Ontoviz and Graphviz questions

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Ontoviz and Graphviz questions

Jos Lehmann-2
Hi there

I'm having very basic interaction problems with the graphic plug-ins:

A- Ontoloviz:

        1. How to correctly display classes? (They shy-off in the top left corner of the screen)
        2. How to display classes individuals?

B- Graphviz:

        1. How to display classes individuals?

Thanks, Jos
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Re: Ontoviz and Graphviz questions

Matthew Horridge-2
Administrator
Hi Jos,

OntoViz uses GraphViz to layout the boxes and lines.  It’s likely that you don’t have GraphViz installed or your path to the dot library (which is part of GraphViz) is not correct.  There are instructions for setting up ontoviz here:


Are you using a Mac?  If so, I recommend that you install “home brew” and from there it’s very easy to install graphviz with “brew install graphviz”.  Installation instructions for GraphViz can be found here:


Cheers,

Matthew



On 18 Oct 2017, at 09:17, Jos Lehmann <[hidden email]> wrote:

Hi there

I'm having very basic interaction problems with the graphic plug-ins:

A- Ontoloviz:

1. How to correctly display classes? (They shy-off in the top left corner of the screen)
2. How to display classes individuals?

B- Graphviz:

1. How to display classes individuals?

Thanks, Jos
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Re: Ontoviz and Graphviz questions

Jos Lehmann-2

Hi Matthew

 

Thank you for your reply. Please note:

 

-          in point B- in my orginal email I meant Ontograf, sorry about the confusion. In Ontograf I don’t seem to be able to visualize all the individuals of a given visualized class.

 

-          as for point A-, I got started with the installation instructions but got stuck: I can‘t find the right version of GraphViz (2.14). Where to find the Graphviz 2.14 (or another compatible version) installer for Windows 10?

 

Thanks, Jos

 

 

Von: protege-user [mailto:[hidden email]] Im Auftrag von Matthew Horridge
Gesendet: Mittwoch, 18. Oktober 2017 20:34
An: User support for WebProtege and Protege Desktop <[hidden email]>
Betreff: Re: [protege-user] Ontoviz and Graphviz questions

 

Hi Jos,

 

OntoViz uses GraphViz to layout the boxes and lines.  It’s likely that you don’t have GraphViz installed or your path to the dot library (which is part of GraphViz) is not correct.  There are instructions for setting up ontoviz here:

 

 

Are you using a Mac?  If so, I recommend that you install “home brew” and from there it’s very easy to install graphviz with “brew install graphviz”.  Installation instructions for GraphViz can be found here:

 

 

Cheers,

 

Matthew

 

 

 

On 18 Oct 2017, at 09:17, Jos Lehmann <[hidden email]> wrote:

 

Hi there

I'm having very basic interaction problems with the graphic plug-ins:

A- Ontoloviz:

1. How to correctly display classes? (They shy-off in the top left corner of the screen)
2. How to display classes individuals?

B- Graphviz:

1. How to display classes individuals?

Thanks, Jos
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https://mailman.stanford.edu/mailman/listinfo/protege-user

 


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Re: Ontoviz and Graphviz questions

samsontu

On Oct 23, 2017, at 3:47 AM, Jos Lehmann <[hidden email]> wrote:

Hi Matthew
 
Thank you for your reply. Please note:
 
-          in point B- in my orginal email I meant Ontograf, sorry about the confusion. In Ontograf I don’t seem to be able to visualize all the individuals of a given visualized class. 

Are you able to see any individuals? My installation of Ontograf shows individuals that I checked.


 
-          as for point A-, I got started with the installation instructions but got stuck: I can‘t find the right version of GraphViz (2.14). Where to find the Graphviz 2.14 (or another compatible version) installer for Windows 10?
 

Google "graphviz 2.14” and you’ll see [1] as the top hit.

With best regards,
Samson

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Re: Ontoviz and Graphviz questions

Jos Lehmann-2

Hi Samson

 

-          On Ontograf:

No, I cant‘ see any individuals.

