protege and web protege questions

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protege and web protege questions

alexandergarciacastrobalu
hi all, I am trying to get a list of features for both web protege and the desktop version of protege (version 5). 

Is there a wiki or webpage with a full list of plugins for protege 5?

Is there a roadmap for future intended developments in web protege?

does protege, either the web version or the desktop one, offers integration with git or with any versioning system?

does protege, either web or desktop, imports from DBs?

does protege, either web or desktop, imports from XLS/CSV files? 

does protege, either web or desktop, support ontology alignment? 

does protege, either web or desktop, support ontology merging? 

does protege, either web or desktop, support exporting to what formats?



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Re: protege and web protege questions

samsontu
Let me try to answer these questions since no one offered to do it so far.

On Nov 4, 2018, at 1:28 AM, alexander garcia <[hidden email]> wrote:

hi all, I am trying to get a list of features for both web protege and the desktop version of protege (version 5). 

Best bet is to look at release notes.


Is there a wiki or webpage with a full list of plugins for protege 5?

https://raw.githubusercontent.com/protegeproject/autoupdate/master/update-info/5.0.0/plugins.repository shows what you can load from within Protege 5. 

In Protege 5, Help/Protege Plugins menu item takes you to a web page that lists Protege plugins past and present. A number of them are compatible with Protege 3.x only.

Is there a roadmap for future intended developments in web protege?

No published roadmap.

does protege, either the web version or the desktop one, offers integration with git or with any versioning system?

Upcoming Protege 5.5 has integration with git.

does protege, either web or desktop, imports from DBs?

No.

does protege, either web or desktop, imports from XLS/CSV files? 

No.

does protege, either web or desktop, support ontology alignment? 

Not that I know of.

does protege, either web or desktop, support ontology merging? 

See menu item Refactor/Merge ontologies ...

does protege, either web or desktop, support exporting to what formats?


See File/Save As…


With best regards,
Samson



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Re: protege and web protege questions

Csongor Nyulas
Administrator
Thank you Samson, for taking a lead on this.
I can add a few things/make some corrections, but Matthew and/or others from our team could elaborate even more, if they have a chance.
In fact, the questions being so broad, and touching so many aspect of our Protégé/WebProtégé software, was one of the reason I found it difficult to take a shot at answering this email.

See my comments below....


On 11/6/18 10:10 AM, Samson Tu wrote:
Let me try to answer these questions since no one offered to do it so far.

On Nov 4, 2018, at 1:28 AM, alexander garcia <[hidden email]> wrote:

hi all, I am trying to get a list of features for both web protege and the desktop version of protege (version 5). 

Best bet is to look at release notes.

That's a definitely a good suggestion. Especially if you are curious of the latest enhancement and features.
Here are links to the release notes:
- for WebProtege: https://github.com/protegeproject/webprotege/releases
- for Protege Desktop: https://github.com/protegeproject/protege-distribution/releases
Note: we are about to release new versions of both Desktop and WebProtege very soon.

If you are curious about a more side-by-side comparison (the way we did for Protege 3 vs Protege 4 here), we do not have such a document. However, it would be a good idea, for sure, to create one such table for Protege 5 and WebProtege, as well.



Is there a wiki or webpage with a full list of plugins for protege 5?

https://raw.githubusercontent.com/protegeproject/autoupdate/master/update-info/5.0.0/plugins.repository shows what you can load from within Protege 5. 

In Protege 5, Help/Protege Plugins menu item takes you to a web page that lists Protege plugins past and present. A number of them are compatible with Protege 3.x only.

Is there a roadmap for future intended developments in web protege?

No published roadmap.

Indeed, we had only an internal road map for WebProtégé.
However, since this may be of interest to the community, we decided to create a wiki page for this on github:
https://github.com/protegeproject/webprotege/wiki/WebProt%C3%A9g%C3%A9-Road-Map


does protege, either the web version or the desktop one, offers integration with git or with any versioning system?

Upcoming Protege 5.5 has integration with git.

This is not a full integration, though. It tries to provide only basic level of integration, which can be very helpful for users, nonetheless.
Basically, Protege recognizes if an ontology is loaded from a project that is under git version control, and shows its git status in the status bar (such as the current branch you are working on, and if the ontology files you have loaded have changed locally since being checked out). It is also possible to use your git user name for "createdBy" annotation in Protege.
We don't offer the capability to use other git commands (such as pull, diffs, commits, pushes, etc.) from within Protege, but you can still use them on the command line and Protege would be aware of their effects.


does protege, either web or desktop, imports from DBs?

No.

It really depends on what you have in mind. Samson's answer is correct, if we interpret your question in the strictest sense, but there are several Protege Desktop plugins that allow you to have certain type of interactions with databases, such as:
- the Ontop plugin, which allows you to run SPARQL query on the combination of your ontology and some data residing in your relational databases (which data, BTW, could be even materialized in your ontology, if you really want to import them): https://github.com/ontop/ontop/wiki
- The Oracle Spacial and Graph Database Backend Plugin for Protege 4.x (which may work for 5.x, as well - haven't tried it): https://protegewiki.stanford.edu/wiki/Protege_4_Plugin_for_Oracle_Database
- The DataMaster Protege 3.x plugin can be used for a importing database structure and data from a relational database: https://protegewiki.stanford.edu/wiki/DataMaster . If the imported ontology is saved in an OWL file it can be reopened and edited in an OWL 2 editor, such the latest Protege 5.x version.


does protege, either web or desktop, imports from XLS/CSV files? 

No.


You could use the Cellfie plugin, which comes bundled with Protege Desktop 5.x, to import from Excel Spreadsheets: https://github.com/protegeproject/cellfie-plugin

does protege, either web or desktop, support ontology alignment? 

Not that I know of.

When I saw the question, two plug-ins popped into my mind, but I am not sure if they would be sophisticated enough for your needs.
One is the Prompt plug-in, which was a very popular Protege 3.x plugin: https://protegewiki.stanford.edu/wiki/PROMPT
And the other is the "OWL Difference" plugin, which is available for Protege 4 and 5 through the auto-update mechanism: https://github.com/protegeproject/owl-diff



does protege, either web or desktop, support ontology merging? 

See menu item Refactor/Merge ontologies ...

does protege, either web or desktop, support exporting to what formats?


See File/Save As…

I would also add that there is also "CSV Export Plugin", available through the auto-update mechanism, which you may find useful.
After installing the plugin, a menu item will be available under the menu Tools > Export to CSV.

I hope this extra info helps a bit.

Best regards,
Csongor



With best regards,
Samson



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