Represent relations other than "is_a"

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suo
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Represent relations other than "is_a"

suo
Dear All:
I have Protege 4.0-OWL. I want to represent ontology relations other than "is_a" in an OWLViz view. For instance,
A RNA derive_from a Protein

How to do it?!
Thanks in advance!


     
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Re: Represent relations other than "is_a"

Thomas Schneider-5
Hi Suo,

I don't know if this is possible in OWLViz, but you can visualise  
models of ontologies (including arbitrary object properties) with  
Johannes Bauer's plugin SuperModel: http://tatome.de/projects/supermodel/

Cheers

Thomas

On 4 Jan 2010, at 09:10, suo wrote:

> Dear All:
> I have Protege 4.0-OWL. I want to represent ontology relations other  
> than "is_a" in an OWLViz view. For instance,
> A RNA derive_from a Protein
>
> How to do it?!
> Thanks in advance!
>
>
>
> _______________________________________________
> 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
+----------------------------------------------------------------------+
|  Dr Thomas Schneider                    schneider (at) cs.man.ac.uk  |
|  School of Computer Science       http://www.cs.man.ac.uk/~schneidt  |
|  Kilburn Building, Room 2.114                 phone +44 161 2756136  |
|  University of Manchester                                            |
|  Oxford Road                                             _///_       |
|  Manchester M13 9PL                                      (o~o)       |
+-----------------------------------------------------oOOO--(_)--OOOo--+

Skagway (n.)
   Sudden outbreak of cones on a motorway.

                   Douglas Adams, John Lloyd: The Deeper Meaning of Liff





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Re: Represent relations other than "is_a"

leyla.garcia
Hi Suo,

You also can use GrOWL http://www.uvm.edu/~skrivov/growl/ for ontology
visualization.

Cheers,

LG

> Hi Suo,
>
> I don't know if this is possible in OWLViz, but you can visualise
> models of ontologies (including arbitrary object properties) with
> Johannes Bauer's plugin SuperModel: http://tatome.de/projects/supermodel/
>
> Cheers
>
> Thomas
>
> On 4 Jan 2010, at 09:10, suo wrote:
>
>> Dear All:
>> I have Protege 4.0-OWL. I want to represent ontology relations other
>> than "is_a" in an OWLViz view. For instance,
>> A RNA derive_from a Protein
>>
>> How to do it?!
>> Thanks in advance!
>>
>>
>>
>> _______________________________________________
>> 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
>
> +----------------------------------------------------------------------+
> |  Dr Thomas Schneider                    schneider (at) cs.man.ac.uk  |
> |  School of Computer Science       http://www.cs.man.ac.uk/~schneidt  |
> |  Kilburn Building, Room 2.114                 phone +44 161 2756136  |
> |  University of Manchester                                            |
> |  Oxford Road                                             _///_       |
> |  Manchester M13 9PL                                      (o~o)       |
> +-----------------------------------------------------oOOO--(_)--OOOo--+
>
> Skagway (n.)
>    Sudden outbreak of cones on a motorway.
>
>                    Douglas Adams, John Lloyd: The Deeper Meaning of Liff
>
>
>
>
> _______________________________________________
> 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: Represent relations other than "is_a"

leyla.garcia
Hi Suo,

Also, if you need to browse more than one ontology and visualize selected
elements, you can use OLS2OWL: http://sourceforge.net/projects/ols2owl/
It uses GrOWL for visualization and allow you to browse elements by name
in predefined repository and those defined by Swoogle and Watson.

Best,

LG

> Hi Suo,
>
> You also can use GrOWL http://www.uvm.edu/~skrivov/growl/ for ontology
> visualization.
>
> Cheers,
>
> LG
>
>> Hi Suo,
>>
>> I don't know if this is possible in OWLViz, but you can visualise
>> models of ontologies (including arbitrary object properties) with
>> Johannes Bauer's plugin SuperModel:
>> http://tatome.de/projects/supermodel/
>>
>> Cheers
>>
>> Thomas
>>
>> On 4 Jan 2010, at 09:10, suo wrote:
>>
>>> Dear All:
>>> I have Protege 4.0-OWL. I want to represent ontology relations other
>>> than "is_a" in an OWLViz view. For instance,
>>> A RNA derive_from a Protein
>>>
>>> How to do it?!
>>> Thanks in advance!
>>>
>>>
>>>
>>> _______________________________________________
>>> 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
>>
>> +----------------------------------------------------------------------+
>> |  Dr Thomas Schneider                    schneider (at) cs.man.ac.uk  |
>> |  School of Computer Science       http://www.cs.man.ac.uk/~schneidt  |
>> |  Kilburn Building, Room 2.114                 phone +44 161 2756136  |
>> |  University of Manchester                                            |
>> |  Oxford Road                                             _///_       |
>> |  Manchester M13 9PL                                      (o~o)       |
>> +-----------------------------------------------------oOOO--(_)--OOOo--+
>>
>> Skagway (n.)
>>    Sudden outbreak of cones on a motorway.
>>
>>                    Douglas Adams, John Lloyd: The Deeper Meaning of Liff
>>
>>
>>
>>
>> _______________________________________________
>> 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
>>
>
>
> _______________________________________________
> 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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suo
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Re: Represent relations other than "is_a"

suo
In reply to this post by Thomas Schneider-5
Hi,

I put supermodel jar into my Protege4 owl plugin folder. But how to enable it? Thanks.

