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[p4-feedback] Custom annotations are lost after save and reload

Thomas Schneider schneidt at cs.man.ac.uk
Thu Apr 16 23:12:02 PDT 2009


Hi Holger,

hmm, the annotations aren't completely lost:

* you've saved your ontology in RDF/XML. After reopening, the  
annotation is gone, but it has been turned into a data property  
assertion prefLabel(ABC, "123 at en") -- just check the "Individuals" and  
"Data Properties" tabs.

* if you save the same ontology in OWL/XML or in OWL Functional  
Syntax, everything is fine after reloading.

* if you save the same ontology in Manchester Syntax, then it can't be  
reopened because the parser chokes on the "skos:prefLabel", see full  
stack trace below.

Matthew, Nick, any comments on this?

Cheers

Thomas

> Encountered skos:prefLabel at line 22 column 8. Expected one of:
> 	owl:backwardCompatibleWith
> 	owl:versionInfo
> 	dc:coverage
> 	dc:title
> 	dc:publisher
> 	dc:creator
> 	dc:contributor
> 	owl:priorVersion
> 	dc:rights
> 	dc:language
> 	owl:incompatibleWith
> 	dc:relation
> 	rdfs:comment
> 	dc:type
> 	dc:subject
> 	dc:source
> 	owl:deprecated
> 	rdfs:label
> 	dc:date
> 	dc:identifier
> 	rdfs:seeAlso
> 	dc:description
> 	rdfs:isDefinedBy
> 	dc:format
>
>
>
> Full Stack Trace
> -----------------------------------------------------------------------------------------
>
> org.semanticweb.owl.expression.ParserException: Encountered  
> skos:prefLabel at line 22 column 8. Expected one of:
> 	owl:backwardCompatibleWith
> 	owl:versionInfo
> 	dc:coverage
> 	dc:title
> 	dc:publisher
> 	dc:creator
> 	dc:contributor
> 	owl:priorVersion
> 	dc:rights
> 	dc:language
> 	owl:incompatibleWith
> 	dc:relation
> 	rdfs:comment
> 	dc:type
> 	dc:subject
> 	dc:source
> 	owl:deprecated
> 	rdfs:label
> 	dc:date
> 	dc:identifier
> 	rdfs:seeAlso
> 	dc:description
> 	rdfs:isDefinedBy
> 	dc:format
>
> 	at  
> org 
> .coode 
> .manchesterowlsyntax 
> .ManchesterOWLSyntaxEditorParser 
> .throwException(ManchesterOWLSyntaxEditorParser.java:2067)
> 	at  
> org 
> .coode 
> .manchesterowlsyntax 
> .ManchesterOWLSyntaxEditorParser 
> .parseAnnotations(ManchesterOWLSyntaxEditorParser.java:1041)
> 	at  
> org 
> .coode 
> .manchesterowlsyntax 
> .ManchesterOWLSyntaxEditorParser 
> .parseAnnotations(ManchesterOWLSyntaxEditorParser.java:1083)
> 	at  
> org 
> .coode 
> .manchesterowlsyntax 
> .ManchesterOWLSyntaxEditorParser 
> .parseClassFrame(ManchesterOWLSyntaxEditorParser.java:1145)
> 	at  
> org 
> .coode 
> .manchesterowlsyntax 
> .ManchesterOWLSyntaxEditorParser 
> .parseClassFrame(ManchesterOWLSyntaxEditorParser.java:1091)
> 	at  
> org 
> .coode 
> .manchesterowlsyntax 
> .ManchesterOWLSyntaxEditorParser 
> .parseOntology(ManchesterOWLSyntaxEditorParser.java:1993)
> 	at  
> org 
> .coode 
> .manchesterowlsyntax 
> .ManchesterOWLSyntaxOntologyParser 
> .parse(ManchesterOWLSyntaxOntologyParser.java:71)
> 	at  
> uk 
> .ac 
> .manchester 
> .cs 
> .owl 
> .ParsableOWLOntologyFactory 
> .loadOWLOntology(ParsableOWLOntologyFactory.java:159)
> 	at  
> uk 
> .ac 
> .manchester 
> .cs 
> .owl.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java: 
> 461)
> 	at  
> uk 
> .ac 
> .manchester 
> .cs 
> .owl.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java: 
> 424)
> 	at  
> org 
> .protege 
> .editor 
> .owl.model.OWLModelManagerImpl.loadOntology(OWLModelManagerImpl.java: 
> 323)
> 	at  
> org 
> .protege 
> .editor 
> .owl 
> .model 
> .OWLModelManagerImpl 
> .loadOntologyFromPhysicalURI(OWLModelManagerImpl.java:385)
> 	at  
