search usage of individuals as values for annotation properties

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search usage of individuals as values for annotation properties

Matthew Brush

Hello.  Could someone tell me if there is a way to view in Protégé all Usages of individuals as values for annotation properties.  As far as I can tell, the standard ‘Usage’ feature in Protege shows only where individuals are used in object properties.  I have followed the IAO practice of using individuals to represent a controlled list of ‘curation status specifications’ for my ontology classes (e.g. individuals for ‘ready for release’, ‘metadata incomplete’, ‘exploratory class’, etc).  As an example use case, I might like to view all classes that have an curation status annotation property with the value ‘exploratory class’.

 

Any suggestions would be appreciated.

 

Thanks!

 

Matt

 

 

---

Matthew H. Brush
NLM Postdoctoral Fellow
Department of Medical Informatics and Clinical Epidemiology
Oregon Health and Science University
phone : 919-452-6914
fax :  503-346-6815
e-mail: [hidden email]

 


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Re: search usage of individuals as values for annotation properties

Carlo Torniai-2
Matt there is the animation search plugin



On Jul 31, 2012, at 6:16 PM, Matthew Brush <[hidden email]> wrote:

Hello.  Could someone tell me if there is a way to view in Protégé all Usages of individuals as values for annotation properties.  As far as I can tell, the standard ‘Usage’ feature in Protege shows only where individuals are used in object properties.  I have followed the IAO practice of using individuals to represent a controlled list of ‘curation status specifications’ for my ontology classes (e.g. individuals for ‘ready for release’, ‘metadata incomplete’, ‘exploratory class’, etc).  As an example use case, I might like to view all classes that have an curation status annotation property with the value ‘exploratory class’.

 

Any suggestions would be appreciated.

 

Thanks!

 

Matt

 

 

---

Matthew H. Brush
NLM Postdoctoral Fellow
Department of Medical Informatics and Clinical Epidemiology
Oregon Health and Science University
phone : 919-452-6914
fax :  503-346-6815
e-mail: [hidden email]

 

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Re: search usage of individuals as values for annotation properties

Alan Ruttenberg-2
Which will find all animated individuals ;)
You may also be interested in the annotation search plugin :)

-Alan


On Tuesday, July 31, 2012, Carlo Torniai <[hidden email]> wrote:
> Matt there is the animation search plugin
>
>
>
> On Jul 31, 2012, at 6:16 PM, Matthew Brush <[hidden email]> wrote:
>
> Hello.  Could someone tell me if there is a way to view in Protégé all Usages of individuals as values for annotation properties.  As far as I can tell, the standard ‘Usage’ feature in Protege shows only where individuals are used in object properties.  I have followed the IAO practice of using individuals to represent a controlled list of ‘curation status specifications’ for my ontology classes (e.g. individuals for ‘ready for release’, ‘metadata incomplete’, ‘exploratory class’, etc).  As an example use case, I might like to view all classes that have an curation status annotation property with the value ‘exploratory class’.
>

>  
>
> Any suggestions would be appreciated.
>
>  
>
> Thanks!
>
>  
>
> Matt
>
>  
>
>  
>
> ---
>
> Matthew H. Brush
> NLM Postdoctoral Fellow
> Department of Medical Informatics and Clinical Epidemiology
> Oregon Health and Science University
> phone : 919-452-6914
> fax :  503-346-6815
> e-mail: [hidden email]
>
>  
>
> _______________________________________________
> protege-owl mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-owl
>
> Instructions for unsubscribing: http://protege.stanford.edu/doc/faq.html#01a.03
>
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Re: search usage of individuals as values for annotation properties

Matthew Brush

Hi. Thanks Carlo, Alan.  Yes, I have tried this plug-in (Annotation Search View), but it seems only able to search on free-text annotations.  I was unable to use it to find usage of a given individual as a value for an annotation (as described in the example in my previous e-mail).  Was hoping there might be some special syntax for a query that would return such cases, or some other functionality I was missing that would allow this. Didn’t find any help in the plug-in documentation, but will  contact the developers directly for any insight here. 

