programmatic access to webprotege ontologies

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programmatic access to webprotege ontologies

Mark Longo
Hi All, 

Is there a programmatic way to download webprotege ontologies?  I'm using some external visualization tooling (leveraging ontobio to convert my ontologies into networkx objects, which then opens up a whole world of custom graph visualization), and would love to be able to access the webprotege ontology files programmatically to be able to visualize changes on the fly. Webprotege's built-in graph view is nice but doesn't quite serve my needs. 

Thank you. 

Cheers,
Mark


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Re: programmatic access to webprotege ontologies

Michael DeBellis-2
Mark, I don't think anyone ever replied to your message. As far as I know there is no way to get programmatic access to the owl files in Web Protege, but I could be wrong. You can of course get access to the files via the UI. You probably know this but to do that go to the History tab. You should see the version numbers for each revision in the upper right corner, something like "R1". Click on that and there should be a drop down menu that includes an option: "Download revision 1" (or whatever version you click on). 

I think people usually write the kind of extensions you are describing (called Plugins) for the desktop version of Protege not Web Protege. There are more graphical views in the desktop version but I think some additional ones could be useful. Here are some links I found related to developing plugins for the desktop version: https://protegewiki.stanford.edu/wiki/Protege5DevDocs#Developing_a_plugin    https://protegewiki.stanford.edu/wiki/SetUpEclipseForPlugin  

Also, if you are looking for additional visualization tools for OWL files you might want to check out WebVOWL: http://vowl.visualdataweb.org/webvowl.html  

Cheers,
Michael


On Tue, Dec 10, 2019 at 12:49 PM Mark Longo <[hidden email]> wrote:
Hi All, 

Is there a programmatic way to download webprotege ontologies?  I'm using some external visualization tooling (leveraging ontobio to convert my ontologies into networkx objects, which then opens up a whole world of custom graph visualization), and would love to be able to access the webprotege ontology files programmatically to be able to visualize changes on the fly. Webprotege's built-in graph view is nice but doesn't quite serve my needs. 

Thank you. 

Cheers,
Mark

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Re: programmatic access to webprotege ontologies

Mark Longo
Thanks very much, Michael. 
I'd prefer to find a solution for Webprotege rather than desktop Protege because I'm building an ontology collaboratively.  I could download the ontology manually as you suggested but I like to visualize the graph after every few additions/modifications - which means I'd be doing that many times a day. I might write a little script to automate the process using Selenium. I could share with whomever is interested. 

Cheers,
Mark

On Mon, Dec 16, 2019 at 5:21 PM Michael DeBellis <[hidden email]> wrote:
Mark, I don't think anyone ever replied to your message. As far as I know there is no way to get programmatic access to the owl files in Web Protege, but I could be wrong. You can of course get access to the files via the UI. You probably know this but to do that go to the History tab. You should see the version numbers for each revision in the upper right corner, something like "R1". Click on that and there should be a drop down menu that includes an option: "Download revision 1" (or whatever version you click on). 

I think people usually write the kind of extensions you are describing (called Plugins) for the desktop version of Protege not Web Protege. There are more graphical views in the desktop version but I think some additional ones could be useful. Here are some links I found related to developing plugins for the desktop version: https://protegewiki.stanford.edu/wiki/Protege5DevDocs#Developing_a_plugin    https://protegewiki.stanford.edu/wiki/SetUpEclipseForPlugin  

Also, if you are looking for additional visualization tools for OWL files you might want to check out WebVOWL: http://vowl.visualdataweb.org/webvowl.html  

Cheers,
Michael


On Tue, Dec 10, 2019 at 12:49 PM Mark Longo <[hidden email]> wrote:
Hi All, 

Is there a programmatic way to download webprotege ontologies?  I'm using some external visualization tooling (leveraging ontobio to convert my ontologies into networkx objects, which then opens up a whole world of custom graph visualization), and would love to be able to access the webprotege ontology files programmatically to be able to visualize changes on the fly. Webprotege's built-in graph view is nice but doesn't quite serve my needs. 

Thank you. 

Cheers,
Mark

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


--
Mark D. Longo, Ph.D.  |  Head of Data Science
Sirona Medical
236 8th Street, San Francisco, CA 94103
Cell: (650) 644-5647

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Re: programmatic access to webprotege ontologies

Michael DeBellis-2
Mark, you probably know this but in case you are new to Protege and OWL I just wanted to mention that there is no reasoner support yet with Web Protege. Unless you are just using Web Protege to define classes in a hierarchy with no DL axioms and properties with no domain or range I would suggest that you take the ontology from Web Protege and bring it into the desktop version every once in a while so you can run the reasoner and make sure there are no inconsistencies with the ontology. I'm always interested in new visualization tools for OWL so I would be interested in your tool. 

Cheers,
Michael

On Tue, Dec 17, 2019 at 11:16 AM Mark Longo <[hidden email]> wrote:
Thanks very much, Michael. 
I'd prefer to find a solution for Webprotege rather than desktop Protege because I'm building an ontology collaboratively.  I could download the ontology manually as you suggested but I like to visualize the graph after every few additions/modifications - which means I'd be doing that many times a day. I might write a little script to automate the process using Selenium. I could share with whomever is interested. 

Cheers,
Mark

On Mon, Dec 16, 2019 at 5:21 PM Michael DeBellis <[hidden email]> wrote:
Mark, I don't think anyone ever replied to your message. As far as I know there is no way to get programmatic access to the owl files in Web Protege, but I could be wrong. You can of course get access to the files via the UI. You probably know this but to do that go to the History tab. You should see the version numbers for each revision in the upper right corner, something like "R1". Click on that and there should be a drop down menu that includes an option: "Download revision 1" (or whatever version you click on). 

I think people usually write the kind of extensions you are describing (called Plugins) for the desktop version of Protege not Web Protege. There are more graphical views in the desktop version but I think some additional ones could be useful. Here are some links I found related to developing plugins for the desktop version: https://protegewiki.stanford.edu/wiki/Protege5DevDocs#Developing_a_plugin    https://protegewiki.stanford.edu/wiki/SetUpEclipseForPlugin  

Also, if you are looking for additional visualization tools for OWL files you might want to check out WebVOWL: http://vowl.visualdataweb.org/webvowl.html  

Cheers,
Michael


On Tue, Dec 10, 2019 at 12:49 PM Mark Longo <[hidden email]> wrote:
Hi All, 

Is there a programmatic way to download webprotege ontologies?  I'm using some external visualization tooling (leveraging ontobio to convert my ontologies into networkx objects, which then opens up a whole world of custom graph visualization), and would love to be able to access the webprotege ontology files programmatically to be able to visualize changes on the fly. Webprotege's built-in graph view is nice but doesn't quite serve my needs. 

Thank you. 

Cheers,
Mark

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


--
Mark D. Longo, Ph.D.  |  Head of Data Science
Sirona Medical
236 8th Street, San Francisco, CA 94103
Cell: (650) 644-5647
_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

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