[protege-owl] viewing bipax owl instances graphically using OWLViz

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[protege-owl] viewing bipax owl instances graphically using OWLViz

dhivyaai
Hello all,
 
I'm using Protege version 3.2 beta and thanks to your help, I've now been able to import a biopax file into protege. But when I try to use the OWLViz plug in to view a diagram of the owl file, I get the following error:
 
A error related to DOT has occured. This error was probably because OWL Viz could not find the DOT application. Please ensure that the path to the DOT application is set properly.
 
The DOT path seems to be set to:
 
C:\Program Files\ATT\GraphViz\bin\Dot This path doesnt seem to exist.
 
Has anyone else had the same problem? Any suggestions about other ways to view the file graphically on protege?
 
thanks
dhivya
 
 
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[protege-owl] Re: viewing bipax owl instances graphically using OWLViz

Asad Bajwa
Hi there,

to use the owlviz you have to install the graphviz. Got it from here
http://www.graphviz.org/Download..php
Remember the path where you have installed graphviz.  now you should
have the tool dot.exe in the path. remember this path. Some algorithm of
Dot.exe is used by owlviz i think.
No you got back into protege and click at the owlviz tab. the error will
occur again, because you have not set the path yet. therefore you need
to go into options (in owlviz tab) and set the path you should have
remembered :-)

And voila you can take a look at the classes and subclasses.

Asad




> Hello all,
>  
> I'm using Protege version 3.2 beta and thanks to your help, I've now
> been able to import a biopax file into protege. But when I try to use
> the OWLViz plug in to view a diagram of the owl file, I get the
> following error:
>  
> A error related to DOT has occured. This error was probably because
> OWL Viz could not find the DOT application. Please ensure that the
> path to the DOT application is set properly.
>  
> The DOT path seems to be set to:
>  
> C:\Program Files\ATT\GraphViz\bin\Dot This path doesnt seem to exist.
>  
> Has anyone else had the same problem? Any suggestions about other ways
> to view the file graphically on protege?
>  
> thanks
> dhivya
>  
>  
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[protege-owl] Re: viewing bipax owl instances graphically using OWLViz

sombhop
In reply to this post by dhivyaai
Hi
   It needs GraphViz to be installed on your machine.

Sombhop

On 2/7/06, Dhivya Arasappan/O/VCU <[hidden email]> wrote:
Hello all,
 
I'm using Protege version 3.2 beta and thanks to your help, I've now been able to import a biopax file into protege. But when I try to use the OWLViz plug in to view a diagram of the owl file, I get the following error:
 
A error related to DOT has occured. This error was probably because OWL Viz could not find the DOT application. Please ensure that the path to the DOT application is set properly.
 
The DOT path seems to be set to:
 
C:\Program Files\ATT\GraphViz\bin\Dot This path doesnt seem to exist.
 
Has anyone else had the same problem? Any suggestions about other ways to view the file graphically on protege?
 
thanks
dhivya
 
 
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[protege-owl] Re: viewing bipax owl instances graphically using OWLViz

Ronnie Valkky
In reply to this post by dhivyaai
Hi dhivya ,
 
 
Cheers,
Ronnie
----- Original Message -----
Sent: Tuesday, February 07, 2006 6:15 PM
Subject: [protege-owl] viewing bipax owl instances graphically using OWLViz

Hello all,
 
I'm using Protege version 3.2 beta and thanks to your help, I've now been able to import a biopax file into protege. But when I try to use the OWLViz plug in to view a diagram of the owl file, I get the following error:
 
A error related to DOT has occured. This error was probably because OWL Viz could not find the DOT application. Please ensure that the path to the DOT application is set properly.
 
The DOT path seems to be set to:
 
C:\Program Files\ATT\GraphViz\bin\Dot This path doesnt seem to exist.
 
Has anyone else had the same problem? Any suggestions about other ways to view the file graphically on protege?
 
thanks
dhivya
 
 
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Re: viewing bipax owl instances graphically using OWLViz

Nick Drummond
Jambalya is a very different type of visualiser to OWLViz.
Both have advantages and disadvantages.

