[protege-owl] importing RDF

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[protege-owl] importing RDF

Paul Prueitt
 
 
 
I have a file which is a pure RDF file, which I build with Altova's new RDF OWL editor.   I am trying to load this into Protege OWL
 
i use the create new project    and then use the create with existing sources by checking the little box..
 
 
the project type list does not make sense ... since I want to create something that is not OWL... but I understand that I should select "OWL files... but there is uncertainty. 
 Andrea's note in the Protege OWL discussion helps me conjecture that OWL is "sameAs" RDF in many practical sense if one does not need to use the OIL part.  ...  but there are some details.....  and these details are a moving target for me....
 
The select file does not allow me to look for only .rdf files (which worries me more) and so I use the select from "all files" to get my rdf file selected
 
 
The language profile window allows me two choices - which I can not make a judgment about so I try Pure RDF Schema without OWL first... and this fails   because  the class names are changed .... "matrix" becomes "p10:atrix" . 
redoing the steps and making the other choice leads to the same result. 
 
 I  think this must be a default namespace issue, but I am not sure.  
 
 
 
Thank you in advance...
 
 
 
 
 
with deepest respects..
 
 
 
 
 
 
 
 
-----Original Message-----
From: Ted Hopper [mailto:[hidden email]]
Sent: Wednesday, February 08, 2006 4:16 PM
To: Paul Prueitt
Cc: Tim Redmond; Jennifer Vendetti
Subject: RE: Message submitted to 'protege-discussion'

Hi Paul,

Please accept my sincerest apologies, as the last thing that I wanted to do was to censor your post.  We have implemented an albeit far from perfect filtering system to detect messages posted to the protege-discussion list that should have been posted to the more specific protege-owl list.  I, not an experienced protege user, then have to make the call as to whether to repost them to discussion or suggest that the sender post to OWL instead, and, being human, I do make mistakes from time to time.  Rest assured our rationale is to help ensure that each post gets routed to the folks most likely to help out.  I am happy to see that you received the answers you sought in the OWL list.

Best,
Ted

At 06:36 AM 2/8/2006, you wrote:
Ted, I posted to the discussion list that I wanted to.  I did not post to be
censored

If I am censored that I will take this up with those who feel that there
should not be censorship in this forum.



-----Original Message-----
From: Ted Hopper [[hidden email]]
Sent: Tuesday, February 07, 2006 10:08 PM
To: Paul Prueitt
Subject: Fwd: Message submitted to 'protege-discussion'


Hello Paul,

The nature of your message is more appropriate for posting to the
[hidden email] list.
Please post your message there.  If you currently not subscribed to this
list, you can browse to
http://protege.stanford.edu/community/subscribe.html to do so.

Thanx,
Ted

>X-Sieve: CMU Sieve 2.2
>Date: Tue, 07 Feb 2006 20:41:34 %z (PST)
>From: Ecartis <[hidden email]>
>Reply-To: [hidden email]
>To: [hidden email]
>X-ecartis-antiloop: crg-gw.Stanford.EDU
>Subject: Message submitted to 'protege-discussion'
>
>This message was received for a list you are a moderator on, and
>was marked for moderation due to the following reason:
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>
>To approve this message and have it go out on the list, forward this to
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>
>If you wish to decline the post, change the 'apppost' below to 'delpost'.
>If you wish to edit the post, change it to 'modpost' and edit the message
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>
>DO NOT DELETE THE FOLLOWING LINE.  Ecartis needs it.
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>
> >From [hidden email] Tue Feb  7 20:41:30 2006
>Received: from harbor.safeport.com (harbor.safeport.com [209.31.154.12])
>         by crg-gw.Stanford.EDU (8.11.5/8.11.5) with SMTP id k184fTW02564
>         for <[hidden email]>; Tue, 7 Feb 2006
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>         Tue, 7 Feb 2006 23:41:20 -0500 (EST)
>         (envelope-from [hidden email])
>From: "Paul Prueitt" <[hidden email]>
>To: <[hidden email]>
>Subject: on properties
>Date: Tue, 7 Feb 2006 21:41:16 -0700
>Message-ID: <[hidden email]>
>MIME-Version: 1.0
>Content-type: text/plain
>X-Priority: 3 (Normal)
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>Importance: Normal
>Content-Transfer-Encoding: 8bit
>
>
>
>in looking at
>
>owl:ObjectProperty
>owl:DatatypeProperty
>and
>rdf:Property
>
>I am trying to understand how to choose one of these in defining a property
>
>The task I am doing is to encode the SOA-IM (service oriented
>architecture-information model) as an RDF file.
>
>The SOA-IM has 38 "enitities" which I have made into "classes"  .  I wish
to

>have no subsumptions relationships, since each of these IM enitities is a
>data object related to a simple XML document.  There are in the OASIS
>standard the notion of class parents... but I wish to flatten the set of
>objects ...
>
>see attached rdf file
>
>
>
>2.1 SOA Information Model Entities
>
>This section covers all SOA IM entities and their attributes.
>
>2.1.1 Action
>
>A consequence of an event taking place.
>
>
>Attribute       Type    Description
>id      String256       Unique ID
>name    String256       Action's name
>description     String4000      Detailed description
>event   String256       Event which this action relates to
>reference       String256       Unique ID of the reference
>type    String256       The type of the Action
>(Alert/Compensation/Information/Insertion/Termination/Trigger Flow)
>
>
>Associated with
>.       An Event where Event is the target object and association type is
>"IsActionOf"
>
>Parent: Event
>
>is the first object.
>
>**********************************
>
>My question is about whether the attributes should be
>
>
>owl:ObjectProperty
>owl:DatatypeProperty
>or
>rdf:Property
>
>
>advice and explaination of why the advise is (as it is) is appreciated,
>greatly.
>
>
>
>
>
>
>-- Attached file removed by Ecartis and put at URL below --
>-- Type: text/xml
>-- Size: 9k (9489 bytes)
>-- URL :
http://protege.stanford.edu/mail_archive/attachments/SOA-Enitities.rdf
>
>
>// eompost 43E9767E:A51.1:cebgrtrqvfphffvba

~~~~~~~~~~~~~~~~~~~~~~~~~~
Ted Hopper, '84, MA '85
Administrative Associate
Stanford Medical Informatics
Medical School Office Building, Room X217
Stanford, CA
Voice: (650) 736-0728
Fax: (650) 725-7944
Mail Code: 5479
Web: http://www.smi.stanford.edu/
~~~~~~~~~~~~~~~~~~~~~~~~~~

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Ted Hopper
Protégé Group Administrative Associate
Stanford Medical Informatics
Medical School Office Building, Room X217
Stanford, CA
Voice: (650) 736-0728
Fax: (650) 725-7944
Mail Code: 5479
URLS: Home: http://protege.stanford.edu
           Wiki:  
http://protege.cim3.net/wiki
Short Course: http://protege.stanford.edu/shortcourse/protege/200603
Conference:    http://protege.stanford.edu/conference/2006
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


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[protege-owl] Re: importing RDF

Paul S Prueitt
I am absolutely stopped on something that I need to finish ... this (really really should be simple) importing of an Altova created simple RDF file.
 
Everyone knows that I am critical of how very complicated the ontology paradigm is that has been created by the Stanford team, and I hope that I do not get attacked (again) by someone who feels that I am being unfair to anyone.   This attacking response in face of critisicm is simple NOT proper. 
 
FIRST the import of a compliant short RDF file into Protege, or the import of the BioPAX file into Protege should not be a problem.  Period.  But there have been at least four different persons who have have a problem importing the BioPAX file.  This is not the BioPAX working group's fault.   It is the fault of the Protege GUI.  Right?
 
 
The design of the import interface seems to be fundamentally flawed.   Why, after 17 years? 
 
The flaws might stem from the Tim Berners-Lee Layer cake itself, and so the difficulty of the import and export may not be merely a result of poor work by the Stanford team.   But the problems themselves are not being exposed, (I conjecture).   
 
In my message, two days ago, to Protege Discussion (which got rejected automatically because I used the word "OWL") I trying to set up a problem, modeling the OASIS SOA IM with RDF !!!or!!! OWL.   This task is huge, because it links the OASIS and IEEE web services and XML standards with semantic web "ontology with inferencing".  So, I am aksing for help.
 
The RDF modeling of OASISA SOA IM task should be a great interest to everyone on this discussion forum, as well as the Protege-discussion forum (where it never got posted).    Can I see a show of hands?  Who in the Protege OWL forum would like to see a simple RDF model (no OIL) of the SOA IM?  Once we have this, who would like to see various ways of adding the OIL?
 
 
 
I want to be clear, since over and over my discussion is treated as if I need for tutorial on something (Jennifer?). 
 
