OntoGraf feature request

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OntoGraf feature request

Daniel Schober
Dear Sean

Thanks for this nice and stable OntoGraf plugin. This looks really promising.

I think this plugin would be even better and more useable if the following feats could be implemented.

a)  an option to export the result-graph as jpg or gif
b)  an option that persistently depicts the relation names (or the full restrictions e.g. in manchester owl syntax) over the edges. At the moment I can't reuse the pics for educational purposes as onyl the relation name is visible when one actively puts the mouse pointer over the edge. At the moment this lack of the relations greatly limits the useability of this great plugin for audit , reporting and didactic purposes.
c) an option to display the direct logical definitions/ restrictions in the node (as long  b) is not implemented).
d) an option to save a view for later re-visualization. E.g. if one is interested to display the same domain areas in an ontology repeatedly. E.g. in the OBI  ontology I want to report on the two following areas/views: 1. the devices (set of classes like device, function, settings, software)  and 2. the Protocols and algorithms. It would be very nice to have the possibility to store such class sets for later reuse in visualising their context.

Two drawbacks I recognised:
1. The most interesting parts of the logical equivalence definitions (e.g. for a 'PharmaceuticalSubstance' node:
 'bearer of' some
    (disposition
     and ('has realization' only 'treating disease'))

seems to be ignored by the plugin and is currently not visualized anywhere. These should at least be seen in the node descriptions.

2. At the moment if I move the mouse over a node all that happends is that the nodes gets a liddle bigger and the label is shown (redundantly). Maybe you could substitute this with another useful functionality, e.g. showing the full class def in Manchester owl Syntax.

Is any of this in the planning ?

Cheers,
    Daniel Schober.
-- 

-------------------------------------------------------------
  Dr. Daniel Schober
  Universitätsklinikum    
  Institut für Medizinische Biometrie und Medizinische Informatik
  Stefan-Meier-Strasse  26	Raum 6
  D-79104 Freiburg		Germany
  Tel: +49 (0)761 2036807	FAX: +49 (0)761 2036711
  
  
          
          
          
          
             
          
          
          

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Re: OntoGraf feature request

Sean Falconer
Hi Daniel,

Thanks for the feedback. Yes, many of the suggestions and issues you
raised are planned as features for the next release. The goal with the
initial version was to get something lightweight and usable out there
for the Protege 4 users.

In the mean time, you can address your first draw back by opening the
OWL definition view in conjunction with the OntoGraf view. Then when
you select a node in your graph, you'll see the full OWL description.
This is available in the menu under View / Class views / Description.

I will make an announcement again when a second version is available
that incorporates some of the requests that you and others have made.

Cheers,

Sean

On Fri, May 14, 2010 at 4:37 AM, Dr. Daniel Schober
<[hidden email]> wrote:

> Dear Sean
>
> Thanks for this nice and stable OntoGraf plugin. This looks really
> promising.
>
> I think this plugin would be even better and more useable if the following
> feats could be implemented.
>
> a)  an option to export the result-graph as jpg or gif
> b)  an option that persistently depicts the relation names (or the full
> restrictions e.g. in manchester owl syntax) over the edges. At the moment I
> can't reuse the pics for educational purposes as onyl the relation name is
> visible when one actively puts the mouse pointer over the edge. At the
> moment this lack of the relations greatly limits the useability of this
> great plugin for audit , reporting and didactic purposes.
> c) an option to display the direct logical definitions/ restrictions in the
> node (as long  b) is not implemented).
> d) an option to save a view for later re-visualization. E.g. if one is
> interested to display the same domain areas in an ontology repeatedly. E.g.
> in the OBI  ontology I want to report on the two following areas/views: 1.
> the devices (set of classes like device, function, settings, software)  and
> 2. the Protocols and algorithms. It would be very nice to have the
> possibility to store such class sets for later reuse in visualising their
> context.
>
> Two drawbacks I recognised:
> 1. The most interesting parts of the logical equivalence definitions (e.g.
> for a 'PharmaceuticalSubstance' node:
>  'bearer of' some
>     (disposition
>      and ('has realization' only 'treating disease'))
> seems to be ignored by the plugin and is currently not visualized anywhere.
> These should at least be seen in the node descriptions.
>
> 2. At the moment if I move the mouse over a node all that happends is that
> the nodes gets a liddle bigger and the label is shown (redundantly). Maybe
> you could substitute this with another useful functionality, e.g. showing
> the full class def in Manchester owl Syntax.
>
> Is any of this in the planning ?
>
> Cheers,
>     Daniel Schober.
>
> --
>
> -------------------------------------------------------------
>   Dr. Daniel Schober
>   Universitätsklinikum
>   Institut für Medizinische Biometrie und Medizinische Informatik
>   Stefan-Meier-Strasse  26 Raum 6
>   D-79104 Freiburg Germany
>   Tel: +49 (0)761 2036807 FAX: +49 (0)761 2036711
>
>
>
>
>
>
>
>
>
>
>