 

-          On Graphviz:

Thank you. Btw I had found that webpage, but wanted to be sure that was what was needed.

Perhaps a direct link from https://protegewiki.stanford.edu/wiki/OntoViz would make things easier.

 

Now I am stuck again because I can’t find the protege.properties file in my Protege 5.2 installation nor do I know how else to set the path to the Grapviz dot library.

 

Thanks, Jos

 

Von: protege-user [mailto:[hidden email]] Im Auftrag von Samson Tu
Gesendet: Dienstag, 24. Oktober 2017 00:08
An: User support for WebProtege and Protege Desktop <[hidden email]>
Betreff: Re: [protege-user] Ontoviz and Graphviz questions

 

 

On Oct 23, 2017, at 3:47 AM, Jos Lehmann <[hidden email]> wrote:

 

Hi Matthew

 

Thank you for your reply. Please note:

 

-          in point B- in my orginal email I meant Ontograf, sorry about the confusion. In Ontograf I don’t seem to be able to visualize all the individuals of a given visualized class. 

 

Are you able to see any individuals? My installation of Ontograf shows individuals that I checked.

 

 

-          as for point A-, I got started with the installation instructions but got stuck: I can‘t find the right version of GraphViz (2.14). Where to find the Graphviz 2.14 (or another compatible version) installer for Windows 10?

 

 

Google "graphviz 2.14” and you’ll see [1] as the top hit.

 

With best regards,

Samson


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Re: Ontoviz and Graphviz questions

Csongor Nyulas
Administrator
Hi Jos,
See inline answers below:

On 10/24/2017 01:25 AM, Jos Lehmann wrote:

Hi Samson

 

-          On Ontograf:

No, I cant‘ see any individuals.


This did work for me. I just had to add the classes that have individuals to the diagram, and double click on them to expand them. This is a screen shot of what I see.
Maybe you need to check what is selected and what isn't in the "Node types" and "Arc types" menus, which you can activate with the little icons in the tool bar, one with the mustard color square + check box and the other showing a blue arrow + check box.




 

-          On Graphviz:

Thank you. Btw I had found that webpage, but wanted to be sure that was what was needed.

Perhaps a direct link from https://protegewiki.stanford.edu/wiki/OntoViz would make things easier.


OntoViz is for Protege 3.x. Protege 5.2 comes with OWLViz, and this is its wiki page:
https://protegewiki.stanford.edu/wiki/OWLViz

Both the OntoViz and the OWLViz wiki page have links to the Graphviz where you can download it.


 

Now I am stuck again because I can’t find the protege.properties file in my Protege 5.2 installation nor do I know how else to set the path to the Grapviz dot library.


The easiest way to do this in Protege 5.2 is to edit the path to the dot application in the preferences (File -> Preferences...) choose the OWLViz tab and update the "Path to DOT". Restart Protege.

Good luck,
Csongor

 

Thanks, Jos

 

Von: protege-user [[hidden email]] Im Auftrag von Samson Tu
Gesendet: Dienstag, 24. Oktober 2017 00:08
An: User support for WebProtege and Protege Desktop [hidden email]
Betreff: Re: [protege-user] Ontoviz and Graphviz questions

 

 

On Oct 23, 2017, at 3:47 AM, Jos Lehmann <[hidden email]> wrote:

 

Hi Matthew

 

Thank you for your reply. Please note:

 

-          in point B- in my orginal email I meant Ontograf, sorry about the confusion. In Ontograf I don’t seem to be able to visualize all the individuals of a given visualized class. 

 

Are you able to see any individuals? My installation of Ontograf shows individuals that I checked.

 

 

-          as for point A-, I got started with the installation instructions but got stuck: I can‘t find the right version of GraphViz (2.14). Where to find the Graphviz 2.14 (or another compatible version) installer for Windows 10?

 

 

Google "graphviz 2.14” and you’ll see [1] as the top hit.

 

With best regards,

Samson



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Re: Ontoviz and Graphviz questions

Jos Lehmann-2

Hi Csongor

 

-          On Ontograf:

I guess it works for me as well… I had not realized that Ontograf only shows individuals of the current ontology, but not of its imports.