The problem is not my knowledge of the problem.  The problem is on the incompeteness of our (the world society) development of tools for modeling "reality".  This problem, as Andrea and I have talked about starts with the narrow (and often misleading) use of terms like inference, and the absence of common understanding of the generalization of the term "inference" ...  "entailment" is both logical "inference" and physical cause.
 
 
And, as has been suggested by several PhDs in knowledge engineering, this is not about one professions right to have their own private language.  The entire world needs to have ontological modeling figured out ... in precisely the way that arithmetic was figured out and is now commonly and everywhere available without "professional interests" trumping "social interests".   Again, I do not deserve to be attacked as being somehow un-poroessional. 
 
It is time to see the limitations and problems of Protege "with eyes open". 
 
We all have many layers of things we are trying to get to .... and the fundamentals of import and export using Protege cannot be so weird as to bend one's mind into contortions. 
 
Right?
 
<gesturing with a puzzled look).
 
As I mentioned, the problem in loading the Altova created RDF file is likely a namespace problem.... 
 
but how this is handled should be made clear in the "software wizard" that is now just poorly designed.
 
Right?
 
 
-----Original Message-----
From: [hidden email] [mailto:[hidden email]]On Behalf Of Paul Prueitt
Sent: Wednesday, February 08, 2006 6:39 PM
To: Protege-Owl
Subject: [protege-owl] importing RDF

 
 
 
I have a file which is a pure RDF file, which I build with Altova's new RDF OWL editor.   I am trying to load this into Protege OWL
 
i use the create new project    and then use the create with existing sources by checking the little box..
 
 
the project type list does not make sense ... since I want to create something that is not OWL... but I understand that I should select "OWL files... but there is uncertainty. 
 Andrea's note in the Protege OWL discussion helps me conjecture that OWL is "sameAs" RDF in many practical sense if one does not need to use the OIL part.  ...  but there are some details.....  and these details are a moving target for me....
 
The select file does not allow me to look for only .rdf files (which worries me more) and so I use the select from "all files" to get my rdf file selected
 
 
The language profile window allows me two choices - which I can not make a judgment about so I try Pure RDF Schema without OWL first... and this fails   because  the class names are changed .... "matrix" becomes "p10:atrix" . 
redoing the steps and making the other choice leads to the same result. 
 
 I  think this must be a default namespace issue, but I am not sure.  
 
 
 
Thank you in advance...
 
 
 
 
 
with deepest respects..
 
 
 
 
 
 
 
 
-----Original Message-----
From: Ted Hopper [mailto:[hidden email]]
Sent: Wednesday, February 08, 2006 4:16 PM
To: Paul Prueitt
Cc: Tim Redmond; Jennifer Vendetti
Subject: RE: Message submitted to 'protege-discussion'

Hi Paul,

Please accept my sincerest apologies, as the last thing that I wanted to do was to censor your post.  We have implemented an albeit far from perfect filtering system to detect messages posted to the protege-discussion list that should have been posted to the more specific protege-owl list.  I, not an experienced protege user, then have to make the call as to whether to repost them to discussion or suggest that the sender post to OWL instead, and, being human, I do make mistakes from time to time.  Rest assured our rationale is to help ensure that each post gets routed to the folks most likely to help out.  I am happy to see that you received the answers you sought in the OWL list.

Best,
Ted

At 06:36 AM 2/8/2006, you wrote:
Ted, I posted to the discussion list that I wanted to.  I did not post to be
censored

If I am censored that I will take this up with those who feel that there
should not be censorship in this forum.



-----Original Message-----
From: Ted Hopper [[hidden email]]
Sent: Tuesday, February 07, 2006 10:08 PM
To: Paul Prueitt
Subject: Fwd: Message submitted to 'protege-discussion'


Hello Paul,

The nature of your message is more appropriate for posting to the
[hidden email] list.
Please post your message there.  If you currently not subscribed to this
list, you can browse to
http://protege.stanford.edu/community/subscribe.html to do so.

Thanx,
Ted

>X-Sieve: CMU Sieve 2.2
>Date: Tue, 07 Feb 2006 20:41:34 %z (PST)
>From: Ecartis <[hidden email]>
>Reply-To: [hidden email]
>To: [hidden email]
>X-ecartis-antiloop: crg-gw.Stanford.EDU
>Subject: Message submitted to 'protege-discussion'
>
>This message was received for a list you are a moderator on, and
>was marked for moderation due to the following reason:
>Failed administrivia check on pattern '^[oO][wW][lL].*$'
>
>To approve this message and have it go out on the list, forward this to
>protege-discussion-repost@(No value set)
>
>If you wish to decline the post, change the 'apppost' below to 'delpost'.
>If you wish to edit the post, change it to 'modpost' and edit the message
>as needed - not all mail programs will work with modpost.
>
>DO NOT DELETE THE FOLLOWING LINE.  Ecartis needs it.
>// apppost 43E9767E:A51.1:cebgrtrqvfphffvba
>
> >From [hidden email] Tue Feb  7 20:41:30 2006
>Received: from harbor.safeport.com (harbor.safeport.com [209.31.154.12])
>         by crg-gw.Stanford.EDU (8.11.5/8.11.5) with SMTP id k184fTW02564
>         for <[hidden email]>; Tue, 7 Feb 2006
20:41:30 -0800 (PST)
>Received: from yourkkxx5rxwd9 (209-188-120-35.taosnet.com [209.188.120.35])
>         by harbor.safeport.com (8.12.11/8.12.11) with SMTP id
k184fFJp071129;

>         Tue, 7 Feb 2006 23:41:20 -0500 (EST)
>         (envelope-from [hidden email])
>From: "Paul Prueitt" <[hidden email]>
>To: <[hidden email]>
>Subject: on properties
>Date: Tue, 7 Feb 2006 21:41:16 -0700
>Message-ID: <[hidden email]>
>MIME-Version: 1.0
>Content-type: text/plain
>X-Priority: 3 (Normal)
>X-MSMail-Priority: Normal
>X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0)
>In-Reply-To: <[hidden email]>
>X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2900.2180
>Importance: Normal
>Content-Transfer-Encoding: 8bit
>
>
>
>in looking at
>
>owl:ObjectProperty
>owl:DatatypeProperty
>and
>rdf:Property
>
>I am trying to understand how to choose one of these in defining a property
>
>The task I am doing is to encode the SOA-IM (service oriented
>architecture-information model) as an RDF file.
>
>The SOA-IM has 38 "enitities" which I have made into "classes"  .  I wish
to

>have no subsumptions relationships, since each of these IM enitities is a
>data object related to a simple XML document.  There are in the OASIS
>standard the notion of class parents... but I wish to flatten the set of
>objects ...
>
>see attached rdf file
>
>
>
>2.1 SOA Information Model Entities
>
>This section covers all SOA IM entities and their attributes.
>
>2.1.1 Action
>
>A consequence of an event taking place.
>
>
>Attribute       Type    Description
>id      String256       Unique ID
>name    String256       Action's name
>description     String4000      Detailed description
>event   String256       Event which this action relates to
>reference       String256       Unique ID of the reference
>type    String256       The type of the Action
>(Alert/Compensation/Information/Insertion/Termination/Trigger Flow)
>
>
>Associated with
>.       An Event where Event is the target object and association type is
>"IsActionOf"
>
>Parent: Event
>
>is the first object.
>
>**********************************
>
>My question is about whether the attributes should be
>
>
>owl:ObjectProperty
>owl:DatatypeProperty
>or
>rdf:Property
>
>
>advice and explaination of why the advise is (as it is) is appreciated,
>greatly.
>
>
>
>
>
>
>-- Attached file removed by Ecartis and put at URL below --
>-- Type: text/xml
>-- Size: 9k (9489 bytes)
>-- URL :
http://protege.stanford.edu/mail_archive/attachments/SOA-Enitities.rdf
>
>
>// eompost 43E9767E:A51.1:cebgrtrqvfphffvba

~~~~~~~~~~~~~~~~~~~~~~~~~~
Ted Hopper, '84, MA '85
Administrative Associate
Stanford Medical Informatics
Medical School Office Building, Room X217
Stanford, CA
Voice: (650) 736-0728
Fax: (650) 725-7944
Mail Code: 5479
Web: http://www.smi.stanford.edu/
~~~~~~~~~~~~~~~~~~~~~~~~~~

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Ted Hopper
Protégé Group Administrative Associate
Stanford Medical Informatics
Medical School Office Building, Room X217
Stanford, CA
Voice: (650) 736-0728
Fax: (650) 725-7944
Mail Code: 5479
URLS: Home: http://protege.stanford.edu
           Wiki:  
http://protege.cim3.net/wiki
Short Course: http://protege.stanford.edu/shortcourse/protege/200603
Conference:    http://protege.stanford.edu/conference/2006
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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[protege-owl] Re: importing RDF

Andrea Proli-2
In reply to this post by Paul Prueitt
Paul,
indeed I have intentionally left out of my post some "details" for the  
sake of clarity, but those details are now emerging in a potentially  
harmful way... so I try to compensate here. However, I have to admit that  
I am not an experienced Protégé user, so I can't tell you what options to  
check or what menu items to select to solve your problems, I can just try  
and guess why are you experiencing some troubles with this RDF/RDFS/OWL  
mess.