--
Sean Falconer, PhD
Postdoctoral Researcher
Stanford Center for Biomedical Informatics Research
http://www.stanford.edu/~sfalc
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Re: OntoGraf feature request

Daniel Schober
Dear Sean,
Nice to see this useful plugin gets more features added in a fast pace ;-) .
  1. How can I make my Ontograf show the full labels in the nodes ? Mine always truncates the longer classnames. Could you implement that the node always shows the full class name (adjust the nodelength according to the name, so it fits).
  2. It would be nice if one can select what more detail one wants to (persistently) display in or with the node. At the moment its just the name, but for display and re-use in documantations one would like to show more info on the node persistently (not only when one moves the mouse over the node, but for the saved graphics and for multiple nodes in parallel).
  3. Minor:  the node and Arc type filter nodes do not show tooltips.
Good stuff...

Cheers,
        Daniel Schober.

Am 17.05.2010 23:21, schrieb Sean Falconer:
Hi Daniel,

Thanks for the feedback. Yes, many of the suggestions and issues you
raised are planned as features for the next release. The goal with the
initial version was to get something lightweight and usable out there
for the Protege 4 users.

In the mean time, you can address your first draw back by opening the
OWL definition view in conjunction with the OntoGraf view. Then when
you select a node in your graph, you'll see the full OWL description.
This is available in the menu under View / Class views / Description.

I will make an announcement again when a second version is available
that incorporates some of the requests that you and others have made.

Cheers,

Sean

On Fri, May 14, 2010 at 4:37 AM, Dr. Daniel Schober
[hidden email] wrote:
  
Dear Sean

Thanks for this nice and stable OntoGraf plugin. This looks really
promising.

I think this plugin would be even better and more useable if the following
feats could be implemented.

a)  an option to export the result-graph as jpg or gif
b)  an option that persistently depicts the relation names (or the full
restrictions e.g. in manchester owl syntax) over the edges. At the moment I
can't reuse the pics for educational purposes as onyl the relation name is
visible when one actively puts the mouse pointer over the edge. At the
moment this lack of the relations greatly limits the useability of this
great plugin for audit , reporting and didactic purposes.
c) an option to display the direct logical definitions/ restrictions in the
node (as long  b) is not implemented).
d) an option to save a view for later re-visualization. E.g. if one is
interested to display the same domain areas in an ontology repeatedly. E.g.
in the OBI  ontology I want to report on the two following areas/views: 1.
the devices (set of classes like device, function, settings, software)  and
2. the Protocols and algorithms. It would be very nice to have the
possibility to store such class sets for later reuse in visualising their
context.

Two drawbacks I recognised:
1. The most interesting parts of the logical equivalence definitions (e.g.
for a 'PharmaceuticalSubstance' node:
 'bearer of' some
    (disposition
     and ('has realization' only 'treating disease'))
seems to be ignored by the plugin and is currently not visualized anywhere.
These should at least be seen in the node descriptions.