--- On Mon, 1/4/10, Thomas Schneider <[hidden email]> wrote:

> From: Thomas Schneider <[hidden email]>
> Subject: Re: [protege-owl] Represent relations other than "is_a"
> To: "User support for the Protege-OWL editor" <[hidden email]>
> Date: Monday, January 4, 2010, 1:35 AM
> Hi Suo,
>
> I don't know if this is possible in OWLViz, but you can
> visualise models of ontologies (including arbitrary object
> properties) with Johannes Bauer's plugin SuperModel: http://tatome.de/projects/supermodel/
>
> Cheers
>
> Thomas
>
> On 4 Jan 2010, at 09:10, suo wrote:
>
> > Dear All:
> > I have Protege 4.0-OWL. I want to represent ontology
> relations other than "is_a" in an OWLViz view. For
> instance,
> > A RNA derive_from a Protein
> >
> > How to do it?!
> > Thanks in advance!
> >
> >
> >
> > _______________________________________________
> > 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
>
> +----------------------------------------------------------------------+
> |  Dr Thomas Schneider       
>             schneider (at)
> cs.man.ac.uk  |
> |  School of Computer Science   
>    http://www.cs.man.ac.uk/~schneidt  |
> |  Kilburn Building, Room 2.114     
>            phone +44 161
> 2756136  |
> |  University of Manchester       
>                
>                
>     |
> |  Oxford Road         
>                
>                
>    _///_       |
> |  Manchester M13 9PL       
>                
>               (o~o) 
>      |
> +-----------------------------------------------------oOOO--(_)--OOOo--+
>
> Skagway (n.)
>   Sudden outbreak of cones on a motorway.
>
>                
>   Douglas Adams, John Lloyd: The Deeper Meaning of
> Liff
>
>
>
>
>
> -----Inline Attachment Follows-----
>
> _______________________________________________
> 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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suo
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Re: Represent relations other than "is_a"

suo
In reply to this post by leyla.garcia
Hi LG:

I installed GrOWL. As suggested by its page,  I need to "select menu item  Project | Configure". But there is no menu item Project and configure.
I use Protege4 owl on Mac os x.
Thanks.

--- On Mon, 1/4/10, [hidden email] <[hidden email]> wrote:

> From: [hidden email] <[hidden email]>
> Subject: Re: [protege-owl] Represent relations other than "is_a"
> To: "User support for the Protege-OWL editor" <[hidden email]>
> Date: Monday, January 4, 2010, 1:45 AM
> Hi Suo,
>
> You also can use GrOWL http://www.uvm.edu/~skrivov/growl/ for ontology
> visualization.
>
> Cheers,
>
> LG
>
> > Hi Suo,
> >
> > I don't know if this is possible in OWLViz, but you
> can visualise
> > models of ontologies (including arbitrary object
> properties) with
> > Johannes Bauer's plugin SuperModel: http://tatome.de/projects/supermodel/
> >
> > Cheers
> >
> > Thomas
> >
> > On 4 Jan 2010, at 09:10, suo wrote:
> >
> >> Dear All:
> >> I have Protege 4.0-OWL. I want to represent
> ontology relations other
> >> than "is_a" in an OWLViz view. For instance,
> >> A RNA derive_from a Protein
> >>
> >> How to do it?!
> >> Thanks in advance!
> >>
> >>
> >>
> >> _______________________________________________
> >> 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
> >
> >
> +----------------------------------------------------------------------+
> > |  Dr Thomas Schneider       
>             schneider (at)
> cs.man.ac.uk  |
> > |  School of Computer Science   
>    http://www.cs.man.ac.uk/~schneidt  |
> > |  Kilburn Building, Room 2.114   
>              phone
> +44 161 2756136  |
> > |  University of Manchester     
>                
>                
>       |
> > |  Oxford Road         
>                
>                
>    _///_       |
> > |  Manchester M13 9PL       
>                
>               (o~o) 
>      |
> >
> +-----------------------------------------------------oOOO--(_)--OOOo--+
> >
> > Skagway (n.)
> >    Sudden outbreak of cones on a motorway.
> >
> >               
>     Douglas Adams, John Lloyd: The Deeper Meaning
> of Liff
> >
> >
> >
> >
> > _______________________________________________
> > 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
> >
>
>
> _______________________________________________
> 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: Represent relations other than "is_a"

Thomas Schneider-5
In reply to this post by suo

On 6 Jan 2010, at 18:03, suo wrote:

> Hi,
>
> I put supermodel jar into my Protege4 owl plugin folder. But how to  
> enable it? Thanks.