First, about the Semantic Web language tower, it is important to note that  
while RDFS is a superset of RDF (in both vocabulary and semantic  
conditions, I mean), the layering of OWL on top of RDFS is a little more  
complicated stuff. Three different flavors of OWL exist, namely (ordered  
by increasingly higher expressivity) OWL-Lite, OWL-DL, and OWL-Full.  
Roughly stated, the reason for this is that the semantic conditions  
attached to the resource names defined by the whole OWL vocabulary  
interact with each other in a way that makes computation and query  
answering with respect to *all of those conditions taken together* too  
much costly, if not unfeasible at all. Thus, three versions of the  
language have been defined supporting different subsets of the semantic  
conditions, each one leading to a different trade-off between expressivity  
and computational properties. The more you can express, the worse  
performance you get. These results come from Description Logics, but  
that's a different story.

Technically, OWL-Full is not decidable (it could take infinite time to  
answer your questions) but is a *proper superset* of the whole RDFS, in  
the sense that its set of semantic conditions properly includes the one of  
RDFS. Instead, the two decidable flavors of OWL (i.e. those for which you  
are always guaranteed to receive an answer in finite time) are supersets  
of *subsets* of RDFS.

Because of this, your document could be perfectly valid "per se", but not  
every set of statements in it that could be legal for a query answering  
program taking into account the semantic conditions of RDFS would also be  
legal for one which takes into account those of OWL-DL and OWL-Lite  
(cumbersome phrase, I am sorry, but if you replace "query answering  
program taking into account the semantic conditions of RDFS" by  
"RDFS-reasoner", and similarly you do for the OWL one, it becomes  
manageable). As you can imagine, this would not be a problem for programs  
taking into account the semantic conditions of OWL-Full and your document  
will always be considered to be legal, but then you would not be sure to  
always obtain an answer.

Most often, the above discourse is shortened and rephrased by saying that  
"not everything you can state in RDF and RDFS can also be stated in OWL",  
which is not precisely true because of what I said here and in my previous  
post, but is more or less effective, provided that you are aware of the  
above details and clarififcations.

I can guess that Protégé is designed to interoperate with other programs  
like Racer or Fact or Pellet, which are concerned with the decidable  
fragments of OWL only, and for this reason does not like documents which  
contain combinations of statements marked as "illegal" by OWL-Lite and/or  
OWL-DL. As far as I know, Protégé cannot handle all of the features of  
OWL-Full, for example instantiation chains spanning more than one  
meta-level (e.g. a rdf:type b, b rdf:type c, c rdf:type d, ...). So, let's  
say, if the RDF document you created with Altova contains such an  
instantiation chain, maybe Protégé would not be happy about that (but I  
repeat, I am just trying to guess), and you won't be free to create  
whatever kind of statement you want in it, no matter if you are not  
interested in OWL. So... pay attention :-)

I hope this helps, please tell me if you need further feedback. I ALSO  
APOLOGIZE IN ADVANCE WITH THE TEAM IN CASE THE INFORMATION I AM GIVING  
ABOUT PROTEGE IS FALSE OR PARTIALLY ERRONEOUS, and if so I would be  
grateful to them if they corrected me.
Best,

Andrea

P.S.: Paul, the usefulness of OWL-Full as a plain, highly expressive  
knowledge representation language breaking the limitations of First Order  
Logics is an interesting topic, and I think it could match your interest  
in "inference-free ontologies". I plan to post something about that, but I  
currently have little time. I would also appreciate private  
communication/feedback from you if you prefer not to bother the whole  
mailing list.

In data Thu, 09 Feb 2006 02:38:47 +0100, Paul Prueitt  
<[hidden email]> ha scritto:

>
>
>
> I have a file which is a pure RDF file, which I build with Altova's new  
> RDF
> OWL editor.   I am trying to load this into Protege OWL
>
> i use the create new project    and then use the create with existing
> sources by checking the little box..
>
>
> the project type list does not make sense ... since I want to create
> something that is not OWL... but I understand that I should select "OWL
> files... but there is uncertainty.
>
>  Andrea's note in the Protege OWL discussion helps me conjecture that  
> OWL is
> "sameAs" RDF in many practical senses  if one does not need to use the  
> OIL
> part.  ...  but there are some details.....  and these details are a  
> moving
> target for me....
>
> The select file does not allow me to look for only .rdf files (which  
> worries
> me more) and so I use the select from "all files" to get my rdf file
> selected
>
>
> The language profile window allows me two choices - which I can not make  
> a
> judgment about so I try Pure RDF Schema without OWL first... and this  
> fails
> because  the class names are changed .... "matrix" becomes "p10:atrix" .
>
> redoing the steps and making the other choice leads to the same result.
>
>  I  think this must be a default namespace issue, but I am not sure.
>
>
>
> Thank you in advance...
>
>
>
>
>
> with deepest respects..
>
>
>
>
>
>
>
>
>   -----Original Message-----
>   From: Ted Hopper [mailto:[hidden email]]
>   Sent: Wednesday, February 08, 2006 4:16 PM
>   To: Paul Prueitt
>   Cc: Tim Redmond; Jennifer Vendetti
>   Subject: RE: Message submitted to 'protege-discussion'
>
>
>   Hi Paul,
>
>   Please accept my sincerest apologies, as the last thing that I wanted  
> to
> do was to censor your post.  We have implemented an albeit far from  
> perfect
> filtering system to detect messages posted to the protege-discussion list
> that should have been posted to the more specific protege-owl list.  I,  
> not
> an experienced protege user, then have to make the call as to whether to
> repost them to discussion or suggest that the sender post to OWL instead,
> and, being human, I do make mistakes from time to time.  Rest assured our
> rationale is to help ensure that each post gets routed to the folks most
> likely to help out.  I am happy to see that you received the answers you
> sought in the OWL list.
>
>   Best,
>   Ted
>
>   At 06:36 AM 2/8/2006, you wrote:
>
>     Ted, I posted to the discussion list that I wanted to.  I did not  
> post
> to be
>     censored
>
>     If I am censored that I will take this up with those who feel that  
> there
>     should not be censorship in this forum.
>
>
>
>     -----Original Message-----
>     From: Ted Hopper [ mailto:[hidden email]]
>     Sent: Tuesday, February 07, 2006 10:08 PM
>     To: Paul Prueitt
>     Subject: Fwd: Message submitted to 'protege-discussion'
>
>
>     Hello Paul,
>
>     The nature of your message is more appropriate for posting to the
>     [hidden email] list.
>     Please post your message there.  If you currently not subscribed to  
> this
>     list, you can browse to
>     http://protege.stanford.edu/community/subscribe.html to do so.
>
>     Thanx,
>     Ted
>
>     >X-Sieve: CMU Sieve 2.2
>     >Date: Tue, 07 Feb 2006 20:41:34 %z (PST)
>     >From: Ecartis <[hidden email]>
>     >Reply-To: [hidden email]
>     >To: [hidden email]
>     >X-ecartis-antiloop: crg-gw.Stanford.EDU
>     >Subject: Message submitted to 'protege-discussion'
>     >
>     >This message was received for a list you are a moderator on, and
>     >was marked for moderation due to the following reason:
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>     >
>     >If you wish to decline the post, change the 'apppost' below to
> 'delpost'.
>     >If you wish to edit the post, change it to 'modpost' and edit the
> message
>     >as needed - not all mail programs will work with modpost.
>     >
>     >DO NOT DELETE THE FOLLOWING LINE.  Ecartis needs it.
>     >// apppost 43E9767E:A51.1:cebgrtrqvfphffvba
>     >
>     > >From [hidden email] Tue Feb  7 20:41:30 2006
>     >Received: from harbor.safeport.com (harbor.safeport.com
> [209.31.154.12])
>     >         by crg-gw.Stanford.EDU (8.11.5/8.11.5) with SMTP id
> k184fTW02564
>     >         for <[hidden email]>; Tue, 7 Feb 2006
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> [209.188.120.35])
>     >         by harbor.safeport.com (8.12.11/8.12.11) with SMTP id
>     k184fFJp071129;
>     >         Tue, 7 Feb 2006 23:41:20 -0500 (EST)
>     >         (envelope-from [hidden email])
>     >From: "Paul Prueitt" <[hidden email]>
>     >To: <[hidden email]>
>     >Subject: on properties
>     >Date: Tue, 7 Feb 2006 21:41:16 -0700
>     >Message-ID: <[hidden email]>
>     >MIME-Version: 1.0
>     >Content-type: text/plain
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>     >Importance: Normal
>     >Content-Transfer-Encoding: 8bit
>     >
>     >
>     >
>     >in looking at
>     >
>     >owl:ObjectProperty
>     >owl:DatatypeProperty
>     >and
>     >rdf:Property
>     >
>     >I am trying to understand how to choose one of these in defining a
> property
>     >
>     >The task I am doing is to encode the SOA-IM (service oriented
>     >architecture-information model) as an RDF file.
>     >
>     >The SOA-IM has 38 "enitities" which I have made into "classes"  .  I
> wish
>     to
>     >have no subsumptions relationships, since each of these IM  
> enitities is
> a
>     >data object related to a simple XML document.  There are in the  
> OASIS
>     >standard the notion of class parents... but I wish to flatten the  
> set
> of
>     >objects ...
>     >
>     >see attached rdf file
>     >
>     >
>     >
>     >2.1 SOA Information Model Entities
>     >
>     >This section covers all SOA IM entities and their attributes.
>     >
>     >2.1.1 Action
>     >
>     >A consequence of an event taking place.
>     >
>     >
>     >Attribute       Type    Description
>     >id      String256       Unique ID
>     >name    String256       Action's name
>     >description     String4000      Detailed description
>     >event   String256       Event which this action relates to
>     >reference       String256       Unique ID of the reference
>     >type    String256       The type of the Action
>     >(Alert/Compensation/Information/Insertion/Termination/Trigger Flow)
>     >
>     >
>     >Associated with
>     >.       An Event where Event is the target object and association  
> type
> is
>     >"IsActionOf"
>     >
>     >Parent: Event
>     >
>     >is the first object.
>     >
>     >**********************************
>     >
>     >My question is about whether the attributes should be
>     >
>     >
>     >owl:ObjectProperty
>     >owl:DatatypeProperty
>     >or
>     >rdf:Property
>     >
>     >
>     >advice and explaination of why the advise is (as it is) is  
> appreciated,
>     >greatly.
>     >
>     >
>     >
>     >
>     >
>     >
>     >-- Attached file removed by Ecartis and put at URL below --
>     >-- Type: text/xml
>     >-- Size: 9k (9489 bytes)
>     >-- URL :
>     http://protege.stanford.edu/mail_archive/attachments/SOA-Enitities.rdf
>     >
>     >
>     >// eompost 43E9767E:A51.1:cebgrtrqvfphffvba
>
>     ~~~~~~~~~~~~~~~~~~~~~~~~~~
>     Ted Hopper, '84, MA '85
>     Administrative Associate
>     Stanford Medical Informatics
>     Medical School Office Building, Room X217
>     Stanford, CA
>     Voice: (650) 736-0728
>     Fax: (650) 725-7944
>     Mail Code: 5479
>     Web: http://www.smi.stanford.edu/
>     ~~~~~~~~~~~~~~~~~~~~~~~~~~
>   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>   Ted Hopper
>   Protégé Group Administrative Associate
>   Stanford Medical Informatics
>   Medical School Office Building, Room X217
>   Stanford, CA
>   Voice: (650) 736-0728
>   Fax: (650) 725-7944
>   Mail Code: 5479
>   URLS: Home: http://protege.stanford.edu
>              Wiki:   http://protege.cim3.net/wiki
>   Short Course: http://protege.stanford.edu/shortcourse/protege/200603
>   Conference:    http://protege.stanford.edu/conference/2006
>   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


