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Comments on WebProtege upgrade

Jade Hotchkiss
Hi

I see today that the Stanford hosted WebProtege has been upgraded overnight.

I like some of the changes:
- The inclusion of Classes in the class annotation panel.
- The new Comments tab.
- The ability to go straight to any entity referred to in a class's annotations.

However, some features that I used quite a lot are no longer there:
- The search function for Class Hierarchy.
- The ability to add certain panels/functionality to tabs, particularly, "Usage" and "Metrics".
- The ability to download versions from the History (old Dashboard) tab.

Is this missing functionality final or might it still be re-included again?

Thanks,
Jade Hotchkiss

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Re: Comments on WebProtege upgrade

Matthew Horridge-2
Administrator
Hi Jade,

Thanks a lot for the comments and feed back.  I’ll answer your point inline.

I like some of the changes:
- The inclusion of Classes in the class annotation panel.
- The new Comments tab.
- The ability to go straight to any entity referred to in a class's annotations.

However, some features that I used quite a lot are no longer there:
- The search function for Class Hierarchy.

This will be implemented in the next couple of days.

- The ability to add certain panels/functionality to tabs, particularly, "Usage" and "Metrics”.

You can do this.  The mechanism is slightly different now.  Select the tab which you want to add a view to and press the three-lined menu icon to the right of the tab name.  This will cause a menu to pop up.  Select the “Add view” item from the menu and in the dialog that appears select the view that you want to add.  Next, move the mouse over the page to position the view where you’d like it to go.  The position will be indicated by the yellow rectangle.


- The ability to download versions from the History (old Dashboard) tab.

This is available.  On the History tab click the small badge icon on the right hand side of the screen that corresponds to the revision that you want to download.   See the screenshot below.

Is this missing functionality final or might it still be re-included again?

The search component will be added this week.  

We removed the metrics due to some overhead in computing them.  We aim to provide this again soon.

Please feel free to let us know if there’s other functionality that you’d like to see.

Cheers,

Matthew



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Re: Comments on WebProtege upgrade

Jade Hotchkiss
Great, thank you for explaining those points, Matthew!
Another thing I was not managing to do as before was to open more than one project and move between them easily, but I see now I can open each project in a new window and then move between those windows.

Thanks again!
Jade


On Wed, Apr 19, 2017 at 4:57 PM, Matthew Horridge <[hidden email]> wrote:
Hi Jade,

Thanks a lot for the comments and feed back.  I’ll answer your point inline.

I like some of the changes:
- The inclusion of Classes in the class annotation panel.
- The new Comments tab.
- The ability to go straight to any entity referred to in a class's annotations.

However, some features that I used quite a lot are no longer there:
- The search function for Class Hierarchy.

This will be implemented in the next couple of days.

- The ability to add certain panels/functionality to tabs, particularly, "Usage" and "Metrics”.

You can do this.  The mechanism is slightly different now.  Select the tab which you want to add a view to and press the three-lined menu icon to the right of the tab name.  This will cause a menu to pop up.  Select the “Add view” item from the menu and in the dialog that appears select the view that you want to add.  Next, move the mouse over the page to position the view where you’d like it to go.  The position will be indicated by the yellow rectangle.


- The ability to download versions from the History (old Dashboard) tab.

This is available.  On the History tab click the small badge icon on the right hand side of the screen that corresponds to the revision that you want to download.   See the screenshot below.

Is this missing functionality final or might it still be re-included again?

The search component will be added this week.  

We removed the metrics due to some overhead in computing them.  We aim to provide this again soon.

Please feel free to let us know if there’s other functionality that you’d like to see.

Cheers,

Matthew



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Re: Comments on WebProtege upgrade

Matthew Horridge-2
Administrator
Hi Jade,

Just a follow up to this.  Search functionality is now available via the class hierarchy.  

You can enter multiple partial words and WebProtege will search for terms containing these partial words (see below).  If you’re working with OBO ontologies then you can also search within OBO Ids (see the second screenshot) by typing the id, or partial id, into the search field.

Cheers,

Matthew





On 21 Apr 2017, at 00:33, Jade Hotchkiss <[hidden email]> wrote:

Great, thank you for explaining those points, Matthew!
Another thing I was not managing to do as before was to open more than one project and move between them easily, but I see now I can open each project in a new window and then move between those windows.

