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[protege-discussion] protege-discussion Digest, Vol 8, Issue 11

Tania Tudorache tudorache at stanford.edu
Wed Mar 14 16:54:45 PDT 2007


You need to start rmiregistry before starting the Protege server. 
Actually, the Protege server start script should start rmiregistry. Did 
you start the run_protege_server.bat in a console window?

You have to start first the server and after the server gives you the 
message "Protege server ready to accept connections..."  in the console, 
you should start a client and connect it to the server.

All these steps are explained in the multi-user tutorial of Protege:

http://protege.cim3.net/cgi-bin/wiki.pl?MultiUserTutorial 
<http://protege.cim3.net/cgi-bin/wiki.pl?MultiUserTutorial>

Tania



Xiaomeng Chang wrote:
>
>      I tried the multi-user Protege, but I found it doesn't work.I
>     don't have a fire wall. 
>
>
> It says in the DOS interface:
>
> SEVERE: server startup failed -- java.rmi.ConnectException: Connection 
> refused t
> o host: 192.168.1.101 <http://192.168.1.101>; nested exception is:
>         java.net.ConnectException: Connection refused: connect
>         at sun.rmi.transport.tcp.TCPEndpoint.newSocket(Unknown Source)
>         at sun.rmi.transport.tcp.TCPChannel.createConnection(Unknown 
> Source)
>         at sun.rmi.transport.tcp.TCPChannel.newConnection(Unknown Source)
>         at sun.rmi.server.UnicastRef.newCall(Unknown Source)
>         at sun.rmi.registry.RegistryImpl_Stub.rebind(Unknown Source)
>         at edu.stanford.smi.protege.server.Server.bindName(Unknown Source)
>         at edu.stanford.smi.protege.server.Server.initialize(Unknown 
> Source)
>         at edu.stanford.smi.protege.server.Server.<init>(Unknown Source)
>         at edu.stanford.smi.protege.server.Server.startServer(Unknown 
> Source)
>         at edu.stanford.smi.protege.server.Server.startServer(Unknown 
> Source)
>         at edu.stanford.smi.protege.server.Server.main(Unknown Source)
> Caused by: java.net.ConnectException: Connection refused: connect
>         at java.net.PlainSocketImpl.socketConnect(Native Method)
>         at java.net.PlainSocketImpl.doConnect(Unknown Source)
>         at java.net.PlainSocketImpl.connectToAddress (Unknown Source)
>         at java.net.PlainSocketImpl.connect(Unknown Source)
>         at java.net.SocksSocketImpl.connect(Unknown Source)
>         at java.net.Socket.connect(Unknown Source)
>         at java.net.Socket.connect (Unknown Source)
>         at java.net.Socket.<init>(Unknown Source)
>         at java.net.Socket.<init>(Unknown Source)
>         at 
> edu.stanford.smi.protege.server.ServerRmiSocketFactory.createSocket(U
> nknown Source)
>         ... 11 more
>
> Do you know the reason?
>
> Xiaomeng
>
>  
>
>        1. Re: how to edited ontology online?- in windows system
>           (Tania Tudorache)
>        2. Re: DISPLAY_SLOT problem (William Bug)
>
>
>     ----------------------------------------------------------------------
>
>     Message: 1
>     Date: Fri, 09 Mar 2007 11:57:15 -0800
>     From: Tania Tudorache <tudorache at stanford.edu
>     <mailto:tudorache at stanford.edu>>
>     Subject: Re: [protege-discussion] how to edited ontology online?- in
>             windows system
>     To: User support for Core Protege and the Protege-Frames editor
>             <protege-discussion at lists.stanford.edu
>     <mailto:protege-discussion at lists.stanford.edu>>
>     Message-ID: < 45F1BC1B.3090901 at stanford.edu
>     <mailto:45F1BC1B.3090901 at stanford.edu>>
>     Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>     If you open a project file from an Apache server, you won't be
>     able to
>     save it.