 

Best,  Matt 

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Alan Ruttenberg
Sent: Wednesday, August 01, 2012 6:25 AM
To: User support for the Protege-OWL editor
Subject: Re: [protege-owl] search usage of individuals as values for annotation properties

 

Which will find all animated individuals ;)
You may also be interested in the annotation search plugin :)

-Alan


On Tuesday, July 31, 2012, Carlo Torniai <[hidden email]> wrote:


> Matt there is the animation search plugin
>
>
>
> On Jul 31, 2012, at 6:16 PM, Matthew Brush <[hidden email]> wrote:
>
> Hello.  Could someone tell me if there is a way to view in Protégé all Usages of individuals as values for annotation properties.  As far as I can tell, the standard ‘Usage’ feature in Protege shows only where individuals are used in object properties.  I have followed the IAO practice of using individuals to represent a controlled list of ‘curation status specifications’ for my ontology classes (e.g. individuals for ‘ready for release’, ‘metadata incomplete’, ‘exploratory class’, etc).  As an example use case, I might like to view all classes that have an curation status annotation property with the value ‘exploratory class’.
>
>  
>
> Any suggestions would be appreciated.
>
>  
>
> Thanks!
>
>  
>
> Matt
>
>  
>
>  
>
> ---
>
> Matthew H. Brush
> NLM Postdoctoral Fellow
> Department of Medical Informatics and Clinical Epidemiology
> Oregon Health and Science University
> phone : 919-452-6914
> fax :  503-346-6815
> e-mail: [hidden email]
>
>  
>
> _______________________________________________
> protege-owl mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-owl
>
> Instructions for unsubscribing: http://protege.stanford.edu/doc/faq.html#01a.03
>

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Re: search usage of individuals as values for annotation properties

Timothy Redmond


> Hello.  Could someone tell me if there is a way to view in Protégé all Usages of individuals as values for annotation properties.  As far as I can tell, the standard ‘Usage’ feature in Protege shows only where individuals are used in object properties.  I have followed the IAO practice of using individuals to represent a controlled list of ‘curation status specifications’ for my ontology classes (e.g. individuals for ‘ready for release’, ‘metadata incomplete’, ‘exploratory class’, etc).  As an example use case, I might like to view all classes that have an curation status annotation property with the value ‘exploratory class’.

The problem here is that an annotation property value that is an OWL individual must be an anonymous individual (http://goo.gl/gvlby).   Unfortunately Protege 4 doesn't handle anonymous individuals well and there is no method for selecting such a thing.   Therefore there is no way to display this individual in the usage view.

There is a bug tracker for this (http://goo.gl/LMcly).   It is not clear how hard this would be to fix but it has a couple of delicate issues.

Alternatively if you are talking about the case where the annotation value is an IRI which is the same as the IRI of some OWL individual then I am not surprised that this does not work as you want.  I can see why you would want this feature.  It hasn't been implemented yet because it really is not a case of finding the usage of the individual.  But there is some other code in Protege (e.g. I think that the refactor code does this) that goes looking for IRI annotation values to do the "right" thing.

-Timothy



On 8/1/12 7:56 AM, Matthew Brush wrote:

Hi. Thanks Carlo, Alan.  Yes, I have tried this plug-in (Annotation Search View), but it seems only able to search on free-text annotations.  I was unable to use it to find usage of a given individual as a value for an annotation (as described in the example in my previous e-mail).  Was hoping there might be some special syntax for a query that would return such cases, or some other functionality I was missing that would allow this. Didn’t find any help in the plug-in documentation, but will  contact the developers directly for any insight here. 