2. At the moment if I move the mouse over a node all that happends is that
the nodes gets a liddle bigger and the label is shown (redundantly). Maybe
you could substitute this with another useful functionality, e.g. showing
the full class def in Manchester owl Syntax.

Is any of this in the planning ?

Cheers,
    Daniel Schober.

--

-------------------------------------------------------------
  Dr. Daniel Schober
  Universitätsklinikum
  Institut für Medizinische Biometrie und Medizinische Informatik
  Stefan-Meier-Strasse  26	Raum 6
  D-79104 Freiburg		Germany
  Tel: +49 (0)761 2036807	FAX: +49 (0)761 2036711











    


  

-- 

-------------------------------------------------------------
  Dr. Daniel Schober
  Universitätsklinikum    
  Institut für Medizinische Biometrie und Medizinische Informatik
  Stefan-Meier-Strasse  26	Raum 6
  D-79104 Freiburg		Germany
  Tel: +49 (0)761 2036807	FAX: +49 (0)761 2036711
  
  
          
          
          
          
             
          
          
          

_______________________________________________
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: OntoGraf feature request

Sean Falconer
Hi Daniel,

> How can I make my Ontograf show the full labels in the nodes ? Mine always
> truncates the longer classnames. Could you implement that the node always
> shows the full class name (adjust the nodelength according to the name, so
> it fits).

This is currently not supported. This is something I could look into
for the next release.

> It would be nice if one can select what more detail one wants to
> (persistently) display in or with the node. At the moment its just the name,
> but for display and re-use in documantations one would like to show more
> info on the node persistently (not only when one moves the mouse over the
> node, but for the saved graphics and for multiple nodes in parallel).

Would you want this to be only for specific nodes in the display or
would you want one setting for all currently visible nodes?

> Minor:  the node and Arc type filter nodes do not show tooltips.

Do you mean in the toolbar?

Sean

On Wed, Jun 16, 2010 at 9:20 AM, Dr. Daniel Schober
<[hidden email]> wrote:

> Dear Sean,
> Nice to see this useful plugin gets more features added in a fast pace ;-) .
>
> How can I make my Ontograf show the full labels in the nodes ? Mine always
> truncates the longer classnames. Could you implement that the node always
> shows the full class name (adjust the nodelength according to the name, so
> it fits).
> It would be nice if one can select what more detail one wants to
> (persistently) display in or with the node. At the moment its just the name,
> but for display and re-use in documantations one would like to show more
> info on the node persistently (not only when one moves the mouse over the
> node, but for the saved graphics and for multiple nodes in parallel).
> Minor:  the node and Arc type filter nodes do not show tooltips.
>
> Good stuff...
>
> Cheers,
>         Daniel Schober.
>
> Am 17.05.2010 23:21, schrieb Sean Falconer:
>
> Hi Daniel,
>
> Thanks for the feedback. Yes, many of the suggestions and issues you
> raised are planned as features for the next release. The goal with the
> initial version was to get something lightweight and usable out there
> for the Protege 4 users.
>
> In the mean time, you can address your first draw back by opening the
> OWL definition view in conjunction with the OntoGraf view. Then when
> you select a node in your graph, you'll see the full OWL description.
> This is available in the menu under View / Class views / Description.
>
> I will make an announcement again when a second version is available
> that incorporates some of the requests that you and others have made.
>
> Cheers,
>
> Sean
>
> On Fri, May 14, 2010 at 4:37 AM, Dr. Daniel Schober
> <[hidden email]> wrote:
>
>
> Dear Sean
>
> Thanks for this nice and stable OntoGraf plugin. This looks really
> promising.
>
> I think this plugin would be even better and more useable if the following
> feats could be implemented.
>
> a)  an option to export the result-graph as jpg or gif
> b)  an option that persistently depicts the relation names (or the full
> restrictions e.g. in manchester owl syntax) over the edges. At the moment I
> can't reuse the pics for educational purposes as onyl the relation name is
> visible when one actively puts the mouse pointer over the edge. At the
> moment this lack of the relations greatly limits the useability of this
> great plugin for audit , reporting and didactic purposes.
> c) an option to display the direct logical definitions/ restrictions in the
> node (as long  b) is not implemented).
> d) an option to save a view for later re-visualization. E.g. if one is
> interested to display the same domain areas in an ontology repeatedly. E.g.
> in the OBI  ontology I want to report on the two following areas/views: 1.
> the devices (set of classes like device, function, settings, software)  and
> 2. the Protocols and algorithms. It would be very nice to have the
> possibility to store such class sets for later reuse in visualising their
> context.
>
> Two drawbacks I recognised:
> 1. The most interesting parts of the logical equivalence definitions (e.g.
> for a 'PharmaceuticalSubstance' node:
>  'bearer of' some
>     (disposition
>      and ('has realization' only 'treating disease'))
> seems to be ignored by the plugin and is currently not visualized anywhere.
> These should at least be seen in the node descriptions.
>
> 2. At the moment if I move the mouse over a node all that happends is that
> the nodes gets a liddle bigger and the label is shown (redundantly). Maybe
> you could substitute this with another useful functionality, e.g. showing
> the full class def in Manchester owl Syntax.
>
> Is any of this in the planning ?
>
> Cheers,
>     Daniel Schober.
>
> --
>
> -------------------------------------------------------------
>   Dr. Daniel Schober
>   Universitätsklinikum
>   Institut für Medizinische Biometrie und Medizinische Informatik
>   Stefan-Meier-Strasse  26 Raum 6
>   D-79104 Freiburg Germany
>   Tel: +49 (0)761 2036807 FAX: +49 (0)761 2036711
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> --
>
> -------------------------------------------------------------
>   Dr. Daniel Schober
>   Universitätsklinikum
>   Institut für Medizinische Biometrie und Medizinische Informatik
>   Stefan-Meier-Strasse  26 Raum 6
>   D-79104 Freiburg Germany
>   Tel: +49 (0)761 2036807 FAX: +49 (0)761 2036711
>
>
>
>
>
>
>
>
>
>
>



