Re: An instance as range of a property.

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WebProtege Question(s)

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Re: An instance as range of a property.

On Jan 1, 2009, at 8:17 AM, Niels Hoogeveen wrote:

> Thank you for your response.
>
> Which leaves me with the question, what is the appropriare way to  
> model a class that has a relation to a particular instance. As for  
> example the States of the US have with respect to the USA. There  
> are properties that only apply to US states and not to any other  
> subdivision of a country, making it impossible to model this in a  
> more general way?

The proper way to model this is to create an anonymous class which is  
defined to be the set consisting of a single individual.

You should be able to do this using the expression editor for the range.
This is the button with the "U" shaped union operator on it.

When it is open, you select the enumeration class type, which has  
curly brackets "{}" on it.  And then put the individual(s) you want  
in the enumeration definition inside the curly brackets.  You can  
find them using the individual (diamond) button.

When you are don, you should have an expression that looks like

    {United_States_of_America}

in the editor.

>
>
> Niels
>
> > To: protege-discussion <at> lists.stanford.edu
> > From: swt <at> stanford.edu
> > Date: Wed, 31 Dec 2008 11:01:38 -0800
> > Subject: Re: [protege-discussion] An instance as range of a  
> property.
> >
> >
> > The range of a property is a set of things, and should not be a  
> specific
> > instance. If you change the OWL file manually to put an instance  
> as the
> > range, then you are stating that the instance is also a class. (The
> > extension of a class is a set of things.) So yes, Protegeis behaving
> > correctly.
> >
> > Samson
> >
> > Niels Hoogeveen wrote:
> > > I am new to Protegé and to OWL and trying to create an ontology  
> I'd like to
> > > use for my website. I'd like to express the following.
> > >
> > > I have a class named "Country".
> > > I have an instance of "Country" named "United States of America"
> > > I have an instance of "Country" named "Netherlands"
> > >
> > > I have a class named "SubNationalTerritory" as a generic class  
> for states,
> > > provinces, departments.
> > >
> > > I have a subclass of "SubNationalTerritory" called "USState"  
> which instances
> > > should be the 50 states of the United States of America.
> > >
> > > I have a subclass of "SubNationalTerritory" called "NLProvince"  
> which
> > > instances should be the 11 provinces of the Netherlands.
> > >
> > > I have a "partOf" property with domain "Thing" and range "Thing".
> > >
> > > I'd like to create the following two sub-properties of "partOf":
> > >
> > > * isNLProviceOf with "NLProvince" as domain and "Netherlands"  
> as range.
> > > * isUSState with "USState" as domain and "United States of  
> America" as range.
> > >
> > > When adding this into Protegé I am not able to set an instance  
> of a class as
> > > range of a property. When I manually change the OWL file and  
> reload it in
> > > Protegé, the instances "United States of America" and  
> "Netherlands" become
> > > classes as well as instances. Is this correct behaviour? Or is  
> there any other
> > > way to model the above scenario?
> > >
> > >
> > >
> > >
> > >  
> ---------------------------------------------------------------------- 
> --
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> > > <http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/>
> > >
> > >
> > >  
> ---------------------------------------------------------------------- 
> --
> > >
> > > _______________________________________________
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> > >
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2009 Protege Conference: Call for participation

My apologies for multiple postings. Please re-distribute as widely as 
possible.

Dear Protege Users,

We are pleased to announce that the 11th International Protege
Conference will be held June 23-26, 2009 in Amsterdam, The
Netherlands.  Please mark these dates on your calendar and plan to
join us for a few days this summer.

The conference is a forum to discuss ontology development and
management, applications using ontologies, common problems and
solutions. The conference is also an opportunity for Protege users to
meet the Protege team, and to learn about our current activities and
plans.

The conference will include one day of tutorials and small focused
workshops on the first day and two and a half days of the main
conference. The main program will include presentations, a poster
session, and a demo session. Thus, we would like to solicit your
contributions for all the events at the conference. You can find the
detailed calls for contributions at the conference Web site:
http://protege.stanford.edu/conference/2009/.  There will be a review
process for abstracts and the number of presentations will be limited.
All events at the conference will address the following topics (the
list is not exhaustive):

- ontology development
- frames vs description logic
- standard terminologies
- biomedical applications
- other innovative applications
- interoperability between different formats
- plug-in development
- visualization tools
- project management
- ontology tools
- reasoning and inference
- collaboration tools
- ontology repository

If you have questions, you can contact the organizers by email at
protege-conf-organizers <at> lists.stanford.edu

We look forward to your contributions and to seeing as many of you as
possible in June 2009!

