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

Xiaomeng Chang changxm at gmail.com
Sun Mar 11 18:02:02 PDT 2007


>
>  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; 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>
> 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>
> Message-ID: <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
>
> 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
>
> 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
> > https://mailman.stanford.edu/mailman/listinfo/protege-discussion
> >
> > Instructions for unsubscribing:
> 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>
> Subject: Re: [protege-discussion] DISPLAY_SLOT problem
> To: tudorache at stanford.edu,     User support for Core Protege and the
>         Protege-Frames editor   <protege-discussion at lists.stanford.edu>
> Message-ID: <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
> >>> 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>
> >>>
> >>>
> >>>
> >>>
> >>> <Picture 15.png>
> >>> <Picture 16.png>
> >>> _______________________________________________
> >>> 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
> >> 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>
> >>
> >>
> >>
> >>
> >> ---------------------------------------------------------------------
> >> ---
> >>
> >> _______________________________________________
> >> protege-discussion mailing list
> >> 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
> > 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
> 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
>
>
>
>
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> 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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