Is that the way it is supposed work?

 

-          On OntoViz:

Sorry, I confused OWLViz with OntoViz, thus I went in search for Graphviz 2.14 (and got lost, as from https://protegewiki.stanford.edu/wiki/OntoViz one is pointed to Graphviz 2.38, which won’t work with OntoViz).

Anyways thanks to your reply I realized Protege now comes with OWLViz rather than with OntoViz, and I successfully installed Graphviz 2.38

 

Thanks, Jos

 

 

 

Von: protege-user [mailto:[hidden email]] Im Auftrag von Csongor Nyulas
Gesendet: Dienstag, 24. Oktober 2017 19:46
An: [hidden email]
Betreff: Re: [protege-user] Ontoviz and Graphviz questions

 

Hi Jos,
See inline answers below:

On 10/24/2017 01:25 AM, Jos Lehmann wrote:

Hi Samson

 

-          On Ontograf:

No, I cant‘ see any individuals.


This did work for me. I just had to add the classes that have individuals to the diagram, and double click on them to expand them. This is a screen shot of what I see.
Maybe you need to check what is selected and what isn't in the "Node types" and "Arc types" menus, which you can activate with the little icons in the tool bar, one with the mustard color square + check box and the other showing a blue arrow + check box.

cid:image001.png@01D34F1E.9064BA90



 

-          On Graphviz:

Thank you. Btw I had found that webpage, but wanted to be sure that was what was needed.

Perhaps a direct link from https://protegewiki.stanford.edu/wiki/OntoViz would make things easier.


OntoViz is for Protege 3.x. Protege 5.2 comes with OWLViz, and this is its wiki page:
https://protegewiki.stanford.edu/wiki/OWLViz

Both the OntoViz and the OWLViz wiki page have links to the Graphviz where you can download it.



 

Now I am stuck again because I can’t find the protege.properties file in my Protege 5.2 installation nor do I know how else to set the path to the Grapviz dot library.


The easiest way to do this in Protege 5.2 is to edit the path to the dot application in the preferences (File -> Preferences...) choose the OWLViz tab and update the "Path to DOT". Restart Protege.

Good luck,
Csongor


 

Thanks, Jos

 

Von: protege-user [[hidden email]] Im Auftrag von Samson Tu
Gesendet: Dienstag, 24. Oktober 2017 00:08
An: User support for WebProtege and Protege Desktop
[hidden email]
Betreff: Re: [protege-user] Ontoviz and Graphviz questions

 

 

On Oct 23, 2017, at 3:47 AM, Jos Lehmann <[hidden email]> wrote:

 

Hi Matthew

 

Thank you for your reply. Please note:

 

-          in point B- in my orginal email I meant Ontograf, sorry about the confusion. In Ontograf I don’t seem to be able to visualize all the individuals of a given visualized class. 

 

Are you able to see any individuals? My installation of Ontograf shows individuals that I checked.

 

 

-          as for point A-, I got started with the installation instructions but got stuck: I can‘t find the right version of GraphViz (2.14). Where to find the Graphviz 2.14 (or another compatible version) installer for Windows 10?

 

 

Google "graphviz 2.14” and you’ll see [1] as the top hit.

 

With best regards,

Samson




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[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

 


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Re: Ontoviz and Graphviz questions

Csongor Nyulas
Administrator
Hi Jos,
Please see answers below...

On 10/27/2017 07:34 AM, Jos Lehmann wrote:

Hi Csongor

 

-          On Ontograf:

I guess it works for me as well… I had not realized that Ontograf only shows individuals of the current ontology, but not of its imports.

Is that the way it is supposed work?


This seems to have been fixed in this issue (I haven't tested it though): https://github.com/protegeproject/ontograf/issues/13
Can you make sure that you are using the latest version of OWLViz on your Protege 5.2?
If you open File -> Check for plugins... you can see if there is new version for OWLViz or not.
Also, the About box (Help -> About on Windows and Linux) would show you which version of OWLViz do you have (mine is 5.0.3).