> org.protege.editor.owl.OWLEditorKit.handleLoadFrom(OWLEditorKit.java: 
> 148)
> 	at  
> org 
> .protege.editor.owl.OWLEditorKit.handleLoadRequest(OWLEditorKit.java: 
> 143)
> 	at  
> org 
> .protege 
> .editor 
> .core.ProtegeManager.openAndSetupEditorKit(ProtegeManager.java:146)
> 	at  
> org 
> .protege 
> .editor.core.ui.action.OpenAction.openInNewWorkspace(OpenAction.java: 
> 51)
> 	at org.protege.editor.core.ui.util.UIUtil.openRequest(UIUtil.java: 
> 169)
> 	at  
> org 
> .protege 
> .editor.core.ui.action.OpenAction.actionPerformed(OpenAction.java:27)
> 	at  
> javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java: 
> 1882)
> 	at javax.swing.AbstractButton 
> $Handler.actionPerformed(AbstractButton.java:2202)
> 	at  
> javax 
> .swing 
> .DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:420)
> 	at  
> javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:258)
> 	at javax.swing.AbstractButton.doClick(AbstractButton.java:334)
> 	at javax.swing.AbstractButton.doClick(AbstractButton.java:282)
> 	at javax.swing.plaf.basic.BasicMenuItemUI 
> $Actions.actionPerformed(BasicMenuItemUI.java:1020)
> 	at javax.swing.SwingUtilities.notifyAction(SwingUtilities.java:1576)
> 	at javax.swing.JComponent.processKeyBinding(JComponent.java:2772)
> 	at  
> javax 
> .swing.JMenuBar.processBindingForKeyStrokeRecursive(JMenuBar.java:656)
> 	at  
> javax 
> .swing.JMenuBar.processBindingForKeyStrokeRecursive(JMenuBar.java:664)
> 	at  
> javax 
> .swing.JMenuBar.processBindingForKeyStrokeRecursive(JMenuBar.java:664)
> 	at javax.swing.JMenuBar.processKeyBinding(JMenuBar.java:640)
> 	at javax.swing.KeyboardManager.fireBinding(KeyboardManager.java:255)
> 	at  
> javax.swing.KeyboardManager.fireKeyboardAction(KeyboardManager.java: 
> 242)
> 	at  
> javax 
> .swing.JComponent.processKeyBindingsForAllComponents(JComponent.java: 
> 2849)
> 	at javax.swing.JComponent.processKeyBindings(JComponent.java:2841)
> 	at javax.swing.JComponent.processKeyEvent(JComponent.java:2735)
> 	at java.awt.Component.processEvent(Component.java:5379)
> 	at java.awt.Container.processEvent(Container.java:2010)
> 	at java.awt.Component.dispatchEventImpl(Component.java:4068)
> 	at java.awt.Container.dispatchEventImpl(Container.java:2068)
> 	at java.awt.Component.dispatchEvent(Component.java:3903)
> 	at  
> java 
> .awt.KeyboardFocusManager.redispatchEvent(KeyboardFocusManager.java: 
> 1826)
> 	at  
> java 
> .awt 
> .DefaultKeyboardFocusManager 
> .dispatchKeyEvent(DefaultKeyboardFocusManager.java:681)
> 	at  
> java 
> .awt 
> .DefaultKeyboardFocusManager 
> .preDispatchKeyEvent(DefaultKeyboardFocusManager.java:938)
> 	at  
> java 
> .awt 
> .DefaultKeyboardFocusManager 
> .typeAheadAssertions(DefaultKeyboardFocusManager.java:810)
> 	at  
> java 
> .awt 
> .DefaultKeyboardFocusManager 
> .dispatchEvent(DefaultKeyboardFocusManager.java:645)
> 	at java.awt.Component.dispatchEventImpl(Component.java:3941)
> 	at java.awt.Container.dispatchEventImpl(Container.java:2068)
> 	at java.awt.Window.dispatchEventImpl(Window.java:1801)
> 	at java.awt.Component.dispatchEvent(Component.java:3903)
> 	at java.awt.EventQueue.dispatchEvent(EventQueue.java:463)
> 	at  
> java 
> .awt 
> .EventDispatchThread 
> .pumpOneEventForHierarchy(EventDispatchThread.java:269)
> 	at  
> java 
> .awt 
> .EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java: 
> 190)
> 	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java: 
> 184)
> 	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java: 
> 176)
> 	at java.awt.EventDispatchThread.run(EventDispatchThread.java:110)
>