 

Best,  Matt 

 

From: [hidden email] [[hidden email]] On Behalf Of Alan Ruttenberg
Sent: Wednesday, August 01, 2012 6:25 AM
To: User support for the Protege-OWL editor
Subject: Re: [protege-owl] search usage of individuals as values for annotation properties

 

Which will find all animated individuals ;)
You may also be interested in the annotation search plugin :)

-Alan


On Tuesday, July 31, 2012, Carlo Torniai <[hidden email]> wrote:
> Matt there is the animation search plugin
>
>
>
> On Jul 31, 2012, at 6:16 PM, Matthew Brush <[hidden email]> wrote:
>
> Hello.  Could someone tell me if there is a way to view in Protégé all Usages of individuals as values for annotation properties.  As far as I can tell, the standard ‘Usage’ feature in Protege shows only where individuals are used in object properties.  I have followed the IAO practice of using individuals to represent a controlled list of ‘curation status specifications’ for my ontology classes (e.g. individuals for ‘ready for release’, ‘metadata incomplete’, ‘exploratory class’, etc).  As an example use case, I might like to view all classes that have an curation status annotation property with the value ‘exploratory class’.
>
>  
>
> Any suggestions would be appreciated.
>
>  
>
> Thanks!
>
>  
>
> Matt
>
>  
>
>  
>
> ---
>
> Matthew H. Brush
> NLM Postdoctoral Fellow
> Department of Medical Informatics and Clinical Epidemiology
> Oregon Health and Science University
> phone : 919-452-6914
> fax :  503-346-6815
> e-mail: [hidden email]
>
>  
>
> _______________________________________________
> protege-owl mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-owl
>
> Instructions for unsubscribing: http://protege.stanford.edu/doc/faq.html#01a.03
>



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Re: search usage of individuals as values for annotation properties

Timothy Redmond
In reply to this post by Matthew Brush
On 8/1/12 7:56 AM, Matthew Brush wrote:
Didn’t find any help in the plug-in documentation, but will  contact the developers directly for any insight here. 

Not really necessary as all the developers are present on this list.  Posting on list is good for the community as well as it allows future users and developers to find answers.

-Timothy


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Re: search usage of individuals as values for annotation properties

Carlo Torniai-2
In reply to this post by Alan Ruttenberg-2
Yup.. darn autocorrect on the iphone 
.I may want to write the animated individuals search plugin tho :-)

C

On Wed, Aug 1, 2012 at 6:24 AM, Alan Ruttenberg <[hidden email]> wrote:
Which will find all animated individuals ;)
You may also be interested in the annotation search plugin :)

-Alan



On Tuesday, July 31, 2012, Carlo Torniai <[hidden email]> wrote:
> Matt there is the animation search plugin
>
>
>
> On Jul 31, 2012, at 6:16 PM, Matthew Brush <[hidden email]> wrote:
>
> Hello.  Could someone tell me if there is a way to view in Protégé all Usages of individuals as values for annotation properties.  As far as I can tell, the standard ‘Usage’ feature in Protege shows only where individuals are used in object properties.  I have followed the IAO practice of using individuals to represent a controlled list of ‘curation status specifications’ for my ontology classes (e.g. individuals for ‘ready for release’, ‘metadata incomplete’, ‘exploratory class’, etc).  As an example use case, I might like to view all classes that have an curation status annotation property with the value ‘exploratory class’.
>

>  
>
> Any suggestions would be appreciated.
>
>  
>
> Thanks!
>
>  
>
> Matt
>
>  
>
>  
>
> ---
>
> Matthew H. Brush
> NLM Postdoctoral Fellow
> Department of Medical Informatics and Clinical Epidemiology
> Oregon Health and Science University
> phone : <a href="tel:919-452-6914" value="+19194526914" target="_blank">919-452-6914
> fax :  <a href="tel:503-346-6815" value="+15033466815" target="_blank">503-346-6815
> e-mail: [hidden email]
>
>  
>
> _______________________________________________
> protege-owl mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-owl
>
> Instructions for unsubscribing: http://protege.stanford.edu/doc/faq.html#01a.03
>

_______________________________________________
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--
Carlo


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search usage of individuals as values for annotation properties

Alan Ruttenberg-2
In reply to this post by Timothy Redmond
I don't believe that to be correct. Annotation properties relate IRIs or anonymous individual to IRIs, literals, or anonymous individuals  Whether that IRI denotes an individual, class, property, or something that is not even an entity in the owl structural model doesn't matter.

