deep clarifications about Protege-Owl

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deep clarifications about Protege-Owl

Raj M Verma
Hi list,

sorry to give you a big list of Qs... but I took some time to accumulate these Qs by doing some initial research on Protege, so that it will benifit me for the long time research that I wana do using Protege...

1. What shud be the main criteria in deciding which of the two paradigms (Frame-based or Owl-based) that I must use for devising my Ontologies? What are the (dis)advantages of one over the other? Is there some specific leterature that talks(compares) in these lines?

2. What is the connection between RDF and OWL? Is OWL-Full and RDF Schema are equivalent in terms of expressivity and other things? If yes, what are these other things?

3. What shud be the main criteria in deciding which flavour of OWL (Lite, DL or Full) to be used for my Ontologies? Is there any specific literature that talks abt these three flavours of OWL in detail, abt the advantages and disadvantages of using each of these flavours, with some intuitive examples?

4. Is it possible that I use OWL-Full for some of my Ontologies, where I really need more expressivity, and I use OWL-Lite for other Ontlogies where computational completeness and a fast classification of the Ontology are more important, and then use these two Ontologies simultaneously? Do I get/encounter any problems in doing this way? If yes, what are the problems? (any literature)

5. Is it possible that we can have subsumptional relationship between simple concepts and non-qualified concepts[*]? as it is shown in the papar "DL-Lite: Tractable Description Logics for Ontologies - Diego Calvanese, Giuseppe De Giacomo, Domenico Lembo, Maurizio Lenzerini, Riccardo Rosati" with the following example...

Example 1: Consider the atomic concepts Professor and Student, the roles TeachesTo and HasTutor, and the following DL-Lite TBox T :
Professor SUBSUMES EXISTS TeachesTo
EXISTS TeachesTo(INVERSE) SUBSUMES Student
Student SUBSUMES EXISTS HasTutor
EXISTS HasTutor(INVERSE)  SUBSUMES Professor
and so on...

where the concept 'Professor' is shown to be subsumed by the concept 'EXISTS TeachesTo'... it is ok in Description Logics as we can consider these 'EXISTS TeachesTo' kind of concepts as non-qualified concepts of the type 'EXISTS TeachesTo True'... but when I try to do this in Protege, I'm not able to, as I can only use qualified concepts like 'EXISTS Role1 Concept1', but not the non-qualified concepts like 'EXISTS Role1 True' for the necessary conditions... So, my question is, can I define something like the above example using the necessary conditions in Protege?

[*] (I don't know whether this kind of categorization, reagarding qualified and non-qualified concepts is correct or not... I just borrowed it from qualified and non-qualified number restrictions)

6. What exactly is the machanism of using the back end Knowledge Bases that are created using OWL? Despite we claim that these are OWL Ontologies (or OWL Knowledge Bases) the paper "DL-Lite: Tractable Description Logics for Ontologies by Diego Calvanese, Giuseppe De Giacomo, Domenico Lembo, Maurizio Lenzerini, Riccardo Rosati" suggests that we still use the Databases with SQL engines to deal with the data/knowledge interaction!!! So, is there any other literature that explains in detail about the background management of knowledge bases in Protege when we start using multiple Ontologies?

7. http://algernon-j.sourceforge.net/doc/algernon-protege.html  Here the author claims that Algernon is compatible with Protege v1.8, v1.9, v2.0, v2.1 and Java versions 1.3 and 1.4. He did not mention abt Protege 3.1 !! Does it mean that Algernon doesn't support the Protege 3.1 version?

8. In the paper "Ontology Management with the Prompt Plugin" by Natalya F. Noy, she talked about the merging, versioning and maintaining multiple Ontologies... but it was not clear whether these multiple ontologies, that she is talking abt, shud share some basic common properties like paradigm(whether the multiple ontologies that want to be shared must 'Either' be Frame-based 'Or' Owl-based), expressivity(whether multiple ontologies with different expressive power can be successfully merged) etc... My question is, can multiple ontologies with different expressive power and are built from different paradigms be merged? or versioned? or managed with a single framework??

9. How do we use/add different tabs like Algernon, OWL-DL Individuals tab etc into the Protege editor? Is it possible to add/open the Owl plugin tab alongside/within the Protege Frames?

10. Is it possible(in Protege) that I can edit a Frame-based Ontology to include(with the help of Owl tab) some Owl-based concepts and roles, and then relate between my new Owl concepts and the Frame-based classes? For example: I first open FMA pprj file with Protege(we know that FMA is a frame-based Ontology) Now, I want to open the Owl tab within the same editor(if this is possible) and add some Owl based concepts and roles... and then, I want to link the FMA classes with my new Owl-based concepts and run the consistency, satisfiability tests etc. using Racer for example... well, I'm not sure whether Racer can classify frame-based Ontologies! So, another question here is whether there is a common framework that can deal both DL based reasoning and Frame-based rule processing FOR the Ontologies that are devised by mixing these two pardigms! [ is this a bizzare question :( ]

Thanx a ton in advance,
Raj.
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Re: deep clarifications about Protege-Owl

Matt Williams-9
Dear Raj et al.,

I've picked off what I can:

> 2. What is the connection between RDF and OWL? Is OWL-Full and RDF Schema
> are equivalent in terms of expressivity and other things? If yes, what are
> these other things?