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Re: importing RDF

Paul S Prueitt

Andrea said

"So, let's
say, if the RDF document you created with Altova contains such an
instantiation chain, maybe Protégé would not be happy about that (but I
repeat, I am just trying to guess), and you won't be free to create
whatever kind of statement you want in it, no matter if you are not
interested in OWL. "



The first task is to creat a single layer set of concepts with no
subsumption relationships at all and thus no instantiation chain.

the file is attached.

the question is how to import this valid RDF file into Protege.

this is a simple as it gets.


SOA-Enitities.rdf (7K) Download Attachment
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Re: importing RDF

Andrea Proli
Paul,
you say "and thus no instantiation chain".
You don't need to have subsumption chains in order to have instantation  
chains, and viceversa. Subsumption chains are kind of "a rdfs:subclassOf b  
. b rdfs:subclassOf c . c rdfs:subclassOf  d ...", while instantiation  
chains are kind of "a rdf:type b . b rdf:type c . c rdf:type  d ...".

The distinction is crucial, because the former is meant to model the  
subset-of relationship between sets of elements where one contains more  
elements than the other, while the latter is meant to model the membership  
of an element (which may in turn be a set) to a set of elements (thus  
creating sets of sets of sets of elements...).

It's just a different kind of chain (hierarchy, actually). I am going to  
have a look at your file as soon as I have time to.
Best regards,

Andrea

On Fri, 10 Feb 2006 01:15:24 +0100, Paul S Prueitt  
<[hidden email]> wrote:

>
> Andrea said
>
> "So, let's
> say, if the RDF document you created with Altova contains such an
> instantiation chain, maybe Protégé would not be happy about that (but I
> repeat, I am just trying to guess), and you won't be free to create
> whatever kind of statement you want in it, no matter if you are not
> interested in OWL. "
>
>
>
> The first task is to creat a single layer set of concepts with no
> subsumption relationships at all and thus no instantiation chain.
>
> the file is attached.
>
> the question is how to import this valid RDF file into Protege.
>
> this is a simple as it gets.
>



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Re: importing RDF

Rinke Hoekstra-3
In reply to this post by Paul S Prueitt
Dear Paul,

Although your RDF file is indeed correct RDF, Protege only *seems* to
import it incorrectly. The result is unexpected, but correct. The reason
for this is that the classes you define all have names with a namespace
prefix 'SOA-Entities:', but this prefix is not defined in your RDF file
and hence the parser does something unexpected by you. This is probably
due to the fairly unrestricted Altova tool (great for RDF/OWL experts,
but not-so-great for those less owly).

What should fix the problem is changing

xmlns:Prefix0="http://www.S2EE.org/ontologies/SOA-Entities#"

to

xmlns:SOA-Entities="http://www.S2EE.org/ontologies/SOA-Entities#"

and to change all your rdf:abouts from e.g.

rdf:about="SOA-Entities:Action"

to

rdf:about="http://www.S2EE.org/ontologies/SOA-Entities#Action"

rdf:about attributes require a fully specified absolute URI, this means
no namespace prefix is parsed (resolved), and the entire string is taken
to be a URI. This is syntactially correct.
You could also change all rdf:about attributes to rdf:ID attributes
(which do require an NCName, and not a URI), e.g.:

rdf:about="SOA-Entities:Action"

to

rdf:ID="SOA-Entities:Action"

Making these changes should help the RDF parser (btw: Jena, and not
Protege-OWL) to understand what you mean.  There's no way any parser
would (or even should) be able to guess the prefix from the namespace
URI you have defined.

Repeat the process for the intended 'attributes' prefix:

xmlns:Prefix1="http://www.S2EE.org/ontologies/attributes#"

to

xmlns:attributes="http://www.S2EE.org/ontologies/attributes#"

and e.g.

rdf:about="attributes:id"

to

rdf:about="http://www.S2EE.org/ontologies/attributes#id"


The resulting file is attached, is valid RDF/XML, and will be loaded by
Protege/Jena as expected.

