I opened Protege and immediately created an ontology in the CoModIDE tab, without doing anything else first, and saved it (File > Save As) as both a ttl and an RDF/XML file. After I close and reopen Protege and try to open the ttl file, I get an error box saying "could not parse the ontology." Under "Turtle Syntax" it says the error is
org.semanticweb.owlapi.rdf.turtle.parser.ParseException: Encountered " <PNAME_LN> ":double "" at line 35, column 36.
Was expecting:
"." ...
When I open the RDF/XML file it opens without errors, but the diagram doesn't look like how I left it. Some boxes are in different places and any classes that had whitespace or special characters in the name are truncated - e.g., xsd:string becomes string.
(For interpreting the log- Wildfire2 was the ttl file, Wildfire3 was the RDF/XML.)
INFO 12:48:49 ------------------------------------ Protege -----------------------------------
INFO 12:48:49 Protege Desktop
INFO 12:48:49 Version 5.5.0, Build
INFO 12:48:49
INFO 12:48:49
INFO 12:48:49 ----------------------------------- Platform -----------------------------------
INFO 12:48:49 Java: JVM 1.8.0_121-b13 Memory: 466M
INFO 12:48:49 Language: en, Country: US
INFO 12:48:49 Framework: Apache Software Foundation (1.8)
INFO 12:48:49 OS: windows8 (6.3)
INFO 12:48:49 Processor: x86-64
INFO 12:48:49
INFO 12:48:49 ------------------------------------ Plugins -----------------------------------
INFO 12:48:49 Plugin: Cellfie Protege 5.0+ Plugin (2.1.0)
INFO 12:48:49 Plugin: OWL Code Generation Plug-in (2.0.0)
INFO 12:48:49 Plugin: CoModIDE (1.1.1)
INFO 12:48:49 Plugin: Existential Query (2.0.0)
INFO 12:48:49 Plugin: Explanation Workbench (3.0.0)
INFO 12:48:49 Plugin: OntoGraf (2.0.3)
INFO 12:48:49 Plugin: OPLa Annotator Protege 5.0+ Plugin (1.0.0)
INFO 12:48:49 Plugin: DL Query (4.0.1)
INFO 12:48:49 Plugin: HermiT Reasoner (1.4.3.456)
INFO 12:48:49 Plugin: OWLAx Protege 5.0+ Plugin (1.2.0)
INFO 12:48:49 Plugin: Browser View (OWLDoc) (3.0.3)
INFO 12:48:49 Plugin: OWLViz (5.0.3)
INFO 12:48:49 Plugin: OWLAPI RDF Library (3.0.0)
INFO 12:48:49 Plugin: SPARQL Query Plugin (3.0.0)
INFO 12:48:49 Plugin: SWRLTab Protege 5.0+ Plugin (2.0.6)
INFO 12:48:49
INFO 12:48:51 Creating and setting up empty (default) editor kit
INFO 12:48:51 OWL API Version: 4.5.9.2019-02-01T07:24:44Z
INFO 12:48:52 [OplaController] Starting Update.
INFO 12:48:52 [OplaController] Update Completed.
WARN 12:48:52 [OplaTab] Abort Update: no active ontology.
INFO 12:48:52 Cannot generate ontology catalog for ontology at http://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-50. URI scheme is not "file"
INFO 12:48:52 [OplaController] Starting Update.
INFO 12:48:52 [OplaController] Active Ontology items updated.
INFO 12:48:52 [OplaController] Update Completed.
INFO 12:48:52 [OplaController] Starting Update.
INFO 12:48:52 [OplaController] 'opla' namespace already present.
INFO 12:48:52 [OplaController] Active Ontology items updated.
INFO 12:48:52 [OplaController] Update Completed.
INFO 12:48:53 ------------------------------- Auto-update Check ------------------------------
INFO 12:48:53 Auto-update last performed: Tue Jul 20 12:40:44 CDT 2021
INFO 12:48:53 Auto-update has been performed today. Not performing it again.
INFO 12:48:53
INFO 12:48:58 OWL API Version: 4.5.9.2019-02-01T07:24:44Z
INFO 12:48:58 [OplaController] Starting Update.
INFO 12:48:58 [OplaController] Update Completed.
WARN 12:48:58 [OplaTab] Abort Update: no active ontology.
INFO 12:49:01 ------------------------------- Loading Ontology -------------------------------
INFO 12:49:01 Loading ontology from file:/C:/Users/Joseph/Desktop/Wildfire2.owl
WARN 12:49:02 LINE: 8 Expected white space at pos: 12 LINE:
@base http://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49 .