Thanks again!
Jade


On Wed, Apr 19, 2017 at 4:57 PM, Matthew Horridge <[hidden email]> wrote:
Hi Jade,

Thanks a lot for the comments and feed back.  I’ll answer your point inline.

I like some of the changes:
- The inclusion of Classes in the class annotation panel.
- The new Comments tab.
- The ability to go straight to any entity referred to in a class's annotations.

However, some features that I used quite a lot are no longer there:
- The search function for Class Hierarchy.

This will be implemented in the next couple of days.

- The ability to add certain panels/functionality to tabs, particularly, "Usage" and "Metrics”.

You can do this.  The mechanism is slightly different now.  Select the tab which you want to add a view to and press the three-lined menu icon to the right of the tab name.  This will cause a menu to pop up.  Select the “Add view” item from the menu and in the dialog that appears select the view that you want to add.  Next, move the mouse over the page to position the view where you’d like it to go.  The position will be indicated by the yellow rectangle.
<PastedGraphic-1.png>
<PastedGraphic-2.png>


- The ability to download versions from the History (old Dashboard) tab.

This is available.  On the History tab click the small badge icon on the right hand side of the screen that corresponds to the revision that you want to download.   See the screenshot below.

<PastedGraphic-3.png>
Is this missing functionality final or might it still be re-included again?

The search component will be added this week.  

We removed the metrics due to some overhead in computing them.  We aim to provide this again soon.

Please feel free to let us know if there’s other functionality that you’d like to see.

Cheers,

Matthew



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Re: Comments on WebProtege upgrade

kotsomit
In reply to this post by Jade Hotchkiss
So, is there a new WebProtege release under the hood?

Dimitrios
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Re: Comments on WebProtege upgrade

Tania Tudorache

Yes, there have been a lot of infrastructure and UI improvements, and these are part of a new WebProtege release.


Tania


From: protege-user <[hidden email]> on behalf of kotsomit <[hidden email]>
Sent: Monday, April 24, 2017 3:07:48 PM
To: [hidden email]
Subject: Re: [protege-user] Comments on WebProtege upgrade
 
So, is there a new WebProtege release under the hood?

Dimitrios



--
View this message in context: http://protege-project.136.n4.nabble.com/Comments-on-WebProtege-upgrade-tp4668176p4668284.html
Sent from the Protege User mailing list archive at Nabble.com.
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Re: Comments on WebProtege upgrade

Jade Hotchkiss
In reply to this post by Matthew Horridge-2
Thanks, Matthew!
Definitely helps having that functionality!
Are there plans to include searching using synonyms? This would also be useful, especially for collaborative work with clinicians.


On Sun, Apr 23, 2017 at 11:49 PM, Matthew Horridge <[hidden email]> wrote:
Hi Jade,

Just a follow up to this.  Search functionality is now available via the class hierarchy.  

You can enter multiple partial words and WebProtege will search for terms containing these partial words (see below).  If you’re working with OBO ontologies then you can also search within OBO Ids (see the second screenshot) by typing the id, or partial id, into the search field.

Cheers,

Matthew





On 21 Apr 2017, at 00:33, Jade Hotchkiss <[hidden email]> wrote:

Great, thank you for explaining those points, Matthew!
Another thing I was not managing to do as before was to open more than one project and move between them easily, but I see now I can open each project in a new window and then move between those windows.

Thanks again!
Jade


On Wed, Apr 19, 2017 at 4:57 PM, Matthew Horridge <[hidden email]> wrote:
Hi Jade,

Thanks a lot for the comments and feed back.  I’ll answer your point inline.

I like some of the changes:
- The inclusion of Classes in the class annotation panel.
- The new Comments tab.
- The ability to go straight to any entity referred to in a class's annotations.

However, some features that I used quite a lot are no longer there:
- The search function for Class Hierarchy.

This will be implemented in the next couple of days.

- The ability to add certain panels/functionality to tabs, particularly, "Usage" and "Metrics”.

You can do this.  The mechanism is slightly different now.  Select the tab which you want to add a view to and press the three-lined menu icon to the right of the tab name.  This will cause a menu to pop up.  Select the “Add view” item from the menu and in the dialog that appears select the view that you want to add.  Next, move the mouse over the page to position the view where you’d like it to go.  The position will be indicated by the yellow rectangle.
<PastedGraphic-1.png>
<PastedGraphic-2.png>


- The ability to download versions from the History (old Dashboard) tab.

This is available.  On the History tab click the small badge icon on the right hand side of the screen that corresponds to the revision that you want to download.   See the screenshot below.