Spec says

Annotation := 'Annotation' '(' annotationAnnotations AnnotationProperty AnnotationValue ')'
annotationAnnotations  := { Annotation }
AnnotationValue := AnonymousIndividual | IRI | Literal



See the structural specification on annotation assertions and the production for annotation value.

-Alan

On Wednesday, August 1, 2012, Timothy Redmond <[hidden email]> wrote:
>
>
>> Hello.  Could someone tell me if there is a way to view in Protégé all Usages of individuals as values for annotation properties.  As far as I can tell, the standard ‘Usage’ feature in Protege shows only where individuals are used in object properties.  I have followed the IAO practice of using individuals to represent a controlled list of ‘curation status specifications’ for my ontology classes (e.g. individuals for ‘ready for release’, ‘metadata incomplete’, ‘exploratory class’, etc).  As an example use case, I might like to view all classes that have an curation status annotation property with the value ‘exploratory class’.
>
> The problem here is that an annotation property value that is an OWL individual must be an anonymous individual (http://goo.gl/gvlby).   Unfortunately Protege 4 doesn't handle anonymous individuals well and there is no method for selecting such a thing.   Therefore there is no way to display this individual in the usage view.
>
> There is a bug tracker for this (http://goo.gl/LMcly).   It is not clear how hard this would be to fix but it has a couple of delicate issues.
>
> Alternatively if you are talking about the case where the annotation value is an IRI which is the same as the IRI of some OWL individual then I am not surprised that this does not work as you want.  I can see why you would want this feature.  It hasn't been implemented yet because it really is not a case of finding the usage of the individual.  But there is some other code in Protege (e.g. I think that the refactor code does this) that goes looking for IRI annotation values to do the "right" thing.
>
> -Timothy
>
>
>
> On 8/1/12 7:56 AM, Matthew Brush wrote:
>
> Hi. Thanks Carlo, Alan.  Yes, I have tried this plug-in (Annotation Search View), but it seems only able to search on free-text annotations.  I was unable to use it to find usage of a given individual as a value for an annotation (as described in the example in my previous e-mail).  Was hoping there might be some special syntax for a query that would return such cases, or some other functionality I was missing that would allow this. Didn’t find any help in the plug-in documentation, but will  contact the developers directly for any insight here. 
>
>  
>
> Best,  Matt 
>
>  
>
> From: [hidden email] [mailto:[hidden email]] On Behalf Of Alan Ruttenberg
> Sent: Wednesday, August 01, 2012 6:25 AM
> To: User support for the Protege-OWL editor
> Subject: Re: [protege-owl] search usage of individuals as values for annotation properties
>
>  
>
> Which will find all animated individuals ;)
> You may also be interested in the annotation search plugin :)
>
> -Alan
>
>
> On Tuesday, July 31, 2012, Carlo Torniai <[hidden email]> wrote:
>> Matt there is the animation search plugin
>>
>>
>>
>> On Jul 31, 2012, at 6:16 PM, Matthew Brush <[hidden email]> wrote:
>>
>> Hello.  Could someone tell me if there is a way to view in Protégé all Usages of individuals as values for annotation properties.  As far as I can tell, the standard ‘Usage’ feature in Protege shows only where individuals are used in object properties.  I have followed the IAO practice of using individuals to represent a controlled list of ‘curation status specifications’ for my ontology classes (e.g. individuals for ‘ready for release’, ‘metadata incomplete’, ‘exploratory class’, etc).  As an example use case, I might like to view all classes that have an curation status annotation property with the value ‘exploratory class’.
>>

>>  
>>
>> Any suggestions would be appreciated.
>>
>>  
>>
>> Thanks!
>>
>>  
>>
>> Matt
>>
>>  
>>
>>  
>>
>> ---
>>
>> Matthew H. Brush
>> NLM Postdoctoral Fellow
>> Department of Medical Informatics and Clinical Epidemiology
>> Oregon Health and Science University
>> phone : 919-452-6914
>> fax :  503-346-6815
>> e-mail: [hidden email]
>>
>>  
>>
>> _______________________________________________
>> protege-owl mailing list
>>
_______________________________________________
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[hidden email]
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Instructions for unsubscribing: http://protege.stanford.edu/doc/faq.html#01a.03
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Re: search usage of individuals as values for annotation properties

Timothy Redmond
On 8/1/12 12:03 PM, Alan Ruttenberg wrote:
I don't believe that to be correct. Annotation properties relate IRIs or anonymous individual to IRIs, literals, or anonymous individuals  Whether that IRI denotes an individual, class, property, or something that is not even an entity in the owl structural model doesn't matter.