The Protege Team

--

-- 
Samson Tu                                   email: swt <at> stanford.edu 
Senior Research Scientist                   web: www.stanford.edu/~swt/
Center for Biomedical Informatics Research  phone: 1-650-725-3391
Stanford University                         fax: 1-650-725-7944

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Re: WebProtege Question(s)

Hello Ron,

Ron Schultz wrote:
>
> I spent some time over the holidays adding in instance editing and 
> instance creation into Web Protege, since my need only requires 
> editing and creating instances of an already stable ontology. The Web 
> Protege base code, after a few Guiness, became pretty straightforward 
> to modify - albeit GWT does throw some twists. One question I have is 
> the handling of slots having multiple values. I noticed that in 
> WebProtege slots with multiple values just show as repeats of the slot 
> name with each new value - which while it works is not very intuitive. 
> I was wondering if the Protege team had yet come up with a user 
> interface pattern or approach to address this issue? If not - then I 
> will experiment on my own.
>

This is something we just haven't gotten to yet.  We anticipate that 
development on WebProtege will become more responsive after we've done 
the 3.4 release for Protege standalone.  We are maintaining a roadmap 
for WebProtege development on our wiki.  There is a section where people 
can add feature requests.  I added your request:

http://protegewiki.stanford.edu/index.php/WebProtegeRoadMap

> Also, is the design of WebProtege documented anywhere? I was 
> considering running doxgen against it but was not sure if I was 
> blazing down an already completed trail.
>

Not really.  We've put most of our documentation efforts so far into the 
installation and run process (the admin's guide) and the developer's 
guide so that developers can compile and run from IDEs.  We next want to 
document the plug-in infrastructure as we hope people will take 
advantage of the extensibility.  If you have more specific questions 
about the design, we could answer them here on the discussion list.

Best,
Jennifer

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WebProtege load failure

(list owner: please ignore an earlier copy sent to the wrong address, 
thanks)

Hello -
I'm just wondering if you could help take a look at the following error 
upon setting up web protege (thanks in advance in taking newbie questions).

Error symptom:
WebProtege ontology list displays fine at an url looking like 
http://server.domain.com:8080/webprotege/WebProtege.html,
      .. logging in seemed to work but there was no username displayed 
on the overview page.
*but *individual ontology files refused to open, with an error box 
saying "load project Collaborative Pizza failed. message: the call 
failed on the server, see server log for details"
enclosed  below are (1) server log message about "Exception while 
dispatching incoming RPC call"; (2) screenshot of the error box.
I tried changing the project location to absolute paths in either or 
both copies of metaproject but did not help.

System setup:
- downloaded and installed copies of stand-alone full Protege (build 
513) + webprotege.war (built Nov 26 16:00, w. Tomcat 5.5)
- edited the metaproject, protege.properties etc according to the 
Protege Client-Server and the WebProtegeAdmin guides.

Q1: could you see why there is an error?
Q2: which copy of metaproject is read (in examples/server or  in 
Tomcat5.5/webapps/webprotege/projects/) ... should they be always kept 
identical? where is relative path example/* resolved ...

Thanks very much!

*(1) error log message* from stdout_20090105.log from Tomcat 5.5 reads 
as follows:

