[protege-discussion] Wanted: user manual (memo) of Protege V4.1 for a novice?

[Timothy Redmond]

On 12/11/2012 07:47 AM, Vitályos Gábor wrote:
> Dear colleagues,
>
> I'm beginner in Protégé, I search a description of the menus and the user
> operations for 4.1.
> The tutorials, e.g. Pizza are not suitable: the menus, commands of theirs
> screen shots differ from that I see in my screen.

You have probably seen [1] but I would still recommend this as a great 
tutorial.  One of the good things about this tutorial is that it doesn't 
just explain the Protege user interface; it also explains the OWL 
language.  Without a good understanding of the OWL language it will be 
difficult to understand the behavior of an OWL editor.

It is true that the screenshots and the commands will differ from what 
you see in Protege but they are generally pretty close.   Even if the 
widgets are not in the right place this tutorial will give you a sense 
of what Protege can do.  Unfortunately this document is controlled 
outside the Protege group but I have heard that there is a new version 
coming soon.

There are also pages on the wiki that provide short descriptions of some 
of the aspects of Protege such as the views guide [3] or the menu guide 
[2] (which is admittedly somewhat brief).

>
> (I see the ProtegeWiki, but I don't find anything for this in it. It 
> need a tutorial also :-) )

I grant that we always need additional documentation.

>
> E.g:
> - what is the difference between Entities and Classes tabs?

The entities and classes tabs come from different editing philosophies.  
The idea of the classes tab is to have a tab that is specialized for 
creating and describing new classes.  In this philosophy, when you want 
to create, edit or view classes, you use the classes tab.  When you want 
to create, edit or view properties, you go to the properties tab and 
when you want to create, edit or view individuals you go to the 
individuals tab.  This was how the older versions of Protege used to 
work and having become used to those older editors, this is often how I 
work.

But the joy of the entities tab is that everything that you need is in 
one place.  You can create, edit and view classes, 
object/data/annotation properties, individuals and datatypes all in one 
tab.  So particularly when you are making a new ontology, this can be 
very useful.  You might start, for instance, creating a few classes, and 
then realize that you need to create some object or data properties to 
write some definitions of the classes.  You can add the properties 
without leaving the entities tab and then go back to editing the class 
definition.

> - Moerever: tabs would need at least one paragraph of explanation. 
> Have they any?

There are some explanations of tabs in various places but I suspect they 
may not be what you are looking for.  In some sense, a tab provides a 
coherent picture of the contents of an ontology.  Thus, for instance, 
the Classes tab is focused on showing the structure of the classes and 
their relationships in an ontology.

A tab is made up of a collection of views [3] combined together in a 
useful layout.  A view is a multi-purpose graphical component that 
specializes in showing one particular aspect of an ontology.  Thus for 
instance, the asserted class hierarchy view [4] is used by the classes 
tab and it specializes in showing the class hierarchy for an ontology.  
The classes tab consists of several views organized to support creating, 
editing and viewing classes:

  * the asserted Class Hierarchy view that shows the class hierarchy in
    a tree structure as specified in the ontology
  * the inferred class hierarchy view that shows what the class
    hierarchy looks like after inference
  * the (class) annotations view that shows the annotations on the class
  * the (class) usage view that shows all the places that a particular
    class is used in the ontology.
  * the description view that shows the logical definitions and
    specifications of a class that can be found in the ontology.

Together these views provide an integrated picture of the structure of 
the classes in the ontology.


> - How to use the Wiews menu? It behaves inconsistently.

The Views menu allows you to add new views to a tab.  When you click on 
a view from the Views menu, it will allow you to place that view 
somewhere on the current Protege tab.  For example, one of the tabs that 
I most consistently modify is the "Active Ontology" tab.  I often add 
views that show the rendering of an ontology in different formats so 
that I can cut and paste examples for this mailing list. Or for 
ontologies which have lots of imports I use the graphical imports views 
to get an idea of the shape of the imports.

> - If the Reasoner makes read something, have any explanation message?


I am not sure what you mean by this but when the reasoner is active, 
then most of the inferred results that Protege shows will have a 
question mark nearby.  If you click on the question mark, Protege will 
construct an explanation of how it arrived at that inference. 
Understanding these explanations will probably take some OWL experience 
and this is where the Protege tutorial [1] comes in handy.

-Timothy

> - Etc.
>
> Have you some help?
>
> Thanx
> Gábor Vitályos
> Vitályos Consulting Ltd.
>

[1] http://owl.cs.manchester.ac.uk/tutorials/protegeowltutorial/
[2]http://protegewiki.stanford.edu/wiki/Protege4Shortcuts
[3]http://protegewiki.stanford.edu/wiki/Protege4Views#Annotations_views
[4]http://protegewiki.stanford.edu/wiki/Protege4Views#Asserted_class_hierarchy

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