 

-          On OntoViz:

Sorry, I confused OWLViz with OntoViz, thus I went in search for Graphviz 2.14 (and got lost, as from https://protegewiki.stanford.edu/wiki/OntoViz one is pointed to Graphviz 2.38, which won’t work with OntoViz).

Anyways thanks to your reply I realized Protege now comes with OWLViz rather than with OntoViz, and I successfully installed Graphviz 2.38


I am glad that this was clarified and works now for you.

Csongor

 

Thanks, Jos

 

 

 

Von: protege-user [[hidden email]] Im Auftrag von Csongor Nyulas
Gesendet: Dienstag, 24. Oktober 2017 19:46
An: [hidden email]
Betreff: Re: [protege-user] Ontoviz and Graphviz questions

 

Hi Jos,
See inline answers below:

On 10/24/2017 01:25 AM, Jos Lehmann wrote:

Hi Samson

 

-          On Ontograf:

No, I cant‘ see any individuals.


This did work for me. I just had to add the classes that have individuals to the diagram, and double click on them to expand them. This is a screen shot of what I see.
Maybe you need to check what is selected and what isn't in the "Node types" and "Arc types" menus, which you can activate with the little icons in the tool bar, one with the mustard color square + check box and the other showing a blue arrow + check box.

imap://csnyulas@csnyulas.pobox.stanford.edu:993/fetch%3EUID%3E/INBOX%3E128638?header=quotebody&part=1.1.2&filename=image001.png



 

-          On Graphviz:

Thank you. Btw I had found that webpage, but wanted to be sure that was what was needed.

Perhaps a direct link from https://protegewiki.stanford.edu/wiki/OntoViz would make things easier.


OntoViz is for Protege 3.x. Protege 5.2 comes with OWLViz, and this is its wiki page:
https://protegewiki.stanford.edu/wiki/OWLViz

Both the OntoViz and the OWLViz wiki page have links to the Graphviz where you can download it.



 

Now I am stuck again because I can’t find the protege.properties file in my Protege 5.2 installation nor do I know how else to set the path to the Grapviz dot library.


The easiest way to do this in Protege 5.2 is to edit the path to the dot application in the preferences (File -> Preferences...) choose the OWLViz tab and update the "Path to DOT". Restart Protege.

Good luck,
Csongor


 

Thanks, Jos

 

Von: protege-user [[hidden email]] Im Auftrag von Samson Tu
Gesendet: Dienstag, 24. Oktober 2017 00:08
An: User support for WebProtege and Protege Desktop
[hidden email]
Betreff: Re: [protege-user] Ontoviz and Graphviz questions

 

 

On Oct 23, 2017, at 3:47 AM, Jos Lehmann <[hidden email]> wrote:

 

Hi Matthew

 

Thank you for your reply. Please note:

 

-          in point B- in my orginal email I meant Ontograf, sorry about the confusion. In Ontograf I don’t seem to be able to visualize all the individuals of a given visualized class. 

 

Are you able to see any individuals? My installation of Ontograf shows individuals that I checked.

 

 

-          as for point A-, I got started with the installation instructions but got stuck: I can‘t find the right version of GraphViz (2.14). Where to find the Graphviz 2.14 (or another compatible version) installer for Windows 10?

 

 

Google "graphviz 2.14” and you’ll see [1] as the top hit.

 

With best regards,

Samson




_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

 



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Re: Ontoviz and Graphviz questions

Jos Lehmann-2

Hi Csongor

 

Thank you for your replies.

 

Yes, my OwlViz is 5.0.3 according to the About of my Protege 5.2.0 (plug-in checking doesn’t work because of failing certificate, possibly due to my firewall).

 

Still can’t visualize individuals of imported ontologies in Ontograf.

 

Cheers, Jos

 

 

Von: protege-user [mailto:[hidden email]] Im Auftrag von Csongor Nyulas
Gesendet: Freitag, 27. Oktober 2017 18:16
An: [hidden email]
Betreff: Re: [protege-user] Ontoviz and Graphviz questions

 

Hi Jos,
Please see answers below...