>
>     If you want to have multiple users editing simultaneously the same
>     ontology,  you could use the multi-user Protege:
>     http://protege.cim3.net/cgi-bin/wiki.pl?MultiUserTutorial
>     <http://protege.cim3.net/cgi-bin/wiki.pl?MultiUserTutorial>
>
>     You could also look at Protege Web Browser, a web-based
>     application for
>     browsing and editing Protege ontologies:
>
>     http://protege.cim3.net/cgi-bin/wiki.pl?WebProtege#nid40
>     <http://protege.cim3.net/cgi-bin/wiki.pl?WebProtege#nid40>
>
>     We currently don't have anyone actively supporting the Protege Web
>     Browser. You can find more details about it from the wiki page.
>
>     Tania
>
>
>     Xiaomeng Chang wrote:
>     > Hi,
>     >
>     > Does anybody know how to make the ontology(type: Call Java
>     > Attachments) be read and edited by users online? I found when we
>     > choose "File->Open" we can input a URL address or specify the
>     server.
>     > But when I open an ontology in a server(apache platform), I can't
>     > saved it to the server.The error message is shown below.And
>     since when
>     > we want to open a project, we can specify the server, does anybody
>     > knows which type of server can work, how to set the server, and
>     how to
>     > read and change the ontology in that server?
>     >
>     >
>     > java.lang.IllegalArgumentException: URI scheme is not "file"
>     >     at java.io.File.<init>(File.java:338)
>     >     at
>     >
>     edu.stanford.smi.protege.model.AbstractKnowledgeBaseFactory.createTempFile(Unknown
>     > Source)
>     >     at
>     >
>     edu.stanford.smi.protege.storage.clips.ClipsKnowledgeBaseFactory.saveKnowledgeBase(Unknown
>     > Source)
>     >     at
>     >
>     de.flumagis.backend.jCall.JCallKnowledgeBaseFactory.saveKnowledgeBase(JCallKnowledgeBaseFactory.java:72)
>     >
>     >     at
>     >
>     edu.stanford.smi.protege.storage.clips.ClipsKnowledgeBaseFactory.saveKnowledgeBase
>     (Unknown
>     > Source)
>     >     at
>     edu.stanford.smi.protege.model.Project.saveDomainKB(Unknown Source)
>     >     at edu.stanford.smi.protege.model.Project.save (Unknown Source)
>     >     at edu.stanford.smi.protege.ui.ProjectManager.save (Unknown
>     Source)
>     >     at
>     >
>     edu.stanford.smi.protege.ui.ProjectManager.saveProjectRequest(Unknown
>     > Source)
>     >     at edu.stanford.smi.protege.action.SaveProject.actionPerformed
>     > (Unknown Source)
>     >     at
>     >
>     javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1849)
>     >     at
>     >
>     javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2169)
>     >     at javax.swing.DefaultButtonModel.fireActionPerformed
>     > (DefaultButtonModel.java:420)
>     >     at
>     >
>     javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:258)
>     >     at
>     >
>     javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java
>     :234)
>     >     at java.awt.AWTEventMulticaster.mouseReleased
>     > (AWTEventMulticaster.java:231)
>     >     at java.awt.Component.processMouseEvent(Component.java:5488)
>     >     at javax.swing.JComponent.processMouseEvent
>     (JComponent.java:3126)
>     >     at java.awt.Component.processEvent(Component.java :5253)
>     >     at java.awt.Container.processEvent(Container.java:1966)
>     >     at java.awt.Component.dispatchEventImpl(Component.java :3955)
>     >     at java.awt.Container.dispatchEventImpl(Container.java:2024)
>     >     at java.awt.Component.dispatchEvent (Component.java:3803)
>     >     at
>     > java.awt.LightweightDispatcher.retargetMouseEvent
>     (Container.java:4212)
>     >     at
>     >
>     java.awt.LightweightDispatcher.processMouseEvent(Container.java:3892)
>     >     at java.awt.LightweightDispatcher.dispatchEvent
>     (Container.java:3822)
>     >     at java.awt.Container.dispatchEventImpl (Container.java:2010)
>     >     at java.awt.Window.dispatchEventImpl(Window.java:1774)
>     >     at java.awt.Component.dispatchEvent(Component.java:3803)
>     >     at java.awt.EventQueue.dispatchEvent(EventQueue.java :463)
>     >     at
>     >
>     java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.java:242)
>     >     at
>     >
>     java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java
>     > :163)
>     >     at
>     >
>     java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:157)
>     >     at
>     >
>     java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:149)
>     >     at java.awt.EventDispatchThread.run
>     (EventDispatchThread.java :110)
>     >
>     >
>     >
>     >
>     > Thanks a lot and waiting help.