Thanks Asad for the instructions - Dhivya, if you need any clarification
please see the docs available from [1]

Nick

[1] http://www.co-ode.org/downloads/owlviz/co-ode-index.php

Ronnie Valkky wrote:

> Hi dhivya ,
>  
> Try
> http://www.cs.uvic.ca/~chisel/projects/shrimp/demo/jambalaya_applet.html 
> <http://www.cs.uvic.ca/%7Echisel/projects/shrimp/demo/jambalaya_applet.html>
>  
> Cheers,
> Ronnie
>
>     ----- Original Message -----
>     *From:* Dhivya Arasappan/O/VCU <mailto:[hidden email]>
>     *To:* [hidden email]
>     <mailto:[hidden email]>
>     *Sent:* Tuesday, February 07, 2006 6:15 PM
>     *Subject:* [protege-owl] viewing bipax owl instances graphically
>     using OWLViz
>
>     Hello all,
>      
>     I'm using Protege version 3.2 beta and thanks to your help, I've
>     now been able to import a biopax file into protege. But when I try
>     to use the OWLViz plug in to view a diagram of the owl file, I get
>     the following error:
>      
>     A error related to DOT has occured. This error was probably
>     because OWL Viz could not find the DOT application. Please ensure
>     that the path to the DOT application is set properly.
>      
>     The DOT path seems to be set to:
>      
>     C:\Program Files\ATT\GraphViz\bin\Dot This path doesnt seem to exist.
>      
>     Has anyone else had the same problem? Any suggestions about other
>     ways to view the file graphically on protege?
>      
>     thanks
>     dhivya
>      
>      
>     -------------------------------------------------------------------------
>     To unsubscribe go to
>     http://protege.stanford.edu/community/subscribe.html 
>

--

Nick Drummond

http://www.cs.man.ac.uk/~drummond/ <http://www.cs.man.ac.uk/%7Edrummond/>
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Re: viewing bipax owl instances graphically using OWLViz

Carver, Steve CIV SPAWARSYSCEN Charleston
In reply to this post by dhivyaai
Yes,
 
I am having the same problem.
 
/R
 
Steve
-----Original Message-----
From: [hidden email] [mailto:[hidden email]]On Behalf Of sombhop
Sent: Tuesday, February 07, 2006 12:08
To: [hidden email]
Subject: [protege-owl] Re: viewing bipax owl instances graphically using OWLViz

Hi
   It needs GraphViz to be installed on your machine.

Sombhop

On 2/7/06, Dhivya Arasappan/O/VCU <[hidden email]> wrote:
Hello all,
 
I'm using Protege version 3.2 beta and thanks to your help, I've now been able to import a biopax file into protege. But when I try to use the OWLViz plug in to view a diagram of the owl file, I get the following error:
 
A error related to DOT has occured. This error was probably because OWL Viz could not find the DOT application. Please ensure that the path to the DOT application is set properly.
 
The DOT path seems to be set to:
 
C:\Program Files\ATT\GraphViz\bin\Dot This path doesnt seem to exist.
 
Has anyone else had the same problem? Any suggestions about other ways to view the file graphically on protege?
 
thanks
dhivya
 
 
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Re: viewing bipax owl instances graphically using OWLViz

Ronnie Valkky
Hi Steve and Sombong,
 
I went trough the following steps and phases and got it to work OK:
Step 1: installation
~ went to home page: http://www.graphviz.org
~ downloaded from URL: http://www.graphviz.org/Download.php
~ downloaded file: J:\Download\GraphViz\graphviz-2.8.exe
~ clicked J:\Download\GraphViz\graphviz-2.8.exe
~ installed to: F:\sw\att
~ discovered that dot.exe is in F:\sw\att\Graphviz\bin\dot.exe
~ activated Protege OWL
~ configured my project
~ selected OWLWizTab
~ got the error message that it could not find DOT (F:\sw\att\Graphviz\bin\dot.exe)
~ no instructions how to tell it that !
~ ProtegeOWL dies/tilts/goes to bananas..
Question 1: should I have extracted to F:\sw\Protege3.2beta\plugins
Answer 1: no, it is enough to tell Protege OWL F:\sw\att\Graphviz\bin\dot.exe