OWL sits on top of RDF (and RDFS). It is more expressive. See
http://www.w3.org/TR/owl-features/ (Secn. 1.2) for details)


> 3. What shud be the main criteria in deciding which flavour of OWL (Lite, DL
> or Full) to be used for my Ontologies? Is there any specific literature that
> talks abt these three flavours of OWL in detail, abt the advantages and
> disadvantages of using each of these flavours, with some intuitive examples?

My personal preference is to keep it as simple as you need. There are
certainly some who need OWL Full, but for many OWL DL will suffice.
Since there are good reasoners for OWL DL, I try and stick within that.
The main practical differences (as I have found them) are that in OWL
DL, Individuals and Classes MUST be disjoint. You therefore cannot use a
class as an individual. Since the RDF statements need to run <Subject
Predicate Object>, where Sub. & Obj. are resources, OWL DL stops you
from putting a Class as a subject/ object. Sometimes, this is annoying,
but it depends what you need.

> > 6. What exactly is the machanism of using the back end Knowledge Bases that
> are created using OWL? Despite we claim that these are OWL Ontologies (or
> OWL Knowledge Bases) the paper "DL-Lite: Tractable Description Logics for
> Ontologies by Diego Calvanese, Giuseppe De Giacomo, Domenico Lembo, Maurizio
> Lenzerini, Riccardo Rosati" suggests that we still use the Databases with
> SQL engines to deal with the data/knowledge interaction!!! So, is there any
> other literature that explains in detail about the background management of
> knowledge bases in Protege when we start using multiple Ontologies?

They are OWL ontologies (if you want). You can also use a DB backend, if
you want. If you want to use multiple ontologies, you use the import
statement.


> 7. http://algernon-j.sourceforge.net/doc/algernon-protege.html  Here the
> author claims that Algernon is compatible with Protege v1.8, v1.9, v2.0,
> v2.1 and Java versions 1.3 and 1.4. He did not mention abt Protege 3.1 !!
> Does it mean that Algernon doesn't support the Protege 3.1 version?

No, it works (and up to Protege 3.2b). Michael just hasn't been updating
the site.


> 8. In the paper "Ontology Management with the Prompt Plugin" by Natalya F.
> Noy, she talked about the merging, versioning and maintaining multiple
> Ontologies... but it was not clear whether these multiple ontologies, that
> she is talking abt, shud share some basic common properties like
> paradigm(whether the multiple ontologies that want to be shared must
> 'Either' be Frame-based 'Or' Owl-based), expressivity(whether multiple
> ontologies with different expressive power can be successfully merged)
> etc... My question is, can multiple ontologies with different expressive
> power and are built from different paradigms be merged? or versioned? or
> managed with a single framework??

Don't know, but the issue of merging ontologies is generally considered
HARD.

> 9. How do we use/add different tabs like Algernon, OWL-DL Individuals tab
> etc into the Protege editor? Is it possible to add/open the Owl plugin tab
> alongside/within the Protege Frames?

Got to Project --> Configure and select which tabs you want open. I
would have though OWL plugin won't work with the frames version of
Protege, but I'm not sure.

HTH,

Matt


Dr. M. Williams MRCP(UK)
Clinical Research Fellow,
Cancer Research UK
+44 (0)7834 899570
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Re: deep clarifications about Protege-Owl

Raj M Verma
thanx Matt,

9. How do we use/add different tabs like Algernon, OWL-DL Individuals tab
> etc into the Protege editor? Is it possible to add/open the Owl plugin tab
> alongside/within the Protege Frames?

Got to Project --> Configure and select which tabs you want open. I
would have though OWL plugin won't work with the frames version of
Protege, but I'm not sure.

Yes, you're right... I can't add the Owl plugin while working with Frames... so does it mean that I can't do Owl based changes on a Frame based ontology and vice versa!!

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[protege-owl] Re: deep clarifications about Protege-Owl

Nick Drummond
Raj,

That's correct - the OWL tabs only work with an OWL project.
There is a certain amount of translation you can do between them using
the export as.. functionality, but the mapping between frames and OWL is
lossy (potentially in both directions)

Nick

Raj M Verma wrote:

> thanx Matt,
>
>     9. How do we use/add different tabs like Algernon, OWL-DL
>     Individuals tab
>
>     > etc into the Protege editor? Is it possible to add/open the Owl
>     plugin tab
>     > alongside/within the Protege Frames?
>
>     Got to Project --> Configure and select which tabs you want open. I
>     would have though OWL plugin won't work with the frames version of
>     Protege, but I'm not sure.
>
>
> Yes, you're right... I can't add the Owl plugin while working with
> Frames... so does it mean that I can't do Owl based changes on a Frame
> based ontology and vice versa!!
>

--

Nick Drummond

http://www.cs.man.ac.uk/~drummond/ <http://www.cs.man.ac.uk/%7Edrummond/>
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