>     >
>     > Xiaomeng
>     >
>     ------------------------------------------------------------------------
>     >
>     > _______________________________________________
>     > protege-discussion mailing list
>     > protege-discussion at lists.stanford.edu
>     <mailto:protege-discussion at lists.stanford.edu>
>     > https://mailman.stanford.edu/mailman/listinfo/protege-discussion
>     >
>     > Instructions for unsubscribing:
>     http://protege.stanford.edu/doc/faq.html#01a.03
>     <http://protege.stanford.edu/doc/faq.html#01a.03>
>     >
>
>
>
>     ------------------------------
>
>     Message: 2
>     Date: Sat, 10 Mar 2007 09:23:24 -0800
>     From: William Bug <William.Bug at DrexelMed.edu
>     <mailto:William.Bug at DrexelMed.edu>>
>     Subject: Re: [protege-discussion] DISPLAY_SLOT problem
>     To: tudorache at stanford.edu <mailto:tudorache at stanford.edu>,    
>     User support for Core Protege and the
>             Protege-Frames editor   <
>     protege-discussion at lists.stanford.edu
>     <mailto:protege-discussion at lists.stanford.edu>>
>     Message-ID: <AFB8F925-0E29-4515-8584-2F0804BCEB29 at DrexelMed.edu
>     <mailto:AFB8F925-0E29-4515-8584-2F0804BCEB29 at DrexelMed.edu>>
>     Content-Type: text/plain; charset="us-ascii"
>
>     Hi Tania,
>
>     Sorry for the inappropriate post.  I guess I'm just way over-
>     subscribed on various lists and crossed wires on where to post for
>     this sort of question.  I'll keep my posts constrained to the
>     Protege-
>     OWL list from now on.
>
>     Just to clarify the issue for the curious on this list who may have
>     read it, I do believe I understand what the outcome of setting any
>     AnnotationProperty to the DISPLAY_SLOT should be across several
>     Protege-OWL features. My problem comes down to the behavior being
>     different when I set the "LANG" attribute for that AnnotationProperty
>     as opposed to when the LANG attribute is left unset.  When unset, the
>     behavior of several Protege-OWL features to setting an
>     AnnotationProperty other than :NAME or rdfs:label to the DISPLAY_SLOT
>     is as it should be according to my understanding.  When the LANG
>     attribute is set for a given class - to any value, as far as I can
>     tell from my ad hoc testing - then the value of that
>     AnnotationProperty for that class is not as advertised.
>
>     This is obviously a problem for an ontology that seeks to include
>     internationalization as a part of their internal lexical support.  In
>     fact, to fully support internationalization, you need to be able to
>     set the DISPLAY_SLOT to a particular localized language for a given
>     property - a feature the OWLDoc plugin appears to be designed to
>     support.
>
>     Regarding the protege:defaultLanguage ontology meta-data
>     AnnotationProperty - thanks for pointing out the inconsistency across
>     our ontology files (the BIRNLex ontology is modularized into a
>     collection of OWL files imported according to a specified
>     hierarchy).  This property turned out to be causing a few problems
>     with various aspects of the integration of the modules.  I tried to
>     fix those problems by including this property in each of the OWL
>     files and setting it to the same value (either 'en' or the more
>     proper according to DC specs 'us-EN').  Neither worked.  If I removed
>     this property from ALL the OWL files, then the import-related
>     problems did go away.