Hope that helps,

        -Rinke



Paul S Prueitt wrote:

> Andrea said
>
> "So, let's
> say, if the RDF document you created with Altova contains such an
> instantiation chain, maybe Protégé would not be happy about that (but I
> repeat, I am just trying to guess), and you won't be free to create
> whatever kind of statement you want in it, no matter if you are not
> interested in OWL. "
>
>
>
> The first task is to creat a single layer set of concepts with no
> subsumption relationships at all and thus no instantiation chain.
>
> the file is attached.
>
> the question is how to import this valid RDF file into Protege.
>
> this is a simple as it gets.
>
>
>
> ------------------------------------------------------------------------
>
> <?xml version="1.0"?>
> <rdf:RDF xmlns:Prefix0="http://www.S2EE.org/ontologies/SOA-Entities#" xmlns:Prefix1="http://www.S2EE.org/ontologies/attributes#" xmlns:owl="http://www.w3.org/2002/07/owl#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
> <rdf:Description rdf:about="SOA-Entities:Action">
> <rdf:type>
> <rdf:Description rdf:about="http://www.w3.org/2000/01/rdf-schema#Class"/>
> </rdf:type>
> </rdf:Description>
> <rdf:Description rdf:about="SOA-Entities:ActiveInputs">
> <rdf:type>
> <rdf:Description rdf:about="http://www.w3.org/2000/01/rdf-schema#Class"/>
> </rdf:type>
> </rdf:Description>
> <rdf:Description rdf:about="SOA-Entities:Activity">
> <rdf:type>
> <rdf:Description rdf:about="http://www.w3.org/2000/01/rdf-schema#Class"/>
> </rdf:type>
> </rdf:Description>
> <rdf:Description rdf:about="SOA-Entities:Agent">
> <rdf:type>
> <rdf:Description rdf:about="http://www.w3.org/2000/01/rdf-schema#Class"/>
> </rdf:type>
> </rdf:Description>
> <rdf:Description rdf:about="SOA-Entities:Application">
> <rdf:type>
> <rdf:Description rdf:about="http://www.w3.org/2000/01/rdf-schema#Class"/>
> </rdf:type>
> </rdf:Description>
> <rdf:Description rdf:about="SOA-Entities:Argument">
> <rdf:type>
> <rdf:Description rdf:about="http://www.w3.org/2000/01/rdf-schema#Class"/>
> </rdf:type>
> </rdf:Description>
> <rdf:Description rdf:about="SOA-Entities:Association">
> <rdf:type>
> <rdf:Description rdf:about="http://www.w3.org/2000/01/rdf-schema#Class"/>
> </rdf:type>
> </rdf:Description>
> <rdf:Description rdf:about="SOA-Entities:Audit">
> <rdf:type>
> <rdf:Description rdf:about="http://www.w3.org/2000/01/rdf-schema#Class"/>
> </rdf:type>
> </rdf:Description>
> <rdf:Description rdf:about="SOA-Entities:Choice">
> <rdf:type>
> <rdf:Description rdf:about="http://www.w3.org/2000/01/rdf-schema#Class"/>
> </rdf:type>
> </rdf:Description>
> <rdf:Description rdf:about="SOA-Entities:ChoiceReference">
> <rdf:type>
> <rdf:Description rdf:about="http://www.w3.org/2000/01/rdf-schema#Class"/>
> </rdf:type>
> </rdf:Description>
> <rdf:Description rdf:about="SOA-Entities:Cluster">
> <rdf:type>
> <rdf:Description rdf:about="http://www.w3.org/2000/01/rdf-schema#Class"/>
> </rdf:type>
> </rdf:Description>
> <rdf:Description rdf:about="SOA-Entities:CollaborativeProcess">
> <rdf:type>
> <rdf:Description rdf:about="http://www.w3.org/2000/01/rdf-schema#Class"/>
> </rdf:type>
> </rdf:Description>
> <rdf:Description rdf:about="SOA-Entities:CProle">
> <rdf:type>
> <rdf:Description rdf:about="http://www.w3.org/2000/01/rdf-schema#Class"/>
> </rdf:type>
> </rdf:Description>
> <rdf:Description rdf:about="SOA-Entities:Criteria">
> <rdf:type>
> <rdf:Description rdf:about="http://www.w3.org/2000/01/rdf-schema#Class"/>
> </rdf:type>
> </rdf:Description>
> <rdf:Description rdf:about="SOA-Entities:Decision">
> <rdf:type>
> <rdf:Description rdf:about="http://www.w3.org/2000/01/rdf-schema#Class"/>
> </rdf:type>
> </rdf:Description>
> <rdf:Description rdf:about="SOA-Entities:Device">
> <rdf:type>
> <rdf:Description rdf:about="http://www.w3.org/2000/01/rdf-schema#Class"/>
> </rdf:type>
> </rdf:Description>
> <rdf:Description rdf:about="SOA-Entities:EmailAddress">
> <rdf:type>
> <rdf:Description rdf:about="http://www.w3.org/2000/01/rdf-schema#Class"/>
> </rdf:type>
> </rdf:Description>
> <rdf:Description rdf:about="SOA-Entities:Event">
> <rdf:type>
> <rdf:Description rdf:about="http://www.w3.org/2000/01/rdf-schema#Class"/>
> </rdf:type>
> </rdf:Description>
> <rdf:Description rdf:about="SOA-Entities:InformationReference">
> <rdf:type>
> <rdf:Description rdf:about="http://www.w3.org/2000/01/rdf-schema#Class"/>
> </rdf:type>
> </rdf:Description>
> <rdf:Description rdf:about="SOA-Entities:InputOutput">
> <rdf:type>
> <rdf:Description rdf:about="http://www.w3.org/2000/01/rdf-schema#Class"/>
> </rdf:type>
> </rdf:Description>
> <rdf:Description rdf:about="SOA-Entities:Matrix">
> <rdf:type>
> <rdf:Description rdf:about="http://www.w3.org/2000/01/rdf-schema#Class"/>
> </rdf:type>
> </rdf:Description>
> <rdf:Description rdf:about="SOA-Entities:Message">
> <rdf:type>
> <rdf:Description rdf:about="http://www.w3.org/2000/01/rdf-schema#Class"/>
> </rdf:type>
> </rdf:Description>
> <rdf:Description rdf:about="SOA-Entities:MessageContent">
> <rdf:type>
> <rdf:Description rdf:about="http://www.w3.org/2000/01/rdf-schema#Class"/>
> </rdf:type>
> </rdf:Description>
> <rdf:Description rdf:about="SOA-Entities:MessageRequest">
> <rdf:type>
> <rdf:Description rdf:about="http://www.w3.org/2000/01/rdf-schema#Class"/>
> </rdf:type>
> </rdf:Description>
> <rdf:Description rdf:about="SOA-Entities:Metric">
> <rdf:type>
> <rdf:Description rdf:about="http://www.w3.org/2000/01/rdf-schema#Class"/>
> </rdf:type>
> </rdf:Description>
> <rdf:Description rdf:about="SOA-Entities:ModelReference">
> <rdf:type>
> <rdf:Description rdf:about="http://www.w3.org/2000/01/rdf-schema#Class"/>
> </rdf:type>
> </rdf:Description>
> <rdf:Description rdf:about="SOA-Entities:Organization">
> <rdf:type>
> <rdf:Description rdf:about="http://www.w3.org/2000/01/rdf-schema#Class"/>
> </rdf:type>
> </rdf:Description>
> <rdf:Description rdf:about="SOA-Entities:PostalAddress">
> <rdf:type>
> <rdf:Description rdf:about="http://www.w3.org/2000/01/rdf-schema#Class"/>
> </rdf:type>
> </rdf:Description>
> <rdf:Description rdf:about="SOA-Entities:ProcedureConfirmation">
> <rdf:type>
> <rdf:Description rdf:about="http://www.w3.org/2000/01/rdf-schema#Class"/>
> </rdf:type>
> </rdf:Description>
> <rdf:Description rdf:about="SOA-Entities:Protocal">
> <rdf:type>
> <rdf:Description rdf:about="http://www.w3.org/2000/01/rdf-schema#Class"/>
> </rdf:type>
> </rdf:Description>
> <rdf:Description rdf:about="SOA-Entities:Rule">
> <rdf:type>
> <rdf:Description rdf:about="http://www.w3.org/2000/01/rdf-schema#Class"/>
> </rdf:type>
> </rdf:Description>
> <rdf:Description rdf:about="SOA-Entities:RuleContent">
> <rdf:type>
> <rdf:Description rdf:about="http://www.w3.org/2000/01/rdf-schema#Class"/>
> </rdf:type>
> </rdf:Description>
> <rdf:Description rdf:about="SOA-Entities:Sequence">
> <rdf:type>
> <rdf:Description rdf:about="http://www.w3.org/2000/01/rdf-schema#Class"/>
> </rdf:type>
> </rdf:Description>
> <rdf:Description rdf:about="SOA-Entities:Service">
> <rdf:type>
> <rdf:Description rdf:about="http://www.w3.org/2000/01/rdf-schema#Class"/>
> </rdf:type>
> </rdf:Description>
> <rdf:Description rdf:about="SOA-Entities:Stage">
> <rdf:type>
> <rdf:Description rdf:about="http://www.w3.org/2000/01/rdf-schema#Class"/>
> </rdf:type>
> </rdf:Description>
> <rdf:Description rdf:about="SOA-Entities:System">
> <rdf:type>
> <rdf:Description rdf:about="http://www.w3.org/2000/01/rdf-schema#Class"/>
> </rdf:type>
> </rdf:Description>
> <rdf:Description rdf:about="SOA-Entities:TelephoneNumber">
> <rdf:type>
> <rdf:Description rdf:about="http://www.w3.org/2000/01/rdf-schema#Class"/>
> </rdf:type>
> </rdf:Description>
> <rdf:Description rdf:about="SOA-Entities:Trigger">
> <rdf:type>
> <rdf:Description rdf:about="http://www.w3.org/2000/01/rdf-schema#Class"/>
> </rdf:type>
> </rdf:Description>
> <rdf:Description rdf:about="SOA-Entities:User">
> <rdf:type>
> <rdf:Description rdf:about="http://www.w3.org/2000/01/rdf-schema#Class"/>
> </rdf:type>
> </rdf:Description>
> </rdf:RDF>
--
--------------------------------------
Rinke Hoekstra         [hidden email]
T: +31-20-5253499    F: +31-20-5253495
Leibniz Center for Law,    Law Faculty
University of Amsterdam,   PO Box 1030
1000 BA  Amsterdam,    The Netherlands
--------------------------------------