On 10/27/2017 07:34 AM, Jos Lehmann wrote:

Hi Csongor

 

-          On Ontograf:

I guess it works for me as well… I had not realized that Ontograf only shows individuals of the current ontology, but not of its imports.

Is that the way it is supposed work?


This seems to have been fixed in this issue (I haven't tested it though): https://github.com/protegeproject/ontograf/issues/13
Can you make sure that you are using the latest version of OWLViz on your Protege 5.2?
If you open File -> Check for plugins... you can see if there is new version for OWLViz or not.
Also, the About box (Help -> About on Windows and Linux) would show you which version of OWLViz do you have (mine is 5.0.3).



 

-          On OntoViz:

Sorry, I confused OWLViz with OntoViz, thus I went in search for Graphviz 2.14 (and got lost, as from https://protegewiki.stanford.edu/wiki/OntoViz one is pointed to Graphviz 2.38, which won’t work with OntoViz).

Anyways thanks to your reply I realized Protege now comes with OWLViz rather than with OntoViz, and I successfully installed Graphviz 2.38


I am glad that this was clarified and works now for you.

Csongor


 

Thanks, Jos

 

 

 

Von: protege-user [[hidden email]] Im Auftrag von Csongor Nyulas
Gesendet: Dienstag, 24. Oktober 2017 19:46
An: [hidden email]
Betreff: Re: [protege-user] Ontoviz and Graphviz questions

 

Hi Jos,
See inline answers below:

On 10/24/2017 01:25 AM, Jos Lehmann wrote:

Hi Samson

 

-          On Ontograf:

No, I cant‘ see any individuals.


This did work for me. I just had to add the classes that have individuals to the diagram, and double click on them to expand them. This is a screen shot of what I see.
Maybe you need to check what is selected and what isn't in the "Node types" and "Arc types" menus, which you can activate with the little icons in the tool bar, one with the mustard color square + check box and the other showing a blue arrow + check box.

imap://csnyulas@csnyulas.pobox.stanford.edu:993/fetch%3EUID%3E/INBOX%3E128638?header=quotebody&part=1.1.2&filename=image001.png




 

-          On Graphviz:

Thank you. Btw I had found that webpage, but wanted to be sure that was what was needed.

Perhaps a direct link from https://protegewiki.stanford.edu/wiki/OntoViz would make things easier.


OntoViz is for Protege 3.x. Protege 5.2 comes with OWLViz, and this is its wiki page:
https://protegewiki.stanford.edu/wiki/OWLViz

Both the OntoViz and the OWLViz wiki page have links to the Graphviz where you can download it.




 

Now I am stuck again because I can’t find the protege.properties file in my Protege 5.2 installation nor do I know how else to set the path to the Grapviz dot library.


The easiest way to do this in Protege 5.2 is to edit the path to the dot application in the preferences (File -> Preferences...) choose the OWLViz tab and update the "Path to DOT". Restart Protege.

Good luck,
Csongor



 

Thanks, Jos

 

Von: protege-user [[hidden email]] Im Auftrag von Samson Tu
Gesendet: Dienstag, 24. Oktober 2017 00:08
An: User support for WebProtege and Protege Desktop
[hidden email]
Betreff: Re: [protege-user] Ontoviz and Graphviz questions

 

 

On Oct 23, 2017, at 3:47 AM, Jos Lehmann <[hidden email]> wrote:

 

Hi Matthew

 

Thank you for your reply. Please note:

 

-          in point B- in my orginal email I meant Ontograf, sorry about the confusion. In Ontograf I don’t seem to be able to visualize all the individuals of a given visualized class. 

 

Are you able to see any individuals? My installation of Ontograf shows individuals that I checked.

 

 

-          as for point A-, I got started with the installation instructions but got stuck: I can‘t find the right version of GraphViz (2.14). Where to find the Graphviz 2.14 (or another compatible version) installer for Windows 10?

 

 

Google "graphviz 2.14” and you’ll see [1] as the top hit.

 

With best regards,

Samson





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protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

 




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