>
>     Thanks for redirecting me to the proper list.
>
>     Cheers,
>     Bill
>
>     On Mar 9, 2007, at 11:26 AM, Tania Tudorache wrote:
>
>     > William,
>     >
>     > The browser slot is working fine in the OWL ontologies that you have
>     > given as example. What version of Protege did you use? We recommend
>     > that
>     > you use the latest release 3.2.1.
>     >
>     > If you set the browser slot to another slot than the name or
>     > rdfs:label,
>     > for example, core:pref-label, then the same rules for computing the
>     > browser text apply as the ones for rdfs:label and name. I just
>     tested
>     > that and it works in Protege 3.2.1.
>     >
>     > One thing that I've observed in your ontologies, was the the
>     > protege:defaultLanguage was set to "en-US" instead of just "en".
>     Maybe
>     > that was the problem.
>     >
>     > Please ask in future OWL related questions on the OWL mailing list.
>     >
>     > Thanks,
>     > Tania
>     >
>     >
>     >
>     > William Bug wrote:
>     >> Sorry to be posting this a second time, but I'm in the midst of a
>     >> meeting, where it would be really good to be able to display the
>     >> "preferred labels" for all the classes in our OWL files.
>     >>
>     >> Am I getting something wrong here?  Can other folks pick a class
>     >> annotation property as the DISPLAY_SLOT and get it to display
>     in the
>     >> class browser as the class name regardless of whether the LANG
>     >> attribute is set to 'en' for that property or not?
>     >>
>     >> Many thanks ahead of time for any assistance others can provide in
>     >> solving this problem.
>     >>
>     >> Cheers,
>     >> Bill
>     >>
>     >>
>     >>
>     >> On Mar 8, 2007, at 1:22 AM, William Bug wrote:
>     >>
>     >>> Dear Protege Support folks,
>     >>>
>     >>> We have been having difficulty using the rdfs:label field as a
>     >>> DISPLAY_SLOT, when the language attribute is set to "en".  For
>     >>> classes where language is left blank, that field value is used as
>     >>> the
>     >>> display name.
>     >>>
>     >>> Is this the expected behavior, when setting the DISPLAY_SLOT to a
>     >>> field other than the class :NAME?  I don't know whether this
>     >>> matters,
>     >>> but this for an imported ontology, but I see the same behavior for
>     >>> classes that exist within the OWL file itself.
>     >>>
>     >>> If you would likely to examine this directly both of these
>     >>> ontologies
>     >>> are available online:
>     >>> main ontology file:
>     >>> http://www.nbirn.net/birnlex/1.2/BIRNLex-Investigation.owl
>     >>> imported file: http://obi.sourceforge.net/ontology/OBI.owl
>     >>>
>     >>> I've attached two screen shots below demonstrating what I mean.
>     >>> These are illustrative examples, but this behavior is observed
>     >>> across
>     >>> the entire ontology.
>     >>>
>     >>> Many thanks for your help with this issue.