--
Sean Falconer, PhD
Postdoctoral Researcher
Stanford Center for Biomedical Informatics Research
http://www.stanford.edu/~sfalc
_______________________________________________
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: OntoGraf feature request

Daniel Schober
Hi Sean,
some answers inline....

Am 16.06.2010 18:28, schrieb Sean Falconer:
Hi Daniel,

  
How can I make my Ontograf show the full labels in the nodes ? Mine always
truncates the longer classnames. Could you implement that the node always
shows the full class name (adjust the nodelength according to the name, so
it fits).
    
This is currently not supported. This is something I could look into
for the next release.

  
This would be quite important, as unambiguously named detailed classes have longer names and these often are the complex ones we want to visualize.

  
It would be nice if one can select what more detail one wants to
(persistently) display in or with the node. At the moment its just the name,
but for display and re-use in documantations one would like to show more
info on the node persistently (not only when one moves the mouse over the
node, but for the saved graphics and for multiple nodes in parallel).
    
Would you want this to be only for specific nodes in the display or
would you want one setting for all currently visible nodes?
  
For our use case it would be for all shown nodes (ideally one could specify for which ones one needs to show the full details). In our use case (and I believe this is an important and abundant one) one wants to create a view on a limited module of the ontology, displaying a set of  around 5 classes with their relationships as shown here http://protegewiki.stanford.edu/wiki/File:OntoViz.gif
Think of it as representations that visualize the requirements for SPARQL queries.
Maybe one could configure it so that a user selects the details he wants to see with the node per default and  then can delete details he deems not needed. This way one could generate nice graphics that show the essentials but are not overly crowded.
  
Minor:  the node and Arc type filter nodes do not show tooltips.
    
Do you mean in the toolbar?
  
yes.
Thanks, Daniel.
Sean

On Wed, Jun 16, 2010 at 9:20 AM, Dr. Daniel Schober
[hidden email] wrote:
  
Dear Sean,
Nice to see this useful plugin gets more features added in a fast pace ;-) .