ERROR [http-8080-1] (ApplicationContext.java:678) - Exception while 
dispatching incoming RPC call
com.google.gwt.user.server.rpc.UnexpectedException: Service method 
'public abstract java.lang.Integer 
edu.stanford.bmir.protege.web.client.rpc.OntologyService.loadProject(java.lang.String)' 
threw an unexpected exception: java.lang.RuntimeException: Cannot open 
project Collaborative Pizza
    at 
com.google.gwt.user.server.rpc.RPC.encodeResponseForFailure(RPC.java:360)
    at 
com.google.gwt.user.server.rpc.RPC.invokeAndEncodeResponse(RPC.java:546)
    at 
com.google.gwt.user.server.rpc.RemoteServiceServlet.processCall(RemoteServiceServlet.java:164)
    at 
com.google.gwt.user.server.rpc.RemoteServiceServlet.doPost(RemoteServiceServlet.java:86)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:647)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:729)
    at 
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269)
    at 
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
    at 
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213)
    at 
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:172)
    at 
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127)
    at 
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117)
    at 
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108)
    at 
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174)
    at 
org.apache.coyote.http11.Http11AprProcessor.process(Http11AprProcessor.java:835)
    at 
org.apache.coyote.http11.Http11AprProtocol$Http11ConnectionHandler.process(Http11AprProtocol.java:640)
    at 
org.apache.tomcat.util.net.AprEndpoint$Worker.run(AprEndpoint.java:1286)
    at java.lang.Thread.run(Unknown Source)
Caused by: java.lang.RuntimeException: Cannot open project Collaborative 
Pizza
    at 
edu.stanford.bmir.protege.web.server.ProjectManager.ensureProjectOpen(Unknown 
Source)
    at 
edu.stanford.bmir.protege.web.server.ProjectManager.getServerProject(Unknown 
Source)
    at 
edu.stanford.bmir.protege.web.server.OntologyServiceImpl.loadProject(Unknown 
Source)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
    at java.lang.reflect.Method.invoke(Unknown Source)
    at 
com.google.gwt.user.server.rpc.RPC.invokeAndEncodeResponse(RPC.java:527)
    ... 16 more

*(2)  error screen-shot*

error message screenshot (see attachment)

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Re: WebProtege load failure

Lexing Xie wrote:
> Error symptom:
> WebProtege ontology list displays fine at an url looking like 
> http://server.domain.com:8080/webprotege/WebProtege.html,
>       .. logging in seemed to work but there was no username displayed 
> on the overview page.
> *but *individual ontology files refused to open, with an error box 
> saying "load project Collaborative Pizza failed. message: the call 
> failed on the server, see server log for details"
> enclosed  below are (1) server log message about "Exception while 
> dispatching incoming RPC call"; (2) screenshot of the error box.
> I tried changing the project location to absolute paths in either or 
> both copies of metaproject but did not help.

Please note that the metaproject must be identical in both places for 
the WebProtege application to work properly.  If you make any changes to 
the metaproject, you must restart the servlet container.

> System setup:
> - downloaded and installed copies of stand-alone full Protege (build 
> 513) + webprotege.war (built Nov 26 16:00, w. Tomcat 5.5)
> - edited the metaproject, protege.properties etc according to the 
> Protege Client-Server and the WebProtegeAdmin guides.
>
> Q1: could you see why there is an error?
> Q2: which copy of metaproject is read (in examples/server or  in 
> Tomcat5.5/webapps/webprotege/projects/) ... should they be always kept 
> identical? where is relative path example/* resolved ...

Both copies of the metaproject are read and must be kept identical.  The 
location of your projects must be either a) absolute in both copies - or 
- b) if they are relative paths, the paths should be relative to where 
the Protege server is executing from (not WebProtege).

Please verify that both copies of the metaproject are identical and that 
both copies list the location of your projects as absolute, or relative 
to the Protege server installation.  Once you have done this, please 
restart your servlet container.

This information is listed in the admin's guide in the following two 
sections:

http://protegewiki.stanford.edu/index.php/WebProtegeAdminGuide#Configure_the_Protege_server.27s_metaproject
http://protegewiki.stanford.edu/index.php/WebProtegeAdminGuide#Copy_the_metaproject_to_your_Servlet_container

... which you may find helpful for reference.

Jennifer

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Re: 2009 Protege Conference: Call for participation

Hi Samson,
I hope I am sending this email to the correct address.
I would very much like to participate in your conference.
I have "resurrected" a second PhD ... that I abandonned quite a few 
years ago as the technology was not so advanced ...
The area of the thesis is concerned with reasoning about clinical 
problems at various levels of detail.
At one level I am constructing Ontologies on
- Compartmental Modeling
- Acid Base and Electrolyte disorders
The original, and still , motivation for choosing this area to work on 
was Patil's thesis in this same area of Clinical Chemistry / Pathology 
If I manage to "put together" a suitable framework then the work can be 
extended in many interesting directions ...
The other aspect of the research is to develop a system that has the 
abilitiy to reason and explain its reasoning at various levels of detail.
One of the problems with Patil's work on ABEL is that the knowledge base 
he created is not available in "some kind of" portable format ... [ in 
fact it does not seem to be available at all apart from some example 
fragments in his thesis ] so that others can then use it as a starting 
point for their own work.
A sub-plot to the research is oriented more towards a "data structures" 
and "algorithms" approach ...
Here again Patil's work does not provide a structured software approach 
.. and this is quite frustrating when trying to recreate some of his 
examples.
Let me know if there is anything of merit here that might be of interest 
to attendees at the conference.
It goes without saying that I am using Protege ...  !!
br
Andrew Eliasz
p.s. Tony Hirst is my thesis supervisor at the OU ( Open University in 
the UK )