SOA-Enitities.rdf (15K) Download Attachment
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Properties

Ronnie Valkky
In reply to this post by Andrea Proli
Dear OWL Modellers,

Due to discussion about PROPERTIES in Protege OWL but with different
subject, I created a new thread,
hopefully that was OK.

To several questions concerning "What is PROPTERTY", I recommend the
following research paper:

http://www.cise.ufl.edu/~mhpark/SCS.pdf Ontology based customizable 3D
modelling for simulation *(21)*
by Minho Park and Paul A. Fishwick,  Department of Computer and Information
Science and Engineering

Their research paper studies specific ways in which models can be
interconnected within the same 3D space
through effective ontology construction and human interaction techniques
They define a formalized scene domain in which multiple model
representations can exist together
 and a certain model type can be transformed into other model types via user
interactions,
 by conceptualizing all objects, that the scene domain contains,
 and specifying properties (i.e., geometry, dynamics, and information) of
objects and relationships between objects.

They define three data type properties, hasGeometry, hasDynamic, and
hasInformation, for providing additional information to each class:
~ hasGeometry refers to each geometric structure of a certain target system
being modeled,
~ hasDynamic indicates a dynamic behavior of the geometric structure
~ hasInformation specifies information, such as the manufacturers, sizes,
and colors of each specific part of the target system

For some OWL Modellers above paper might be useful.

Cheers,
Ronnie


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Re: importing RDF

Michael McDougall
In reply to this post by Paul S Prueitt
Paul S Prueitt wrote:
> the file is attached.
>
> the question is how to import this valid RDF file into Protege.
>
> this is a simple as it gets.
>
>  

I can open it in Protege 3.2 beta as follows:

Start Protege
Click "Create New Project.."
Select "Create from Existing Sources"
Select "OWL/RDF Files"
Click the icon with a big square and little '+' in the top right corner,
and select your RDF file.
Click "Finish"

There seems to be some problem with your rdf:about ids. In
"SOA-Entities:TelephoneNumber", Protege treats the "SOA-Entities:T" as a
prefix. I don't know if that's a Protege quirk or if your RDF is badly
formed.

I agree that the GUI for loading RDF and OWL is not very
straightforward. Like many research software applications, Protege seems
to have emphasized features over usability, so it can take a lot of
practice before you know how to use it well. It would be great if
someone could go through and simplify the UI, but based on my own
experience in projects like this, its often hard to find the time and
usability expertise necessary to do a decent redesign.


Michael
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Re: importing RDF

Rinke Hoekstra-3
In reply to this post by Paul S Prueitt
Dear Paul,

I really hope this mail clarifies some of the things that have been
bothering you over the past few days. Hopefully thereby quenching that
which is (in my humble opinion) gradually turning into a flame war
agains the innocent (on both sides!).

Paul S Prueitt wrote:
> I am absolutely stopped on something that I need to finish ... this
> (really really should be simple) importing of an Altova created simple
> RDF file.

Please, see my other response on your original problem report. (I hope
it suffices)
>  
> Everyone knows that I am critical of how very complicated the ontology
> paradigm is that has been created by the Stanford team, and I hope that
> I do not get attacked (again) by someone who feels that I am being
> unfair to anyone.   This attacking response in face of critisicm is
> simple NOT proper.

First off, I believe your fairly agressive criticism of Protege is often
indeed unfair. Some people have a natural reaction to react in the same
tone if they believe something they have a high regard for is criticized
in this way. But, yes... let's keep the discussion pleasant ;)

The KR paradigm used for Protege hinges on two representation languages:
Protege-Frames (developed by Stanford, and indeed 17 years old), and the
OWL language (developed by esteemed scientists, and a W3C
recommendation, only several years old). This distinction has often been
a source for confusion (especially in loading files, such as your BioPax
problem), of which the Protege team is aware. Unfortunately some
bugs/features have a higher priority than others.

The ontology paradigm that you are talking about (I assume it's OWL), is
based on description logics. The people at Stanford and Manchester took
it as their mission to build a tool for this complex language, that
would make ontology development relatively easy (compaired to
hand-coding). As starting point, they took their well established Frames
editor, and turned it into the OWL powerhouse it is now. However, OWL
still is no easy language...

> FIRST the import of a compliant short RDF file into Protege, or the
> import of the BioPAX file into Protege should not be a problem.  
> Period.  But there have been at least four different persons who have
> have a problem importing the BioPAX file.  This is not the BioPAX
> working group's fault.   It is the fault of the Protege GUI.  Right?

Yes, to some extent it is: the distinction between Protege Frames and
OWL is not clear to everybody. Please keep in mind that the OWL support
for Protege is developed as a plugin. The core protege is still
frames-based (CLIPS).

> The design of the import interface seems to be fundamentally flawed.  
> Why, after 17 years?

It really is fairly young (younger than OWL is), actually. And I agree
the process of importing OWL files could be more clear. I believe
Matthew Horridge is currently developing support for double-click
opening of owl files.

> The flaws might stem from the Tim Berners-Lee Layer cake itself, and so
> the difficulty of the import and export may not be merely a result of
> poor work by the Stanford team.   But the problems themselves are not
> being exposed, (I conjecture).  

The 'flaws' are the result of many things really, but the layer cake is
not one of them. One reason is (again) frames vs. owl, and the other is
the apparent refusal of many owl/protege users to RTFM. OWL is a complex
language, yes, and it requires more in-depth knowledge of knowledge
representation and its formalisms than say, UML. (and note that XMI is
non-standard)

>  
> In my message, two days ago, to Protege Discussion (which got rejected
> automatically because I used the word "OWL") I trying to set up a
> problem, modeling the OASIS SOA IM with RDF !!!or!!! OWL.   This task is
> huge, because it links the OASIS and IEEE web services and XML standards
> with semantic web "ontology with inferencing".  So, I am aksing for help.

Renaming mailing-lists is not always a good idea, but protege-owl should
really be called 'the ultimate mailinglist for those who want to do
something roughly semantic-webby with Protege (including rdf/rdfs and
ofcourse owl)'. The protege-discussion mailinglist is really only for
frames users.

> The RDF modeling of OASISA SOA IM task should be a great interest to
> everyone on this discussion forum, as well as the Protege-discussion
> forum (where it never got posted).    Can I see a show of hands?  Who in
> the Protege OWL forum would like to see a simple RDF model (no OIL) of
> the SOA IM?  Once we have this, who would like to see various ways of
> adding the OIL?

I abstain ;)

> I want to be clear, since over and over my discussion is treated as if I
> need for tutorial on something (Jennifer?).

Perhaps this is not such a bad/insulting idea. Please bear in mind that
*any* tool has its specific problems, tweaks and quirks. Reading the
tutorial might help to prevent some of the problems you have
experienced. This is not because we don't regard you as a 'leading
researcher in this field' (your own words: I've never heard of you
before personally...), but because we *know* protege is not really
mature yet and needs some introduction.

> The problem is not my knowledge of the problem.  The problem is on the
> incompeteness of our (the world society) development of tools for
> modeling "reality".  This problem, as Andrea and I have talked about
> starts with the narrow (and often misleading) use of terms like
> inference, and the absence of common understanding of the generalization
> of the term "inference" ...  "entailment" is both logical "inference"
> and physical cause.