>     >>>
>     >>> Cheers,
>     >>> Bill
>     >>>
>     >>> <Picture 15.png>
>     >>> <Picture 16.png>
>     >>>
>     >>>
>     >>>
>     >>> Bill Bug
>     >>> Senior Research Analyst/Ontological Engineer
>     >>>
>     >>> Laboratory for Bioimaging  & Anatomical Informatics
>     >>> www.neuroterrain.org <http://www.neuroterrain.org>
>     >>> Department of Neurobiology & Anatomy
>     >>> Drexel University College of Medicine
>     >>> 2900 Queen Lane
>     >>> Philadelphia, PA    19129
>     >>> 215 991 8430 (ph)
>     >>> 610 457 0443 (mobile)
>     >>> 215 843 9367 (fax)
>     >>>
>     >>>
>     >>> Please Note: I now have a new email -
>     William.Bug at DrexelMed.edu <mailto:William.Bug at DrexelMed.edu>
>     >>> <mailto: William.Bug at DrexelMed.edu
>     <mailto:William.Bug at DrexelMed.edu>>
>     >>>
>     >>>
>     >>>
>     >>>
>     >>> <Picture 15.png>
>     >>> <Picture 16.png>
>     >>> _______________________________________________
>     >>> protege-discussion mailing list
>     >>> protege-discussion at lists.stanford.edu
>     <mailto:protege-discussion at lists.stanford.edu>
>     >>> <mailto: protege-discussion at lists.stanford.edu
>     <mailto:protege-discussion at lists.stanford.edu>>
>     >>> https://mailman.stanford.edu/mailman/listinfo/protege-discussion
>     >>>
>     >>> Instructions for unsubscribing:
>     >>> http://protege.stanford.edu/doc/faq.html#01a.03
>     >>
>     >>
>     >>
>     >> Bill Bug
>     >> Senior Research Analyst/Ontological Engineer
>     >>
>     >> Laboratory for Bioimaging  & Anatomical Informatics
>     >> www.neuroterrain.org <http://www.neuroterrain.org>
>     >> Department of Neurobiology & Anatomy
>     >> Drexel University College of Medicine
>     >> 2900 Queen Lane
>     >> Philadelphia, PA    19129
>     >> 215 991 8430 (ph)
>     >> 610 457 0443 (mobile)
>     >> 215 843 9367 (fax)
>     >>
>     >>
>     >> Please Note: I now have a new email - William.Bug at DrexelMed.edu
>     <mailto:William.Bug at DrexelMed.edu>
>     >> <mailto:William.Bug at DrexelMed.edu
>     <mailto:William.Bug at DrexelMed.edu>>
>     >>
>     >>
>     >>
>     >>
>     >>
>     ---------------------------------------------------------------------
>     >> ---
>     >>
>     >> _______________________________________________
>     >> protege-discussion mailing list
>     >> protege-discussion at lists.stanford.edu
>     <mailto:protege-discussion at lists.stanford.edu>
>     >> https://mailman.stanford.edu/mailman/listinfo/protege-discussion
>     >>
>     >> Instructions for unsubscribing: http://protege.stanford.edu/doc/
>     >> faq.html#01a.03
>     >>
>     >
>     > _______________________________________________
>     > protege-discussion mailing list
>     > protege-discussion at lists.stanford.edu
>     <mailto:protege-discussion at lists.stanford.edu>
>     > https://mailman.stanford.edu/mailman/listinfo/protege-discussion
>     >
>     > Instructions for unsubscribing: http://protege.stanford.edu/doc/
>     > faq.html#01a.03
>
>
>
>     Bill Bug
>     Senior Research Analyst/Ontological Engineer
>
>     Laboratory for Bioimaging  & Anatomical Informatics
>     www.neuroterrain.org <http://www.neuroterrain.org>
>     Department of Neurobiology & Anatomy
>     Drexel University College of Medicine
>     2900 Queen Lane
>     Philadelphia, PA    19129
>     215 991 8430 (ph)
>     610 457 0443 (mobile)
>     215 843 9367 (fax)
>
>
>     Please Note: I now have a new email - William.Bug at DrexelMed.edu
>     <mailto:William.Bug at DrexelMed.edu>
>
>
>
>
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>
>     ------------------------------
>
>     _______________________________________________
>     protege-discussion mailing list
>     protege-discussion at lists.stanford.edu
>     <mailto:protege-discussion at lists.stanford.edu>
>     https://mailman.stanford.edu/mailman/listinfo/protege-discussion
>
>
>     End of protege-discussion Digest, Vol 8, Issue 11
>     *************************************************
>
>
> ------------------------------------------------------------------------
>
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