If I remember correctly, you have to create a view for it:

* Go to some tab where you want to see it; presumably the OWLViz tab
* Select View -> Class views -> SuperModel from the menu and click  
with the mouse to a place in your Protégé window where you want the  
view to appear.

In lieu of a manual, there's a brief description on Pages 35f of  
Johannes's thesis: http://tatome.de/uni/d_thesis.pdf

Cheers

Thomas

>
> --- On Mon, 1/4/10, Thomas Schneider <[hidden email]> wrote:
>
>> From: Thomas Schneider <[hidden email]>
>> Subject: Re: [protege-owl] Represent relations other than "is_a"
>> To: "User support for the Protege-OWL editor" <[hidden email]
>> >
>> Date: Monday, January 4, 2010, 1:35 AM
>> Hi Suo,
>>
>> I don't know if this is possible in OWLViz, but you can
>> visualise models of ontologies (including arbitrary object
>> properties) with Johannes Bauer's plugin SuperModel: http://tatome.de/projects/supermodel/
>>
>> Cheers
>>
>> Thomas
>>
>> On 4 Jan 2010, at 09:10, suo wrote:
>>
>>> Dear All:
>>> I have Protege 4.0-OWL. I want to represent ontology
>> relations other than "is_a" in an OWLViz view. For
>> instance,
>>> A RNA derive_from a Protein
>>>
>>> How to do it?!
>>> Thanks in advance!
>>>
>>>
>>>
>>> _______________________________________________
>>> 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
>>
>> +
>> ----------------------------------------------------------------------+
>> |  Dr Thomas Schneider
>>             schneider (at)
>> cs.man.ac.uk  |
>> |  School of Computer Science
>>    http://www.cs.man.ac.uk/~schneidt  |
>> |  Kilburn Building, Room 2.114
>>            phone +44 161
>> 2756136  |
>> |  University of Manchester
>>
>>
>>     |
>> |  Oxford Road
>>
>>
>>    _///_       |
>> |  Manchester M13 9PL
>>
>>               (o~o)
>>      |
>> +-----------------------------------------------------oOOO--(_)--
>> OOOo--+
>>
>> Skagway (n.)
>>   Sudden outbreak of cones on a motorway.
>>
>>
>>   Douglas Adams, John Lloyd: The Deeper Meaning of
>> Liff
>>
>>
>>
>>
>>
>> -----Inline Attachment Follows-----
>>
>> _______________________________________________
>> 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
>>
>
>
>
> _______________________________________________
> 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
+----------------------------------------------------------------------+
|  Dr Thomas Schneider                    schneider (at) cs.man.ac.uk  |
|  School of Computer Science       http://www.cs.man.ac.uk/~schneidt  |
|  Kilburn Building, Room 2.114                 phone +44 161 2756136  |
|  University of Manchester                                            |
|  Oxford Road                                             _///_       |
|  Manchester M13 9PL                                      (o~o)       |
+-----------------------------------------------------oOOO--(_)--OOOo--+

Treewofe (n.)
   A very thick and heavy drift of snow balanced precariously on the
   edge of a door porch awaiting for what it judges to be the correct
   moment to fall.
   From the ancient Greek legend 'The Treewofe of Damocles'.

                   Douglas Adams, John Lloyd: The Deeper Meaning of Liff





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Re: Represent relations other than "is_a"

Leyla Jael García Castro
In reply to this post by suo
Hi Suo, 

I am not sure about what the GrOWL page means but it seams it is talking about Protégé 3.x.x. However, as far as I know, GrOWL can be used in Protégé 4.x.x

So, for both, GrOWL or Supermodel, you need to active the tab in the Tabs Menu, then you will have the tabs activated.
Hope it works.