<PastedGraphic-3.png>
Is this missing functionality final or might it still be re-included again?

The search component will be added this week.  

We removed the metrics due to some overhead in computing them.  We aim to provide this again soon.

Please feel free to let us know if there’s other functionality that you’d like to see.

Cheers,

Matthew



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protege-user mailing list
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https://mailman.stanford.edu/mailman/listinfo/protege-user


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https://mailman.stanford.edu/mailman/listinfo/protege-user


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Re: Comments on WebProtege upgrade

kotsomit
In reply to this post by Tania Tudorache
Hi Tania,

Thank you for your reply.
Is there any specific branch on github we could try? Some documentation on what's new? Is this "version 3.0"?

Dimitrios
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Re: Comments on WebProtege upgrade

Matthew Horridge-2
Administrator
In reply to this post by Jade Hotchkiss
Hi Jade,

Yes, I’ll evolve the search to fit with user requirements over the next month.  If you have specific requirements please feel free to pass them along (either on or off list, or via our GitHub issue tracker) - we will certainly consider them.

Cheers,

Matthew



On 25 Apr 2017, at 00:00, Jade Hotchkiss <[hidden email]> wrote:

Thanks, Matthew!
Definitely helps having that functionality!
Are there plans to include searching using synonyms? This would also be useful, especially for collaborative work with clinicians.


On Sun, Apr 23, 2017 at 11:49 PM, Matthew Horridge <[hidden email]> wrote:
Hi Jade,

Just a follow up to this.  Search functionality is now available via the class hierarchy.  

You can enter multiple partial words and WebProtege will search for terms containing these partial words (see below).  If you’re working with OBO ontologies then you can also search within OBO Ids (see the second screenshot) by typing the id, or partial id, into the search field.

Cheers,

Matthew



<PastedGraphic-1.png>

<PastedGraphic-2.png>

On 21 Apr 2017, at 00:33, Jade Hotchkiss <[hidden email]> wrote:

Great, thank you for explaining those points, Matthew!
Another thing I was not managing to do as before was to open more than one project and move between them easily, but I see now I can open each project in a new window and then move between those windows.

Thanks again!
Jade


On Wed, Apr 19, 2017 at 4:57 PM, Matthew Horridge <[hidden email]> wrote:
Hi Jade,

Thanks a lot for the comments and feed back.  I’ll answer your point inline.

I like some of the changes:
- The inclusion of Classes in the class annotation panel.
- The new Comments tab.
- The ability to go straight to any entity referred to in a class's annotations.

However, some features that I used quite a lot are no longer there:
- The search function for Class Hierarchy.

This will be implemented in the next couple of days.

- The ability to add certain panels/functionality to tabs, particularly, "Usage" and "Metrics”.

You can do this.  The mechanism is slightly different now.  Select the tab which you want to add a view to and press the three-lined menu icon to the right of the tab name.  This will cause a menu to pop up.  Select the “Add view” item from the menu and in the dialog that appears select the view that you want to add.  Next, move the mouse over the page to position the view where you’d like it to go.  The position will be indicated by the yellow rectangle.
<PastedGraphic-1.png>
<PastedGraphic-2.png>


- The ability to download versions from the History (old Dashboard) tab.

This is available.  On the History tab click the small badge icon on the right hand side of the screen that corresponds to the revision that you want to download.   See the screenshot below.

<PastedGraphic-3.png>
Is this missing functionality final or might it still be re-included again?

The search component will be added this week.  

We removed the metrics due to some overhead in computing them.  We aim to provide this again soon.

Please feel free to let us know if there’s other functionality that you’d like to see.

Cheers,

Matthew



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Re: Comments on WebProtege upgrade

Matthew Horridge-2
Administrator
In reply to this post by kotsomit
Hi Dimitrios,

Yes… there’s been substantial backend and front end changes.  This version will officially be released in the next month or so once we’ve monitored performance in a production setting (i.e. on our servers).

Cheers,

Matthew


> On 24 Apr 2017, at 15:07, kotsomit <[hidden email]> wrote:
>
> So, is there a new WebProtege release under the hood?
>
> Dimitrios
>
>
>
> --
> View this message in context: http://protege-project.136.n4.nabble.com/Comments-on-WebProtege-upgrade-tp4668176p4668284.html
> Sent from the Protege User mailing list archive at Nabble.com.
> _______________________________________________
> protege-user mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-user

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