It is indeed that very problem. But it feels unfair to blame those who
are trying to do something about that... even if it is on US *and* EU/UK
research money. I am a Dutch citizen ;)

> And, as has been suggested by several PhDs in knowledge engineering,
> this is not about one professions right to have their own private
> language.  The entire world needs to have ontological modeling figured
> out ... in precisely the way that arithmetic was figured out and is now
> commonly and everywhere available without "professional interests"
> trumping "social interests".   Again, I do not deserve to be attacked as
> being somehow un-poroessional.

Agreed. This understanding of arithmetic is done through education
though: both of the problem and of the formalism (formulas etc.).
Wouldn't you agree that this holds for ontology engineering too? Even if
the words used may be confusing to the 'uneducated', they might very
well be adequate within context, oops here we go again... ;)

> It is time to see the limitations and problems of Protege "with eyes
> open".

Have a look at what's being done at Manchester in the co-ode project.
They have taken their experiences in teaching owl/ontology engineering
and turned them into invaluable tools and plugins for Protege. The
problem *is* taken seriously. Perhaps you haven't really had a chance to
   notice.

> We all have many layers of things we are trying to get to .... and the
> fundamentals of import and export using Protege cannot be so weird as to
> bend one's mind into contortions.
>  
> Right?
>  
> <gesturing with a puzzled look).

... please give it some time. It's a two-way street: most of the import
problems stem from other tools not exporting the right format. Or people
trying to import the wrong kind of file using the wrong wizard.

> As I mentioned, the problem in loading the Altova created RDF file is
> likely a namespace problem....

Indeed it was, plus a problem with Altova producing syntactically
correct, but semantically incorrect rdf:about attributes. (semantically
incorrect as in not corresponding with the meaning you intended to give
them)

> but how this is handled should be made clear in the "software wizard"
> that is now just poorly designed.
>  
> Right?

If the files presented to the import wizard are syntactically correct,
and correct with respect to the RDF specification, the wizard has no way
of knowing something went wrong. Really. This is just the way computers
work.

All the best,

        Rinke


>  
>  
>
>     -----Original Message-----
>     *From:* [hidden email]
>     [mailto:[hidden email]]*On Behalf Of *Paul
>     Prueitt
>     *Sent:* Wednesday, February 08, 2006 6:39 PM
>     *To:* Protege-Owl
>     *Subject:* [protege-owl] importing RDF
>
>      
>      
>      
>     I have a file which is a pure RDF file, which I build with Altova's
>     new RDF OWL editor.   I am trying to load this into Protege OWL
>      
>     i use the create new project    and then use the create with
>     existing sources by checking the little box..
>      
>      
>     the project type list does not make sense ... since I want to create
>     something that is not OWL... but I understand that I should select
>     "OWL files... but there is uncertainty.
>      Andrea's note in the Protege OWL discussion helps me conjecture
>     that OWL is "sameAs" RDF in many practical senses  if one does not
>     need to use the OIL part.  ...  but there are some details.....  and
>     these details are a moving target for me....
>      
>     The select file does not allow me to look for only .rdf files (which
>     worries me more) and so I use the select from "all files" to get my
>     rdf file selected
>      
>      
>     The language profile window allows me two choices - which I can not
>     make a judgment about so I try Pure RDF Schema without OWL first...
>     and this fails   because  the class names are changed .... "matrix"
>     becomes "p10:atrix" .
>     redoing the steps and making the other choice leads to the same result.
>      
>      I  think this must be a default namespace issue, but I am not sure.  
>      
>      
>      
>     Thank you in advance...
>      
>      
>      
>      
>      
>     with deepest respects..
>      
>      
>      
>      
>      
>      
>      
>      
>
>         -----Original Message-----
>         *From:* Ted Hopper [mailto:[hidden email]]
>         *Sent:* Wednesday, February 08, 2006 4:16 PM
>         *To:* Paul Prueitt
>         *Cc:* Tim Redmond; Jennifer Vendetti
>         *Subject:* RE: Message submitted to 'protege-discussion'
>
>         Hi Paul,
>
>         Please accept my sincerest apologies, as the last thing that I
>         wanted to do was to censor your post.  We have implemented an
>         albeit far from perfect filtering system to detect messages
>         posted to the protege-discussion list that should have been
>         posted to the more specific protege-owl list.  I, not an
>         experienced protege user, then have to make the call as to
>         whether to repost them to discussion or suggest that the sender
>         post to OWL instead, and, being human, I do make mistakes from
>         time to time.  Rest assured our rationale is to help ensure that
>         each post gets routed to the folks most likely to help out.  I
>         am happy to see that you received the answers you sought in the
>         OWL list.
>
>         Best,
>         Ted
>
>         At 06:36 AM 2/8/2006, you wrote:
>>         Ted, I posted to the discussion list that I wanted to.  I did
>>         not post to be
>>         censored
>>
>>         If I am censored that I will take this up with those who feel
>>         that there
>>         should not be censorship in this forum.
>>
>>
>>
>>         -----Original Message-----
>>         From: Ted Hopper [ mailto:[hidden email]]
>>         Sent: Tuesday, February 07, 2006 10:08 PM
>>         To: Paul Prueitt
>>         Subject: Fwd: Message submitted to 'protege-discussion'
>>
>>
>>         Hello Paul,
>>
>>         The nature of your message is more appropriate for posting to the
>>         [hidden email] list.
>>         Please post your message there.  If you currently not
>>         subscribed to this
>>         list, you can browse to
>>         http://protege.stanford.edu/community/subscribe.html to do so.
>>
>>         Thanx,
>>         Ted
>>
>>         >X-Sieve: CMU Sieve 2.2
>>         >Date: Tue, 07 Feb 2006 20:41:34 %z (PST)
>>         >From: Ecartis <[hidden email]>
>>         >Reply-To: [hidden email]
>>         >To: [hidden email]
>>         >X-ecartis-antiloop: crg-gw.Stanford.EDU
>>         >Subject: Message submitted to 'protege-discussion'
>>         >
>>         >This message was received for a list you are a moderator on, and
>>         >was marked for moderation due to the following reason:
>>         >Failed administrivia check on pattern '^[oO][wW][lL].*$'
>>         >
>>         >To approve this message and have it go out on the list,
>>         forward this to
>>         >protege-discussion-repost@(No value set)
>>         >
>>         >If you wish to decline the post, change the 'apppost' below
>>         to 'delpost'.
>>         >If you wish to edit the post, change it to 'modpost' and edit
>>         the message
>>         >as needed - not all mail programs will work with modpost.
>>         >
>>         >DO NOT DELETE THE FOLLOWING LINE.  Ecartis needs it.
>>         >// apppost 43E9767E:A51.1:cebgrtrqvfphffvba
>>         >
>>         > >From [hidden email] Tue Feb  7 20:41:30 2006
>>         >Received: from harbor.safeport.com (harbor.safeport.com
>>         [209.31.154.12])
>>         >         by crg-gw.Stanford.EDU (8.11.5/8.11.5) with SMTP id
>>         k184fTW02564
>>         >         for <[hidden email]>; Tue, 7
>>         Feb 2006
>>         20:41:30 -0800 (PST)
>>         >Received: from yourkkxx5rxwd9 (209-188-120-35.taosnet.com
>>         [209.188.120.35])
>>         >         by harbor.safeport.com (8.12.11/8.12.11) with SMTP id
>>         k184fFJp071129;
>>         >         Tue, 7 Feb 2006 23:41:20 -0500 (EST)
>>         >         (envelope-from [hidden email])
>>         >From: "Paul Prueitt" <[hidden email]>
>>         >To: <[hidden email]>
>>         >Subject: on properties
>>         >Date: Tue, 7 Feb 2006 21:41:16 -0700
>>         >Message-ID: <[hidden email]>
>>         >MIME-Version: 1.0
>>         >Content-type: text/plain
>>         >X-Priority: 3 (Normal)
>>         >X-MSMail-Priority: Normal
>>         >X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0)
>>         >In-Reply-To: <[hidden email]>
>>         >X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2900.2180
>>         >Importance: Normal
>>         >Content-Transfer-Encoding: 8bit
>>         >
>>         >
>>         >
>>         >in looking at
>>         >
>>         >owl:ObjectProperty
>>         >owl:DatatypeProperty
>>         >and
>>         >rdf:Property
>>         >
>>         >I am trying to understand how to choose one of these in
>>         defining a property
>>         >
>>         >The task I am doing is to encode the SOA-IM (service oriented
>>         >architecture-information model) as an RDF file.
>>         >
>>         >The SOA-IM has 38 "enitities" which I have made into
>>         "classes"  .  I wish
>>         to
>>         >have no subsumptions relationships, since each of these IM
>>         enitities is a
>>         >data object related to a simple XML document.  There are in
>>         the OASIS
>>         >standard the notion of class parents... but I wish to flatten
>>         the set of
>>         >objects ...
>>         >
>>         >see attached rdf file
>>         >
>>         >
>>         >
>>         >2.1 SOA Information Model Entities
>>         >
>>         >This section covers all SOA IM entities and their attributes.
>>         >
>>         >2.1.1 Action
>>         >
>>         >A consequence of an event taking place.
>>         >
>>         >
>>         >Attribute       Type    Description
>>         >id      String256       Unique ID
>>         >name    String256       Action's name
>>         >description     String4000      Detailed description
>>         >event   String256       Event which this action relates to
>>         >reference       String256       Unique ID of the reference
>>         >type    String256       The type of the Action
>>         >(Alert/Compensation/Information/Insertion/Termination/Trigger
>>         Flow)
>>         >
>>         >
>>         >Associated with
>>         >.       An Event where Event is the target object and
>>         association type is
>>         >"IsActionOf"
>>         >
>>         >Parent: Event
>>         >
>>         >is the first object.
>>         >
>>         >**********************************
>>         >
>>         >My question is about whether the attributes should be
>>         >
>>         >
>>         >owl:ObjectProperty
>>         >owl:DatatypeProperty
>>         >or
>>         >rdf:Property
>>         >
>>         >
>>         >advice and explaination of why the advise is (as it is) is
>>         appreciated,
>>         >greatly.
>>         >
>>         >
>>         >
>>         >
>>         >
>>         >
>>         >-- Attached file removed by Ecartis and put at URL below --
>>         >-- Type: text/xml
>>         >-- Size: 9k (9489 bytes)
>>         >-- URL :
>>         http://protege.stanford.edu/mail_archive/attachments/SOA-Enitities.rdf
>>
>>         >
>>         >
>>         >// eompost 43E9767E:A51.1:cebgrtrqvfphffvba
>>
>>         ~~~~~~~~~~~~~~~~~~~~~~~~~~
>>         Ted Hopper, '84, MA '85
>>         Administrative Associate
>>         Stanford Medical Informatics
>>         Medical School Office Building, Room X217
>>         Stanford, CA
>>         Voice: (650) 736-0728
>>         Fax: (650) 725-7944
>>         Mail Code: 5479
>>         Web: http://www.smi.stanford.edu/
>>         ~~~~~~~~~~~~~~~~~~~~~~~~~~
>
>         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>         Ted Hopper
>         Protégé Group Administrative Associate
>         Stanford Medical Informatics
>         Medical School Office Building, Room X217
>         Stanford, CA
>         Voice: (650) 736-0728
>         Fax: (650) 725-7944
>         Mail Code: 5479
>         URLS: Home: http://protege.stanford.edu
>         <http://protege.stanford.edu/>           Wiki:  
>         http://protege.cim3.net/wiki
>         Short Course: http://protege.stanford.edu/shortcourse/protege/200603
>         Conference:    http://protege.stanford.edu/conference/2006
>         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>