How can I make my Ontograf show the full labels in the nodes ? Mine always
truncates the longer classnames. Could you implement that the node always
shows the full class name (adjust the nodelength according to the name, so
it fits).
It would be nice if one can select what more detail one wants to
(persistently) display in or with the node. At the moment its just the name,
but for display and re-use in documantations one would like to show more
info on the node persistently (not only when one moves the mouse over the
node, but for the saved graphics and for multiple nodes in parallel).
Minor:  the node and Arc type filter nodes do not show tooltips.

Good stuff...

Cheers,
        Daniel Schober.

Am 17.05.2010 23:21, schrieb Sean Falconer:

Hi Daniel,

Thanks for the feedback. Yes, many of the suggestions and issues you
raised are planned as features for the next release. The goal with the
initial version was to get something lightweight and usable out there
for the Protege 4 users.

In the mean time, you can address your first draw back by opening the
OWL definition view in conjunction with the OntoGraf view. Then when
you select a node in your graph, you'll see the full OWL description.
This is available in the menu under View / Class views / Description.

I will make an announcement again when a second version is available
that incorporates some of the requests that you and others have made.

Cheers,

Sean

On Fri, May 14, 2010 at 4:37 AM, Dr. Daniel Schober
[hidden email] wrote:


Dear Sean

Thanks for this nice and stable OntoGraf plugin. This looks really
promising.

I think this plugin would be even better and more useable if the following
feats could be implemented.

a)  an option to export the result-graph as jpg or gif
b)  an option that persistently depicts the relation names (or the full
restrictions e.g. in manchester owl syntax) over the edges. At the moment I
can't reuse the pics for educational purposes as onyl the relation name is
visible when one actively puts the mouse pointer over the edge. At the
moment this lack of the relations greatly limits the useability of this
great plugin for audit , reporting and didactic purposes.
c) an option to display the direct logical definitions/ restrictions in the
node (as long  b) is not implemented).
d) an option to save a view for later re-visualization. E.g. if one is
interested to display the same domain areas in an ontology repeatedly. E.g.
in the OBI  ontology I want to report on the two following areas/views: 1.
the devices (set of classes like device, function, settings, software)  and
2. the Protocols and algorithms. It would be very nice to have the
possibility to store such class sets for later reuse in visualising their
context.

Two drawbacks I recognised:
1. The most interesting parts of the logical equivalence definitions (e.g.
for a 'PharmaceuticalSubstance' node:
 'bearer of' some
    (disposition
     and ('has realization' only 'treating disease'))
seems to be ignored by the plugin and is currently not visualized anywhere.
These should at least be seen in the node descriptions.

2. At the moment if I move the mouse over a node all that happends is that
the nodes gets a liddle bigger and the label is shown (redundantly). Maybe
you could substitute this with another useful functionality, e.g. showing
the full class def in Manchester owl Syntax.

Is any of this in the planning ?

Cheers,
    Daniel Schober.

--

-------------------------------------------------------------
  Dr. Daniel Schober
  Universitätsklinikum
  Institut für Medizinische Biometrie und Medizinische Informatik
  Stefan-Meier-Strasse  26	Raum 6
  D-79104 Freiburg		Germany
  Tel: +49 (0)761 2036807	FAX: +49 (0)761 2036711















--

-------------------------------------------------------------
  Dr. Daniel Schober
  Universitätsklinikum
  Institut für Medizinische Biometrie und Medizinische Informatik
  Stefan-Meier-Strasse  26	Raum 6
  D-79104 Freiburg		Germany
  Tel: +49 (0)761 2036807	FAX: +49 (0)761 2036711











    


  

-- 

-------------------------------------------------------------
  Dr. Daniel Schober
  Universitätsklinikum    
  Institut für Medizinische Biometrie und Medizinische Informatik
  Stefan-Meier-Strasse  26	Raum 6
  D-79104 Freiburg		Germany
  Tel: +49 (0)761 2036807	FAX: +49 (0)761 2036711
  
  
          
          
          
          
             
          
          
          

_______________________________________________
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