Spec says

Annotation := 'Annotation' '(' annotationAnnotations AnnotationProperty AnnotationValue ')'
annotationAnnotations  := { Annotation }
AnnotationValue := AnonymousIndividual | IRI | Literal

Yes this is correct - there are three disjoint types of annotation values.  The only type of annotation value that is an individual is the AnonymousIndividual.

-Timothy






See the structural specification on annotation assertions and the production for annotation value.

-Alan

On Wednesday, August 1, 2012, Timothy Redmond <[hidden email]> wrote:
>
>
>> Hello.  Could someone tell me if there is a way to view in Protégé all Usages of individuals as values for annotation properties.  As far as I can tell, the standard ‘Usage’ feature in Protege shows only where individuals are used in object properties.  I have followed the IAO practice of using individuals to represent a controlled list of ‘curation status specifications’ for my ontology classes (e.g. individuals for ‘ready for release’, ‘metadata incomplete’, ‘exploratory class’, etc).  As an example use case, I might like to view all classes that have an curation status annotation property with the value ‘exploratory class’.
>
> The problem here is that an annotation property value that is an OWL individual must be an anonymous individual (http://goo.gl/gvlby).   Unfortunately Protege 4 doesn't handle anonymous individuals well and there is no method for selecting such a thing.   Therefore there is no way to display this individual in the usage view.
>
> There is a bug tracker for this (http://goo.gl/LMcly).   It is not clear how hard this would be to fix but it has a couple of delicate issues.
>
> Alternatively if you are talking about the case where the annotation value is an IRI which is the same as the IRI of some OWL individual then I am not surprised that this does not work as you want.  I can see why you would want this feature.  It hasn't been implemented yet because it really is not a case of finding the usage of the individual.  But there is some other code in Protege (e.g. I think that the refactor code does this) that goes looking for IRI annotation values to do the "right" thing.
>
> -Timothy
>
>
>
> On 8/1/12 7:56 AM, Matthew Brush wrote:
>
> Hi. Thanks Carlo, Alan.  Yes, I have tried this plug-in (Annotation Search View), but it seems only able to search on free-text annotations.  I was unable to use it to find usage of a given individual as a value for an annotation (as described in the example in my previous e-mail).  Was hoping there might be some special syntax for a query that would return such cases, or some other functionality I was missing that would allow this. Didn’t find any help in the plug-in documentation, but will  contact the developers directly for any insight here. 
>
>  
>
> Best,  Matt 
>
>  
>
> From: [hidden email] [mailto:[hidden email]] On Behalf Of Alan Ruttenberg
> Sent: Wednesday, August 01, 2012 6:25 AM
> To: User support for the Protege-OWL editor
> Subject: Re: [protege-owl] search usage of individuals as values for annotation properties
>
>  
>
> Which will find all animated individuals ;)
> You may also be interested in the annotation search plugin :)
>
> -Alan
>
>
> On Tuesday, July 31, 2012, Carlo Torniai <[hidden email]> wrote:
>> Matt there is the animation search plugin
>>
>>
>>
>> On Jul 31, 2012, at 6:16 PM, Matthew Brush <[hidden email]> wrote:
>>
>> Hello.  Could someone tell me if there is a way to view in Protégé all Usages of individuals as values for annotation properties.  As far as I can tell, the standard ‘Usage’ feature in Protege shows only where individuals are used in object properties.  I have followed the IAO practice of using individuals to represent a controlled list of ‘curation status specifications’ for my ontology classes (e.g. individuals for ‘ready for release’, ‘metadata incomplete’, ‘exploratory class’, etc).  As an example use case, I might like to view all classes that have an curation status annotation property with the value ‘exploratory class’.
>>
>>  
>>
>> Any suggestions would be appreciated.
>>
>>  
>>
>> Thanks!
>>
>>  
>>
>> Matt
>>
>>  
>>
>>  
>>
>> ---
>>
>> Matthew H. Brush
>> NLM Postdoctoral Fellow
>> Department of Medical Informatics and Clinical Epidemiology
>> Oregon Health and Science University
>> phone : 919-452-6914
>> fax :  503-346-6815
>> e-mail: [hidden email]
>>
>>  
>>
>> _______________________________________________
>> protege-owl mailing list
>>