Best, 

Leyla

> Date: Wed, 6 Jan 2010 10:07:11 -0800
> From: [hidden email]
> To: [hidden email]
> Subject: Re: [protege-owl] Represent relations other than "is_a"
>
> Hi LG:
>
> I installed GrOWL. As suggested by its page, I need to "select menu item Project | Configure". But there is no menu item Project and configure.
> I use Protege4 owl on Mac os x.
> Thanks.
>
> --- On Mon, 1/4/10, [hidden email] <[hidden email]> wrote:
>
> > From: [hidden email] <[hidden email]>
> > Subject: Re: [protege-owl] Represent relations other than "is_a"
> > To: "User support for the Protege-OWL editor" <[hidden email]>
> > Date: Monday, January 4, 2010, 1:45 AM
> > Hi Suo,
> >
> > You also can use GrOWL http://www.uvm.edu/~skrivov/growl/ for ontology
> > visualization.
> >
> > Cheers,
> >
> > LG
> >
> > > Hi Suo,
> > >
> > > I don't know if this is possible in OWLViz, but you
> > can visualise
> > > models of ontologies (including arbitrary object
> > properties) with
> > > Johannes Bauer's plugin SuperModel: http://tatome.de/projects/supermodel/
> > >
> > > Cheers
> > >
> > > Thomas
> > >
> > > On 4 Jan 2010, at 09:10, suo wrote:
> > >
> > >> Dear All:
> > >> I have Protege 4.0-OWL. I want to represent
> > ontology relations other
> > >> than "is_a" in an OWLViz view. For instance,
> > >> A RNA derive_from a Protein
> > >>
> > >> How to do it?!
> > >> Thanks in advance!
> > >>
> > >>
> > >>
> > >> _______________________________________________
> > >> 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
> > >
> > >
> > +----------------------------------------------------------------------+
> > > |  Dr Thomas Schneider       
> >             schneider (at)
> > cs.man.ac.uk  |
> > > |  School of Computer Science   
> >    http://www.cs.man.ac.uk/~schneidt  |
> > > |  Kilburn Building, Room 2.114   
> >              phone
> > +44 161 2756136  |
> > > |  University of Manchester     
> >                
> >                
> >       |
> > > |  Oxford Road         
> >                
> >                
> >    _///_       |
> > > |  Manchester M13 9PL       
> >                
> >               (o~o) 
> >      |
> > >
> > +-----------------------------------------------------oOOO--(_)--OOOo--+
> > >
> > > Skagway (n.)
> > >    Sudden outbreak of cones on a motorway.
> > >
> > >               
> >     Douglas Adams, John Lloyd: The Deeper Meaning
> > of Liff
> > >
> > >
> > >
> > >
> > > _______________________________________________
> > > 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
> > >
> >
> >
> > _______________________________________________
> > 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
> >
>
>
>
> _______________________________________________
> 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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Entity rendering through mireoting

suo
In reply to this post by Thomas Schneider-5
Hello all,

I use Protege 4. When I mireoted some IAO entities to my ontology, I prefer the entity name in mine looks like IAO: information content entity, but it is  "IAO: information content entity". I need to get rid of ""(double quote).
Thanks.


     
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Re: Represent relations other than "is_a"

Tania Tudorache
In reply to this post by Thomas Schneider-5
There is a new very nice visualization plugin for Protege 4.1 that allows you to browse other relationships than is-a. The plugin is called OntoGraf and you can get it by the Update mechanism.

See a video and documentation about the plugin:
http://protegewiki.stanford.edu/wiki/OntoGraf

As I said, you need to install Protege 4.1.

Tania


On 01/06/2010 11:04 AM, Thomas Schneider wrote:

On 6 Jan 2010, at 18:03, suo wrote:

Hi,

I put supermodel jar into my Protege4 owl plugin folder. But how to enable it? Thanks.

If I remember correctly, you have to create a view for it:

* Go to some tab where you want to see it; presumably the OWLViz tab
* Select View -> Class views -> SuperModel from the menu and click with the mouse to a place in your Protégé window where you want the view to appear.

In lieu of a manual, there's a brief description on Pages 35f of Johannes's thesis: http://tatome.de/uni/d_thesis.pdf

Cheers

Thomas


--- On Mon, 1/4/10, Thomas Schneider [hidden email] wrote:

From: Thomas Schneider [hidden email]
Subject: Re: [protege-owl] Represent relations other than "is_a"
To: "User support for the Protege-OWL editor" [hidden email]
Date: Monday, January 4, 2010, 1:35 AM
Hi Suo,

I don't know if this is possible in OWLViz, but you can
visualise models of ontologies (including arbitrary object
properties) with Johannes Bauer's plugin SuperModel: http://tatome.de/projects/supermodel/

Cheers

Thomas

On 4 Jan 2010, at 09:10, suo wrote:

Dear All:
I have Protege 4.0-OWL. I want to represent ontology
relations other than "is_a" in an OWLViz view. For
instance,
A RNA derive_from a Protein

How to do it?!
Thanks in advance!



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|  Dr Thomas Schneider                    schneider (at) cs.man.ac.uk  |
|  School of Computer Science       http://www.cs.man.ac.uk/~schneidt  |
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