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[protege-owl] Deleting Individuals

Robert A. Elliott,Sr. robertelliottsr at yahoo.com
Wed Aug 12 13:29:18 PDT 2009


With what you have stated, I think I know what happened in my situation. I did a refactor(rename) on a member and it didn't complete perfectly.Thats why some members type could not be resolved. Protege gave me an error and I SORTA ignored  it because I did see the name change. Lesson learned. Thanks for your help, its been very useful information.
Regards,Robert

______________________________



--- On Wed, 8/12/09, Timothy Redmond <tredmond at stanford.edu> wrote:

From: Timothy Redmond <tredmond at stanford.edu>
Subject: Re: [protege-owl] Deleting Individuals
To: "User support for the Protege-OWL editor" <protege-owl at lists.stanford.edu>
Date: Wednesday, August 12, 2009, 12:49 PM


On Aug 12, 2009, at 5:20 AM, Robert A. Elliott,Sr. wrote:

> 
> Three questions.
> 
> 1. Did the RequirementsEngineer_1 and
> RequirementsEngineer_One individuals show up in the Instance Browser for you? Only RequirementsEngineer_One shows up in Protege as I view the Instance Browser yet  RequirementsEngineer_1 shows up in the .owl file.

RequirementsEngineer_1 shows up in the instance browser under the class protege:ExternalResource.  This is what happens when Protege can't determine its type.  What ever happened to RequirementsEngineer_1 seemed to involve it losing its type.  There are several individuals in protege:ExternalResource and I am wondering if these are also individuals that you somehow had trouble with.

> 
> 2. Can I manually delete RequirementsEngineer_1 from the .owl file and not corrupt the ontology?

If you mean using a text editor then the answer is a guarded yes.  Editing rdf directly is dangerous though and experience helps.

You can also delete it in Protege 3.4 and it seems to work fine.

> 
> 3. What is the relationship between the .owl file and the url of the ontology? (http://pluto.cse.msstate.edu/~rae20/SRSontology#).
> Are they in sync with one another? ie updated automatically by Protege? I actually FTP a copy of the .owl file to the hosting server(pluto) randomly.


This is a surprisingly complicated question and the answer is changing between OWL 1/1.1 and OWL 2.0.  Much of the naming complexity comes when people want to import ontologies.

The easiest case is when the name of an ontology can also be used as a url to retrieve the ontology.  This should also be the name that is used in import statements.  This is the recommended practice.  But because urls move, people work off their hard drive and other such issues the story has become more complicated.  I have described a version of the owl 1.0 situation here [1].

The OWL 2.0 story is simpler. It is recommended but not required that an ontology can be retrieved by its name or version IRI (see [3] for a more accurate description).  However, experience with the web suggests that this will often not be the case.  Imports statements are like I/O directives or html links.  Whatever they find is the import that they should load.  There is also an allowance for an import statement to be redirected by some mechanism such as XML catalogs [2].  This redirection mechanism is going to be very important (people often want to edit their ontologies on their computer but deploy to the web) but I don't know if anyone has implemented a tool that handles this with OWL 2.0 ontologies.

Note that - approximately - Protege 3.4 works with the OWL 1.0 specification, Protege 4.0 works with the OWL 1.1 specification and Protege 4.1 (not released yet) works with the OWL 2.0 specification.