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Re: search usage of individuals as values for annotation properties

Timothy Redmond
On 8/1/12 12:07 PM, Timothy Redmond wrote:
On 8/1/12 12:03 PM, Alan Ruttenberg wrote:
I don't believe that to be correct. Annotation properties relate IRIs or anonymous individual to IRIs, literals, or anonymous individuals  Whether that IRI denotes an individual, class, property, or something that is not even an entity in the owl structural model doesn't matter.

Spec says

Annotation := 'Annotation' '(' annotationAnnotations AnnotationProperty AnnotationValue ')'
annotationAnnotations  := { Annotation }
AnnotationValue := AnonymousIndividual | IRI | Literal

Yes this is correct - there are three disjoint types of annotation values.  The only type of annotation value that is an individual is the AnonymousIndividual.

I can see this question getting messy because it is really more about the intent of the specification.   I also don't think that it is the right question.  We agree that the usage view should be modified to look for the IRI's in annotation property values that correspond to entities in the ontology.

-Timothy





-Timothy






See the structural specification on annotation assertions and the production for annotation value.

-Alan

On Wednesday, August 1, 2012, Timothy Redmond <[hidden email]> wrote:
>
>
>> Hello.  Could someone tell me if there is a way to view in Protégé all Usages of individuals as values for annotation properties.  As far as I can tell, the standard ‘Usage’ feature in Protege shows only where individuals are used in object properties.  I have followed the IAO practice of using individuals to represent a controlled list of ‘curation status specifications’ for my ontology classes (e.g. individuals for ‘ready for release’, ‘metadata incomplete’, ‘exploratory class’, etc).  As an example use case, I might like to view all classes that have an curation status annotation property with the value ‘exploratory class’.
>
> The problem here is that an annotation property value that is an OWL individual must be an anonymous individual (http://goo.gl/gvlby).   Unfortunately Protege 4 doesn't handle anonymous individuals well and there is no method for selecting such a thing.   Therefore there is no way to display this individual in the usage view.
>
> There is a bug tracker for this (http://goo.gl/LMcly).   It is not clear how hard this would be to fix but it has a couple of delicate issues.
>
> Alternatively if you are talking about the case where the annotation value is an IRI which is the same as the IRI of some OWL individual then I am not surprised that this does not work as you want.  I can see why you would want this feature.  It hasn't been implemented yet because it really is not a case of finding the usage of the individual.  But there is some other code in Protege (e.g. I think that the refactor code does this) that goes looking for IRI annotation values to do the "right" thing.
>
> -Timothy
>
>
>
> On 8/1/12 7:56 AM, Matthew Brush wrote:
>
> Hi. Thanks Carlo, Alan.  Yes, I have tried this plug-in (Annotation Search View), but it seems only able to search on free-text annotations.  I was unable to use it to find usage of a given individual as a value for an annotation (as described in the example in my previous e-mail).  Was hoping there might be some special syntax for a query that would return such cases, or some other functionality I was missing that would allow this. Didn’t find any help in the plug-in documentation, but will  contact the developers directly for any insight here. 
>
>  
>
> Best,  Matt 
>
>  
>
> From: [hidden email] [mailto:[hidden email]] On Behalf Of Alan Ruttenberg
> Sent: Wednesday, August 01, 2012 6:25 AM
> To: User support for the Protege-OWL editor
> Subject: Re: [protege-owl] search usage of individuals as values for annotation properties
>
>  
>
> Which will find all animated individuals ;)
> You may also be interested in the annotation search plugin :)
>
> -Alan
>
>
> On Tuesday, July 31, 2012, Carlo Torniai <[hidden email]> wrote:
>> Matt there is the animation search plugin
>>
>>
>>
>> On Jul 31, 2012, at 6:16 PM, Matthew Brush <[hidden email]> wrote:
>>
>> Hello.  Could someone tell me if there is a way to view in Protégé all Usages of individuals as values for annotation properties.  As far as I can tell, the standard ‘Usage’ feature in Protege shows only where individuals are used in object properties.  I have followed the IAO practice of using individuals to represent a controlled list of ‘curation status specifications’ for my ontology classes (e.g. individuals for ‘ready for release’, ‘metadata incomplete’, ‘exploratory class’, etc).  As an example use case, I might like to view all classes that have an curation status annotation property with the value ‘exploratory class’.
>>
>>  
>>
>> Any suggestions would be appreciated.
>>
>>  
>>
>> Thanks!
>>
>>  
>>
>> Matt
>>
>>  
>>
>>  
>>
>> ---
>>
>> Matthew H. Brush
>> NLM Postdoctoral Fellow
>> Department of Medical Informatics and Clinical Epidemiology
>> Oregon Health and Science University
>> phone : 919-452-6914
>> fax :  503-346-6815
>> e-mail: [hidden email]
>>
>>  
>>
>> _______________________________________________
>> protege-owl mailing list
>>