On 16 Apr 2009, at 21:50, Holger Stenzhorn wrote:

> Hi,
>
> I have a problem when adding a custom annotation to a class.
>
> First, I create a new class "ABC" and then I add to this class the
> custom annotation URI "http://www.w3.org/2004/02/skos/core#prefLabel"
> with the value "123" and "Lang" set to "en".
> As a result, "prefLabel - "123"@en" appears in the annotations section
> on the right for "123".
>
> Now I save the ontology and get the source [1].
> When I reload it, the annotations section is empty for "123".
> Saving the ontology now again results in [2].
>
> I am sorry if this issue has been on the list before and I  
> overlooked it...
> (Checked in build 109 and build from latest SVN checkout)
>
> Cheers,
> Holger
>
> [1]
>
> <?xml version="1.0"?>
>
> <!DOCTYPE rdf:RDF [
>   <!ENTITY baz "http://foo.bar/baz#" >
>   <!ENTITY owl "http://www.w3.org/2002/07/owl#" >
>   <!ENTITY xsd "http://www.w3.org/2001/XMLSchema#" >
>   <!ENTITY owl2xml "http://www.w3.org/2006/12/owl2-xml#" >
>   <!ENTITY skos "http://www.w3.org/2004/02/skos/core#" >
>   <!ENTITY rdfs "http://www.w3.org/2000/01/rdf-schema#" >
>   <!ENTITY rdf "http://www.w3.org/1999/02/22-rdf-syntax-ns#" >
> ]>
>
> <rdf:RDF xmlns="http://foo.bar/baz#"
>    xml:base="http://foo.bar/baz"
>    xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
>    xmlns:owl2xml="http://www.w3.org/2006/12/owl2-xml#"
>    xmlns:baz="http://foo.bar/baz#"
>    xmlns:owl="http://www.w3.org/2002/07/owl#"
>    xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
>    xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
>    xmlns:skos="http://www.w3.org/2004/02/skos/core#">
>   <owl:Ontology rdf:about=""/>
>
>   <!--
>
> ///////////////////////////////////////////////////////////////////////////////////////
>   //
>   // Annotation properties
>   //
>
> ///////////////////////////////////////////////////////////////////////////////////////
>    -->
>   <owl:AnnotationProperty rdf:about="&skos;prefLabel"/>
>
>   <!--
>
> ///////////////////////////////////////////////////////////////////////////////////////
>   //
>   // Classes
>   //
>
> ///////////////////////////////////////////////////////////////////////////////////////
>    -->
>
>   <!-- http://foo.bar/baz#ABC -->
>
>   <owl:Class rdf:about="#ABC">
>       <skos:prefLabel>123</skos:prefLabel>
>   </owl:Class>
> </rdf:RDF>
>
> <!-- Generated by the OWL API (version 2.2.1.974)
> http://owlapi.sourceforge.net -->
>
>
>
>
>
> [2]
>
> <?xml version="1.0"?>
>
> <!DOCTYPE rdf:RDF [
>   <!ENTITY baz "http://foo.bar/baz#" >
>   <!ENTITY owl "http://www.w3.org/2002/07/owl#" >
>   <!ENTITY xsd "http://www.w3.org/2001/XMLSchema#" >
>   <!ENTITY owl2xml "http://www.w3.org/2006/12/owl2-xml#" >
>   <!ENTITY skos "http://www.w3.org/2004/02/skos/core#" >
>   <!ENTITY rdfs "http://www.w3.org/2000/01/rdf-schema#" >
>   <!ENTITY rdf "http://www.w3.org/1999/02/22-rdf-syntax-ns#" >
> ]>
>
> <rdf:RDF xmlns="http://foo.bar/baz#"
>    xml:base="http://foo.bar/baz"
>    xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
>    xmlns:owl2xml="http://www.w3.org/2006/12/owl2-xml#"
>    xmlns:baz="http://foo.bar/baz#"
>    xmlns:owl="http://www.w3.org/2002/07/owl#"
>    xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
>    xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
>    xmlns:skos="http://www.w3.org/2004/02/skos/core#">
>   <owl:Ontology rdf:about=""/>
>
>   <!--
>
> ///////////////////////////////////////////////////////////////////////////////////////
>   //
>   // Data properties
>   //
>
> ///////////////////////////////////////////////////////////////////////////////////////
>    -->
>
>   <!-- http://www.w3.org/2004/02/skos/core#prefLabel -->
>
>   <owl:DatatypeProperty rdf:about="&skos;prefLabel"/>
>
>   <!--
>
> ///////////////////////////////////////////////////////////////////////////////////////
>   //
>   // Classes
>   //
>
> ///////////////////////////////////////////////////////////////////////////////////////
>    -->
>
>   <!-- http://foo.bar/baz#ABC -->
>
>   <owl:Class rdf:about="#ABC"/>
>
>   <!--
>
> ///////////////////////////////////////////////////////////////////////////////////////
>   //
>   // Individuals
>   //
>
> ///////////////////////////////////////////////////////////////////////////////////////
>    -->
>
>   <!-- http://foo.bar/baz#ABC -->
>
>   <rdf:Description rdf:about="#ABC">
>       <skos:prefLabel>123</skos:prefLabel>
>   </rdf:Description>
> </rdf:RDF>
>
> <!-- Generated by the OWL API (version 2.2.1.974)
> http://owlapi.sourceforge.net -->
> _______________________________________________
> p4-feedback mailing list
> p4-feedback at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/p4-feedback

+----------------------------------------------------------------------+
|  Dr Thomas Schneider                         schneider at cs.man.ac.uk  |
|  School of Computer Science       http://www.cs.man.ac.uk/~schneidt  |
|  Kilburn Building, Room 2.114                 phone +44 161 2756136  |
|  University of Manchester                                            |
|  Oxford Road                                             _///_       |
|  Manchester M13 9PL                                      (o~o)       |
+-----------------------------------------------------oOOO--(_)--OOOo--+

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