Unfortunately I did not make much progress! Going forward, in exercise 38, after creating a  closure axiom, I get the following information:

"Protects terminated reasoner.
An error occurred during reasoning: Unsupported axiom: Ignoring transitivity and / or complex subproperty axioms for isIngredientOf.
Org.mindswap.pellet.exceptions.UnsupportedFeatureException: Unsupported axiom: Ignoring transitivity and / or complex subproperty axioms for isIngredientOf"

After this message the Protégé tool comes to lock some times (I repeat several times the exercise 38). I tried (naively) to minify the reasoner's effort by removing options from the "Reasoner" tab present in Configuration. I removed them all, but the error persists. I tried to return the original options with the "Reset Preferences" button, but there was no change in the "Reasoner" tab. Then, I activated some options considering my memory of the original options.

Now, I am ignoring the error and following forward in the Tutorial aware that I can not activate Reasoner plugin again.

Comment: I know that the versions of Protégé 4.x and 5.x are very similar. However, for a beginner, small changes in the use of the Tutorial can represent an insurmountable obstacle. Even something simple like the exchange of "SuperClasses by "Subclass of" in the class hierarchy creates doubts in the learner is following the correct path.
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Re: Tutorial for Protege 5.0

Csongor Nyulas
Administrator
What reasoner were you using when you got the error message? Have you
tried to change the reasoner (in the Reasoner menu)? Would you get the
same exception with Hermit?

Regarding the difficulties of following the tutorial, we really
appreciate your feedback. We do have plans to update the tutorial, but
at the moment we have more urgent things to address.

Csongor


On 05/12/2017 12:46 PM, hazevedo wrote:

> Hi Matthew
>
> Thanks for your answer.
>
> You're right. I deleted ProbeInconsistentTopping and got to advance in the
> Tutorial ...
>
> Unfortunately I did not make much progress! Going forward, in exercise 38,
> after creating a  closure axiom, I get the following information:
>
> "Protects terminated reasoner.
> An error occurred during reasoning: Unsupported axiom: Ignoring transitivity
> and / or complex subproperty axioms for isIngredientOf.
> Org.mindswap.pellet.exceptions.UnsupportedFeatureException: Unsupported
> axiom: Ignoring transitivity and / or complex subproperty axioms for
> isIngredientOf"
>
> After this message the Protégé tool comes to lock some times (I repeat
> several times the exercise 38). I tried (naively) to minify the reasoner's
> effort by removing options from the "Reasoner" tab present in Configuration.
> I removed them all, but the error persists. I tried to return the original
> options with the "Reset Preferences" button, but there was no change in the
> "Reasoner" tab. Then, I activated some options considering my memory of the
> original options.
>
> Now, I am ignoring the error and following forward in the Tutorial aware
> that I can not activate Reasoner plugin again.
>
> Comment: I know that the versions of Protégé 4.x and 5.x are very similar.
> However, for a beginner, small changes in the use of the Tutorial can
> represent an insurmountable obstacle. Even something simple like the
> exchange of "SuperClasses by "Subclass of" in the class hierarchy creates
> doubts in the learner is following the correct path.
>
>
>
> --
> View this message in context: http://protege-project.136.n4.nabble.com/Tutorial-for-Protege-5-0-tp4662396p4668466.html
> Sent from the Protege User mailing list archive at Nabble.com.
> _______________________________________________
> protege-user mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-user


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Re: Tutorial for Protege 5.0

Lorenz B.
In reply to this post by hazevedo


Hi Matthew

Thanks for your answer.

You're right. I deleted ProbeInconsistentTopping and got to advance in the
Tutorial ... 

Unfortunately I did not make much progress! Going forward, in exercise 38,
after creating a  closure axiom, I get the following information:

"Protects terminated reasoner.
An error occurred during reasoning: Unsupported axiom: Ignoring transitivity
and / or complex subproperty axioms for isIngredientOf.
Org.mindswap.pellet.exceptions.UnsupportedFeatureException: Unsupported
axiom: Ignoring transitivity and / or complex subproperty axioms for
isIngredientOf"
That exception is because in OWL 2 it's not allowed to define a property that is transitive and used in a  sub-property chain axiom, see [1] 

[1] https://www.w3.org/TR/owl2-syntax/#Property_Hierarchy_and_Simple_Object_Property_Expressions

After this message the Protégé tool comes to lock some times (I repeat
several times the exercise 38). I tried (naively) to minify the reasoner's
effort by removing options from the "Reasoner" tab present in Configuration.
I removed them all, but the error persists. I tried to return the original
options with the "Reset Preferences" button, but there was no change in the
"Reasoner" tab. Then, I activated some options considering my memory of the
original options.

Now, I am ignoring the error and following forward in the Tutorial aware
that I can not activate Reasoner plugin again.

Comment: I know that the versions of Protégé 4.x and 5.x are very similar.
However, for a beginner, small changes in the use of the Tutorial can
represent an insurmountable obstacle. Even something simple like the
exchange of "SuperClasses by "Subclass of" in the class hierarchy creates
doubts in the learner is following the correct path.