Step2:
~ restarted protege OWL
~ loaded project
~ selected configure project
~ selected OWLWizTab
~ got the error message, clicked several times to close error window
~ got OWLWizTab to my screen
Question2: how to define F:\sw\att\Graphviz\bin\dot.exe to OWLWizTab?
Answer2: once you click OWLWizTab, click under OWLWizTab icon which is the second icon from the right
~ I gave F:\sw\att\Graphviz\bin\dot.exe
SOLVED
Step3:
~ restarted Protege OWL

Above has my settings for drives where I keep software.
Hopefully at least gave you some help!
 
cheers,
Ronnie
 
 
----- Original Message -----
Sent: Thursday, February 16, 2006 7:12 PM
Subject: [Norton AntiSpam] [protege-owl] Re: viewing bipax owl instances graphically using OWLViz

Yes,
 
I am having the same problem.
 
/R
 
Steve
-----Original Message-----
From: [hidden email] [mailto:[hidden email]]On Behalf Of sombhop
Sent: Tuesday, February 07, 2006 12:08
To: [hidden email]
Subject: [protege-owl] Re: viewing bipax owl instances graphically using OWLViz

Hi
   It needs GraphViz to be installed on your machine.

Sombhop

On 2/7/06, Dhivya Arasappan/O/VCU <[hidden email]> wrote:
Hello all,
 
I'm using Protege version 3.2 beta and thanks to your help, I've now been able to import a biopax file into protege. But when I try to use the OWLViz plug in to view a diagram of the owl file, I get the following error:
 
A error related to DOT has occured. This error was probably because OWL Viz could not find the DOT application. Please ensure that the path to the DOT application is set properly.
 
The DOT path seems to be set to:
 
C:\Program Files\ATT\GraphViz\bin\Dot This path doesnt seem to exist.
 
Has anyone else had the same problem? Any suggestions about other ways to view the file graphically on protege?
 
thanks
dhivya
 
 
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Re: viewing bipax owl instances graphically using OWLViz

nini-2
In reply to this post by Carver, Steve CIV SPAWARSYSCEN Charleston

Me, too.

 

*****************************************************
Nwe Ni Tun
Knowledge Engineering Laboratory
School of Information Science
Japan Advanced Institute of Science and Technology
www: http://www.jaist.ac.jp/~nitun/index.html
*****************************************************

-----Original Message-----
From: [hidden email] [mailto:[hidden email]] On Behalf Of Carver, Steve CIV SPAWARSYSCEN Charleston
Sent: Friday, February 17, 2006 2:12 AM
To:
[hidden email]
Subject: [protege-owl] Re: viewing bipax owl instances graphically using OWLViz

 

Yes,

 

I am having the same problem.

 

/R

 

Steve

-----Original Message-----
From: [hidden email] [mailto:[hidden email]]On Behalf Of sombhop
Sent: Tuesday, February 07, 2006 12:08
To: [hidden email]
Subject: [protege-owl] Re: viewing bipax owl instances graphically using OWLViz

Hi
   It needs
GraphViz to be installed on your machine.

Sombhop

On 2/7/06, Dhivya Arasappan/O/VCU <[hidden email]> wrote:

Hello all,

 

I'm using Protege version 3.2 beta and thanks to your help, I've now been able to import a biopax file into protege. But when I try to use the OWLViz plug in to view a diagram of the owl file, I get the following error:

 

A error related to DOT has occured. This error was probably because OWL Viz could not find the DOT application. Please ensure that the path to the DOT application is set properly.

 

The DOT path seems to be set to:

 

C:\Program Files\ATT\GraphViz\bin\Dot This path doesnt seem to exist.

 

Has anyone else had the same problem? Any suggestions about other ways to view the file graphically on protege?

 

thanks

dhivya

 

 

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