-Timothy

[1] http://protegewiki.stanford.edu/index.php/How_Owl_Imports_Work
[2] http://www.oasis-open.org/committees/entity/spec-2001-08-06.html
[3] http://www.w3.org/TR/2009/CR-owl2-syntax-20090611/#Ontology_Documents
> 
> ______________________________
> Robert A. Elliott,Sr.
> 
> (601) 597-2786
> 
> --- On Tue, 8/11/09, Timothy Redmond <tredmond at stanford.edu> wrote:
> 
> From: Timothy Redmond <tredmond at stanford.edu>
> Subject: Re: [protege-owl] Deleting Individuals
> To: "User support for the Protege-OWL editor" <protege-owl at lists.stanford.edu>
> Date: Tuesday, August 11, 2009, 4:33 PM
> 
> 
> I am sorry - I still haven't been able to replicate what you have done.
> Using Protege 3.4, I deleted the RequirementsEngineer_1 and
> RequirementsEngineer_One from the ontology and when I go back with a
> text editor they are really gone.
> 
> One thing that I did notice in the ontology that you sent was that there
> were several individuals in the protege:ExternalResource class.  The
> RequirementsEngineer_1 was there but there were also others
> (Mr_Orris_Vester_Hester, OV_Hester, RequirementsAnalysis_1).  I would
> almost guess that these are  individuals that  you also thought you
> deleted which are still present.  I am not sure of the status of the
> exernal resource dublin core stuff but that is probably not important.
> 
> But I don't know why your deletes were incomplete.
> 
> -Timothy
> 
> 
> On Tue, 2009-08-11 at 06:46 -0700, Robert A. Elliott,Sr. wrote:
> > Tim,
> > It is from an ontology that I'm progressively working on
> > (http://pluto.cse.msstate.edu/~rae20/SRSontology#). I'm using an XSLT
> > application to extract particular members from an identical text
> > backup(SRSontologyTEST.ow).
> > The particular member is:
> > <rdf:Description rdf:ID="RequirementsEngineer_1">
> >     <SRS:hasRequirementsEngineerIDNumber>
> >       <SRS:RequirementsEngineerID rdf:ID="RequirementsEngineerID_1">
> >         <SRS:RequirementsEngineerIdentificationNumber rdf:datatype=
> >
> >  "http://www.w3.org/2001/XMLSchema#int">11</SRS:RequirementsEngineerIdentificationNumber>
> >       </SRS:RequirementsEngineerID>
> >     </SRS:hasRequirementsEngineerIDNumber>
> >     <SRS:RequirementsEngineerName
> > rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >     >Epluribus Elliott</SRS:RequirementsEngineerName>
> >   </rdf:Description>
> >
> >
> > I did rename this individual :RequirementsEngineer_1
> >  to RequirementsEngineer_One.  Both are in the .owl file. After
> > deleting all of the indiduals in the RequirementsEngineer
> > class, RequirementsEngineer_1 was the only individual I was not able
> > to delete in the instance browser because it would not show up. But it
> > is in the .owl file. Hope I'm not confusing my issue. Thansk for  your
> > response and I really do need to resolve this. I can send you any
> > files that you need.
> >
> >
> > Robert.
> >
> >
> >
> >
> >
> > ______________________________
> > Robert A. Elliott,Sr.
> > (601) 597-2786
> >
> > --- On Mon, 8/10/09, Timothy Redmond <tredmond at stanford.edu> wrote:
> >
> >         From: Timothy Redmond <tredmond at stanford.edu>
> >         Subject: Re: [protege-owl] Deleting Individuals
> >         To: "User support for the Protege-OWL editor"
> >         <protege-owl at lists.stanford.edu>
> >         Date: Monday, August 10, 2009, 6:45 PM
> >
> >
> >         I did not replicate this problem.  I did the following steps:
> >
> >         1. Opened  the standard pizza ontology that comes with a
> >         Protege
> >         distribution.
> >
> >         2. Went to the individual tab, selected the country class and
> >         selected
> >         a country.
> >
> >         3. deleted the country with the X-like icon at the top of the
> >         asserted
> >         instances panel.
> >
> >         4. saved the ontology
> >
> >         5. opened the ontology in a text editor.  The country that I
> >         deleted
> >         was gone.
> >
> >         Is this problem specific to a particular ontology?
> >
> >         -Timothy
> >
> >         On Mon, 2009-08-10 at 10:59 -0500, Robert A. Elliott, Sr.
> >         wrote:
> >         > Hi,
> >         > I'm using Protege 3.4. I delete individuals using the delete
> >         icon
> >         > inside the Instance Browser. The individuals still show up
> >         inside of
> >         > my ontology .owl file.
> >         > I have shut down Protege and restarted several times yet the
> >         deleted
> >         > individual doesn't show up inside the  Protege tool but does
> >         show up
> >         > inside the ontology .owl file.
> >         > Why are the deleted individuals still inside the .owl file?
> >         I would
> >         > think they would disappear from this file which is what I
> >         need them to
> >         > do.
> >         > I hope I explained this well enough for a solution. Thanks.
> >         >
> >         >
> >         > Robert
> >         > --
> >         > Robert A. Elliott, Sr.
> >         > raesr20 at gmail.com
> >         >
> >         > _______________________________________________
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