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Re: search usage of individuals as values for annotation properties

Alan Ruttenberg-2


On Wed, Aug 1, 2012 at 3:28 PM, Timothy Redmond <[hidden email]> wrote:
On 8/1/12 12:07 PM, Timothy Redmond wrote:
On 8/1/12 12:03 PM, Alan Ruttenberg wrote:
I don't believe that to be correct. Annotation properties relate IRIs or anonymous individual to IRIs, literals, or anonymous individuals  Whether that IRI denotes an individual, class, property, or something that is not even an entity in the owl structural model doesn't matter.

Spec says

Annotation := 'Annotation' '(' annotationAnnotations AnnotationProperty AnnotationValue ')'
annotationAnnotations  := { Annotation }
AnnotationValue := AnonymousIndividual | IRI | Literal

Yes this is correct - there are three disjoint types of annotation values.  The only type of annotation value that is an individual is the AnonymousIndividual.

I can see this question getting messy because it is really more about the intent of the specification.   I also don't think that it is the right question.  We agree that the usage view should be modified to look for the IRI's in annotation property values that correspond to entities in the ontology.

Yes. The back story is that this ties into the architecture of the www document and the idea that IRIs mean one thing. So in RDF the single IRI denotes an individual and also has a class extension and a property extension. OWL 2 both supports this and breaks it slightly, primarily in that if you say that two IRIs are sameAs, then you would expect that their class extensions and property extensions are the same too. That isn't the case in OWL 2 using the direct semantics. 

So Annotations were designed so as to to commit to either the seemingly different class/individual/property "puns" - the different senses in OWL that are are more unified in RDF/OWL 2 using the RDF semantics. The intention is that if you are adding an annotation, it is to the "one thing" that is the resource that the IRI identifies. For example, you can't have a different rdfs:label for the IRI used as a class as compared to the IRI used as an individual.

The expected behavior in the interface is that annotations on an IRI would appear for all the "puns", i.e. in the property view if the IRI was declared a property, in the class view if the IRI was declared a class, in the individual view if declared a named individual. 

Similarly when offering to fill in the values of an annotation property, all the IRIs for entities in the ontology would be offered (as well as the ability to type in a new IRI). I think a reasonable display would be to render the label, and have parenthetical keywords indicating the various ways the IRI was "punned" in the current ontology. However this does break one of Protege's visual assumptions, namely that there is a little icon beside each name saying what kind of entity it is, because it is perfectly reasonable that an IRI is used both as class and individual. It also means it would be desirable that there be a view and record of IRIs used in annotation properties that *do not* correspond to entities in the ontology, from which already used IRIs could be selected and which could show annotations on them that otherwise are invisible because they are not to a class, individual, property, datatype...