--
--------------------------------------
Rinke Hoekstra         [hidden email]
T: +31-20-5253499    F: +31-20-5253495
Leibniz Center for Law,    Law Faculty
University of Amsterdam,   PO Box 1030
1000 BA  Amsterdam,    The Netherlands
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Re: importing RDF

Paul S Prueitt
In reply to this post by Michael McDougall


yes, it loads.....

There is an unexpected treatment of the first part of what I thought was a
namespace I have to create in order to define the "concepts" in RDF using
the Altova RDF - OWL editor.

Some people in Washington DC, and elsewhere, feel that the Stanford based
Protege team needs to assume responsibility for producing a product that is
not a research program.    The reason is simple.

The world is attmepting to use Protege as a real world tool.  To ignore this
responsiblity is to be "academic" almost by definition.

And I have little faith that the team at Stanford cares.  So we are looking
for commerical RDF / OWL editors, and some sense of clarity over the issues
of OWL indexing of information (which is NOT "reasoning" if we consider that
nature of "human reasoning".)

see :

http://www.cs.man.ac.uk/mig/people/rector/alr-papers.html

for a discussion of the issue.



The government is requiring that Protege be used in huge projects often
involving Billions (as in the eCP Customs project)

http://www.datawarehouse.com/search/?FREETXT=Prueitt


So, my personal problem is that I do not understand the use of namespaces
...  as explained in the Altova software.  (I do not start out agreeing that
namespaces solves the problems in scope that namespaces are claimed to
solve.)

There is some mismatch between how the Altova RDF editor treates namespaces
and how Protege treats namespace.  I thought that the use of namespaces by
Altova was natural.

The understanding of this problem requires detailed awaressness of where
specific information is on RDF and OWL standards and an understanding that
may only exist in the minds of current or former Stanford team members.

I am trying to find this specific information.

One of these team members could open the small file as you did, and likely
immediately understand the issue.  But I do not understand the issue as yet.





-----Original Message-----
From: [hidden email]
[mailto:[hidden email]]On Behalf Of Michael
McDougall
Sent: Friday, February 10, 2006 8:03 AM
To: [hidden email]
Subject: [protege-owl] Re: importing RDF


Paul S Prueitt wrote:
> the file is attached.
>
> the question is how to import this valid RDF file into Protege.
>
> this is a simple as it gets.
>
>

I can open it in Protege 3.2 beta as follows:

Start Protege
Click "Create New Project.."
Select "Create from Existing Sources"
Select "OWL/RDF Files"
Click the icon with a big square and little '+' in the top right corner,
and select your RDF file.
Click "Finish"

There seems to be some problem with your rdf:about ids. In
"SOA-Entities:TelephoneNumber", Protege treats the "SOA-Entities:T" as a
prefix. I don't know if that's a Protege quirk or if your RDF is badly
formed.

I agree that the GUI for loading RDF and OWL is not very
straightforward. Like many research software applications, Protege seems
to have emphasized features over usability, so it can take a lot of
practice before you know how to use it well. It would be great if
someone could go through and simplify the UI, but based on my own
experience in projects like this, its often hard to find the time and
usability expertise necessary to do a decent redesign.


Michael
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a posting to both Protege forums

Paul S Prueitt
In reply to this post by Rinke Hoekstra-3

Please excuse the posting to both forums, as this discussion belongs in both
forums.


Rinke,

Thank you for your thoughtful message.  I posted this at

http://www.bcngroup.org/beadgames/generativeMethodology/163.htm

with a few short footnotes..

At

http://www.bcngroup.org/beadgames/generativeMethodology/164.htm

I posted a more extensive discussion of the issues you raise.

I hope that we might take this discussion off the Protege - owl forum, but
we are interested in continuing to talk about and reveal the issues related
to translation of other paradigms, such as the OASIS SOA-IM (service
oriented architecture information model) to OWL.  So perhaps some discusison
here will be tolerated.

While we realize that Protege is a research environment, the current
critical market need is for interoperability between the W3C based
(lay-cake) logic based ontology, and other representations of human or
computer transaction spaces - such as IEEE and OASIS information models and
metadata registries, such as the ISO/IEC 11170 - which has been recently
discussed on the Protege discussion forum.

The effort my group is making exposes some difficulties in simply taking a
simple RDF file, produced using the new commercial Altova RDF editor, and
importing this to Protege as pure RDF.  It is likely that the difficulty
stems from our misunderstanding of how namespaces are used, but that is
conjectural on my part.

Andrea has made several very helpful communications regarding the nature of
RDF and RDF schema (RDFS) and the notion of a "language".  I am posting some
of his discussion along with other's contributions into the BCNGroup Galss
Bead Games - for the record.

The import-export issue arises in other context, such as the import of the
BioPAX ontology.  This import can be done but one has to understand a
complicated process having many decisions, where each decision requires the
"researcher's" understanding of the state of the current version.  It is a
moving target, which I am sure is well known by the Stanford team members.

I do not speak for the BioPAX working group.  But I know that they have
chosen to use Protege-OWL rather than Protege-frames for various reasons, in
spite the traditional choice of Protege-frames for bio-medical ontology.

Part of the reason is that BioPAX is designed to be consistent with the
notions that Alan Rector uses in "Defaults, Context, and Knowledge
Alternatives for OWL-Indexed Knowledge bases" ...

<Quote>

Page 2

".. despite the benefits of logic-based formalisms such as OWL, the
inability to express defaults and exceptions is a serious limitations"

One can down load this paper and read the full paragraph, and text.


Many individuals see the limitations, not only as discussed by Alan Rector,
but also the deeper root causes of these limitations as expressed in the
philosophy of mathematics.

In spite of this, we see the possibility that OWL constructions are "almost"
ready to instrument a "Semantic Web" so that (quoting Rector) "the use of
the logic based ontology as an index to contingent information ..."  is
available within various fields including medicine.




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