Samson Tu wrote:
> My apologies for multiple postings. Please re-distribute as widely as 
> possible.
> 
> Dear Protege Users,
> 
> We are pleased to announce that the 11th International Protege
> Conference will be held June 23-26, 2009 in Amsterdam, The
> Netherlands.  Please mark these dates on your calendar and plan to
> join us for a few days this summer.
> 
> The conference is a forum to discuss ontology development and
> management, applications using ontologies, common problems and
> solutions. The conference is also an opportunity for Protege users to
> meet the Protege team, and to learn about our current activities and
> plans.
> 
> The conference will include one day of tutorials and small focused
> workshops on the first day and two and a half days of the main
> conference. The main program will include presentations, a poster
> session, and a demo session. Thus, we would like to solicit your
> contributions for all the events at the conference. You can find the
> detailed calls for contributions at the conference Web site:
> http://protege.stanford.edu/conference/2009/.  There will be a review
> process for abstracts and the number of presentations will be limited.
> All events at the conference will address the following topics (the
> list is not exhaustive):
> 
> - ontology development
> - frames vs description logic
> - standard terminologies
> - biomedical applications
> - other innovative applications
> - interoperability between different formats
> - plug-in development
> - visualization tools
> - project management
> - ontology tools
> - reasoning and inference
> - collaboration tools
> - ontology repository
> 
> If you have questions, you can contact the organizers by email at
> protege-conf-organizers <at> lists.stanford.edu
> 
> We look forward to your contributions and to seeing as many of you as
> possible in June 2009!
> 
> The Protege Team
> 

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Re: 2009 Protege Conference: Call for participation

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Re: 2009 Protege Conference: Call for participation

I apologize if the call for participation I sent out was not clear.

Please go to http://protege.stanford.edu/conference/2009/index.html to 
find detailed information on the submission procedures for 
presentations/posters/demos/tutorials/workshops.

Please don't post submissions to protege-discussion  <at>  lists.stanford.edu.

In particular, the procedure for submitting presentation/posters/demos 
is as follows:

Submission procedure:

We solicit 3 types of contributions:
Presentation abstracts (3 pages, at least 10-point font)
Poster descriptions (1 page)
Demo descriptions (1 page)

Important dates:
Submission deadline: April 6, 2009
Notification of abstract acceptance: April 20, 2009
Conference: June 23-26, 2009

Submission instructions:
Please send your submissions in PDF or ASCII to 
protege-conf-organizers <at> lists.stanford.edu

Andrew Eliasz wrote:
> Hi Samson,
> I hope I am sending this email to the correct address.
> I would very much like to participate in your conference.
> I have "resurrected" a second PhD ... that I abandonned quite a few 
> years ago as the technology was not so advanced ...
> The area of the thesis is concerned with reasoning about clinical 
> problems at various levels of detail.
> At one level I am constructing Ontologies on
> - Compartmental Modeling
> - Acid Base and Electrolyte disorders
> The original, and still , motivation for choosing this area to work on 
> was Patil's thesis in this same area of Clinical Chemistry / Pathology 
> If I manage to "put together" a suitable framework then the work can be 
> extended in many interesting directions ...
> The other aspect of the research is to develop a system that has the 
> abilitiy to reason and explain its reasoning at various levels of detail.
> One of the problems with Patil's work on ABEL is that the knowledge base 
> he created is not available in "some kind of" portable format ... [ in 
> fact it does not seem to be available at all apart from some example 
> fragments in his thesis ] so that others can then use it as a starting 
> point for their own work.
> A sub-plot to the research is oriented more towards a "data structures" 
> and "algorithms" approach ...
> Here again Patil's work does not provide a structured software approach 
> .. and this is quite frustrating when trying to recreate some of his 
> examples.
> Let me know if there is anything of merit here that might be of interest 
> to attendees at the conference.
> It goes without saying that I am using Protege ...  !!
> br
> Andrew Eliasz
> p.s. Tony Hirst is my thesis supervisor at the OU ( Open University in 
> the UK )
> 

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