--
View this message in context: http://protege-project.136.n4.nabble.com/Tutorial-for-Protege-5-0-tp4662396p4668466.html
Sent from the Protege User mailing list archive at Nabble.com.
_______________________________________________
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-- 
Lorenz Bühmann
AKSW group, University of Leipzig
Group: http://aksw.org - semantic web research center

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Re: Tutorial for Protege 5.0

hazevedo
Thanks for your answers.

Just for update the issue:
- I am using Pellet reasoner (no reason in particular).
- I will test the pizza ontology without using transitive property.


In this meanwhile, I have made some additional tests.


After the message that lock Protégé sometimes:
"Protects terminated reasoner.
An error occurred during reasoning: Unsupported axiom: Ignoring transitivity and / or complex subproperty axioms for isIngredientOf.
Org.mindswap.pellet.exceptions.UnsupportedFeatureException: Unsupported axiom: Ignoring transitivity and / or complex subproperty axioms for isIngredientOf "

1) I tried (naively) to minify the reasoner's effort by removing options from the "Reasoner" tab present in Configuration.
I removed them all, but the error persists. I tried to return the original options with the "Reset Preferences" button present at "Reasoner" tab, but there was no change in the "Reasoner" options. Then, I removed and re-installed Protege to gain access to the original configuration.

2) I figured out that I had made a mistake in previous Tutorial exercises, so I re-made all 38 exercises ever activating and deactivating Reasoner to identify when the problem occurred. I also saved the file Pizza.owl for each exercise performed. Again, upon arriving at Exercise 39 the problem was repeated. Then, I undo each step of exercise 39 to restore the final condition present at end of the exercise 38. Curiously even in this condition the Reasoner still presented the same problem. A diff between the Pizza_ex38.owl and Pizza_ex39_undone.owl versions reveals the following differences:
87a88.95
> <! - http://www.w3.org/2002/07/owl#topObjectProperty ->
>
> <Rdf: Description rdf: about = "http://www.w3.org/2002/07/owl#topObjectProperty">
<Rdf: type rdf: resource = "http://www.w3.org/2002/07/owl#FunctionalProperty" />
> </ Rdf: Description>
>

3) I was obsessed with figuring out the exact step of the exercise 39 that caused the error. So I performed the exercise step by step always using Reasoner and restarting Protégé. Under these conditions the error was not repeated.
I will try to move forward in the learning process.
Grateful.
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Re: Tutorial for Protege 5.0

Matthew Horridge-2
Administrator
Thanks for the update.  Glad you got it sorted!

Cheers,

Matthew

> On 14 May 2017, at 07:31, hazevedo <[hidden email]> wrote:
>
> Thanks for your answers.
>
> Just for update the issue:
> - I am using Pellet reasoner (no reason in particular).
> - I will test the pizza ontology without using transitive property.
>
>
> In this meanwhile, I have made some additional tests.
>
>
> After the message that lock Protégé sometimes:
> "Protects terminated reasoner.
> An error occurred during reasoning: Unsupported axiom: Ignoring transitivity
> and / or complex subproperty axioms for isIngredientOf.
> Org.mindswap.pellet.exceptions.UnsupportedFeatureException: Unsupported
> axiom: Ignoring transitivity and / or complex subproperty axioms for
> isIngredientOf "
>
> 1) I tried (naively) to minify the reasoner's effort by removing options
> from the "Reasoner" tab present in Configuration.
> I removed them all, but the error persists. I tried to return the original
> options with the "Reset Preferences" button present at "Reasoner" tab, but
> there was no change in the "Reasoner" options. Then, I removed and
> re-installed Protege to gain access to the original configuration.
>
> 2) I figured out that I had made a mistake in previous Tutorial exercises,
> so I re-made all 38 exercises ever activating and deactivating Reasoner to
> identify when the problem occurred. I also saved the file Pizza.owl for each
> exercise performed. Again, upon arriving at Exercise 39 the problem was
> repeated. Then, I undo each step of exercise 39 to restore the final
> condition present at end of the exercise 38. Curiously even in this
> condition the Reasoner still presented the same problem. A diff between the
> Pizza_ex38.owl and Pizza_ex39_undone.owl versions reveals the following
> differences:
> 87a88.95
>> <! - http://www.w3.org/2002/07/owl#topObjectProperty ->
>>
>> <Rdf: Description rdf: about =
>> "http://www.w3.org/2002/07/owl#topObjectProperty">
> <Rdf: type rdf: resource =
> "http://www.w3.org/2002/07/owl#FunctionalProperty" />
>> </ Rdf: Description>
>>
>
> 3) I was obsessed with figuring out the exact step of the exercise 39 that
> caused the error. So I performed the exercise step by step always using
> Reasoner and restarting Protégé. Under these conditions the error was not
> repeated.
> I will try to move forward in the learning process.
> Grateful.
>
>
>
> --
> View this message in context: http://protege-project.136.n4.nabble.com/Tutorial-for-Protege-5-0-tp4662396p4668472.html
> Sent from the Protege User mailing list archive at Nabble.com.
> _______________________________________________
> protege-user mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-user

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