Hope this makes sense,
Alan


 


-Timothy






-Timothy






See the structural specification on annotation assertions and the production for annotation value.

-Alan

On Wednesday, August 1, 2012, Timothy Redmond <[hidden email]> wrote:
>
>
>> Hello.  Could someone tell me if there is a way to view in Protégé all Usages of individuals as values for annotation properties.  As far as I can tell, the standard ‘Usage’ feature in Protege shows only where individuals are used in object properties.  I have followed the IAO practice of using individuals to represent a controlled list of ‘curation status specifications’ for my ontology classes (e.g. individuals for ‘ready for release’, ‘metadata incomplete’, ‘exploratory class’, etc).  As an example use case, I might like to view all classes that have an curation status annotation property with the value ‘exploratory class’.
>
> The problem here is that an annotation property value that is an OWL individual must be an anonymous individual (http://goo.gl/gvlby).   Unfortunately Protege 4 doesn't handle anonymous individuals well and there is no method for selecting such a thing.   Therefore there is no way to display this individual in the usage view.
>
> There is a bug tracker for this (http://goo.gl/LMcly).   It is not clear how hard this would be to fix but it has a couple of delicate issues.
>
> Alternatively if you are talking about the case where the annotation value is an IRI which is the same as the IRI of some OWL individual then I am not surprised that this does not work as you want.  I can see why you would want this feature.  It hasn't been implemented yet because it really is not a case of finding the usage of the individual.  But there is some other code in Protege (e.g. I think that the refactor code does this) that goes looking for IRI annotation values to do the "right" thing.
>
> -Timothy
>
>
>
> On 8/1/12 7:56 AM, Matthew Brush wrote:
>
> Hi. Thanks Carlo, Alan.  Yes, I have tried this plug-in (Annotation Search View), but it seems only able to search on free-text annotations.  I was unable to use it to find usage of a given individual as a value for an annotation (as described in the example in my previous e-mail).  Was hoping there might be some special syntax for a query that would return such cases, or some other functionality I was missing that would allow this. Didn’t find any help in the plug-in documentation, but will  contact the developers directly for any insight here. 
>
>  
>
> Best,  Matt 
>
>  
>
> From: [hidden email] [mailto:[hidden email]] On Behalf Of Alan Ruttenberg
> Sent: Wednesday, August 01, 2012 6:25 AM
> To: User support for the Protege-OWL editor
> Subject: Re: [protege-owl] search usage of individuals as values for annotation properties
>
>  
>
> Which will find all animated individuals ;)
> You may also be interested in the annotation search plugin :)
>
> -Alan
>
>
> On Tuesday, July 31, 2012, Carlo Torniai <[hidden email]> wrote:
>> Matt there is the animation search plugin
>>
>>
>>
>> On Jul 31, 2012, at 6:16 PM, Matthew Brush <[hidden email]> wrote:
>>
>> Hello.  Could someone tell me if there is a way to view in Protégé all Usages of individuals as values for annotation properties.  As far as I can tell, the standard ‘Usage’ feature in Protege shows only where individuals are used in object properties.  I have followed the IAO practice of using individuals to represent a controlled list of ‘curation status specifications’ for my ontology classes (e.g. individuals for ‘ready for release’, ‘metadata incomplete’, ‘exploratory class’, etc).  As an example use case, I might like to view all classes that have an curation status annotation property with the value ‘exploratory class’.
>>
>>  
>>
>> Any suggestions would be appreciated.
>>
>>  
>>
>> Thanks!
>>
>>  
>>
>> Matt
>>
>>  
>>
>>  
>>
>> ---
>>
>> Matthew H. Brush
>> NLM Postdoctoral Fellow
>> Department of Medical Informatics and Clinical Epidemiology
>> Oregon Health and Science University
>> phone : <a href="tel:919-452-6914" value="+19194526914" target="_blank">919-452-6914
>> fax :  <a href="tel:503-346-6815" value="+15033466815" target="_blank">503-346-6815
>> e-mail: [hidden email]
>>
>>  
>>
>> _______________________________________________
>> protege-owl mailing list
>>

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