WARN 12:49:02 LINE: 10 Expected white space at pos: 6 LINE:
http://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49 rdf:type owl:Ontology .
INFO 12:49:02 Finished loading file:/C:/Users/Joseph/Desktop/Wildfire2.owl
INFO 12:49:07 ---------------------------- Disposing of Workspace ----------------------------
INFO 12:49:07 Saved tab state for 'Entities' tab
INFO 12:49:07 Saved tab state for 'Data properties' tab
INFO 12:49:07 Saved tab state for 'CoModIDE' tab
INFO 12:49:07 Saved tab state for 'OWLAx' tab
INFO 12:49:07 Saved tab state for 'Individuals by class' tab
INFO 12:49:07 Saved tab state for 'OPLa' tab
INFO 12:49:07 Saved workspace
INFO 12:49:07 Disposed of 'Entities' tab
INFO 12:49:07 Disposed of 'Data properties' tab
INFO 12:49:07 Disposed of 'CoModIDE' tab
INFO 12:49:07 Disposed of 'OWLAx' tab
INFO 12:49:07 Disposed of 'Individuals by class' tab
INFO 12:49:07 Disposed of 'OPLa' tab
INFO 12:49:07 Disposed of workspace
INFO 12:49:07
INFO 12:49:21 OWL API Version: 4.5.9.2019-02-01T07:24:44Z
INFO 12:49:21 [OplaController] Starting Update.
INFO 12:49:21 [OplaController] Update Completed.
WARN 12:49:21 [OplaTab] Abort Update: no active ontology.
INFO 12:49:23 ------------------------------- Loading Ontology -------------------------------
INFO 12:49:23 Loading ontology from file:/C:/Users/Joseph/Desktop/Wildfire3.owl
INFO 12:49:23 Finished loading file:/C:/Users/Joseph/Desktop/Wildfire3.owl
INFO 12:49:23 [OplaController] Starting Update.
INFO 12:49:23 [OplaController] 'opla' namespace already present.
INFO 12:49:23 [OplaController] Active Ontology items updated.
INFO 12:49:23 [OplaController] Update Completed.
INFO 12:49:23 [OplaController] Starting Update.
INFO 12:49:23 [OplaController] 'opla' namespace already present.
INFO 12:49:23 [OplaController] Active Ontology items updated.
INFO 12:49:23 [OplaController] Update Completed.
INFO 12:49:23 Loading for ontology and imports closure successfully completed in 104 ms
INFO 12:49:23
INFO 12:49:23 [OplaController] Starting Update.
INFO 12:49:23 [OplaController] 'opla' namespace already present.
INFO 12:49:23 [OplaController] Active Ontology items updated.
INFO 12:49:23 [OplaController] Update Completed.
INFO 12:49:23 ---------------------------- Disposing of Workspace ----------------------------
INFO 12:49:23 Saved tab state for 'Data properties' tab
INFO 12:49:23 Saved tab state for 'CoModIDE' tab
INFO 12:49:23 Saved tab state for 'Individuals by class' tab
INFO 12:49:23 Saved tab state for 'OWLAx' tab
INFO 12:49:23 Saved tab state for 'Entities' tab
INFO 12:49:23 Saved tab state for 'OPLa' tab
INFO 12:49:23 Saved workspace
INFO 12:49:23 Disposed of 'Data properties' tab
INFO 12:49:23 Disposed of 'CoModIDE' tab
INFO 12:49:23 Disposed of 'Individuals by class' tab
INFO 12:49:23 Disposed of 'OWLAx' tab
INFO 12:49:23 Disposed of 'Entities' tab
INFO 12:49:23 Disposed of 'OPLa' tab
INFO 12:49:23 Disposed of workspace
INFO 12:49:23
INFO 12:49:25 Cannot generate ontology catalog for ontology at file://null/C:/Users/Joseph/Desktop/Wildfire3-comodide-metadata.owl. URI has an authority component
INFO 12:49:25 [CoModIDE:OPLaAnnotationManager] successfully initialized.
INFO 12:49:25 [CoModIDE:SchemaDiagram] Successfully initialized.
INFO 12:49:25 [CoModIDE:SchemaDiagram] Adding OWL Classhttp://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#Fire
INFO 12:49:25 [CoModIDE:SchemaDiagram] Adding OWL Classhttp://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#Wildfire%20OR%20Prescribed%20Fire%20OR%20Incident%20Complex
INFO 12:49:25 [CoModIDE:SchemaDiagram] Adding OWL Classhttp://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#xsd:datetime
INFO 12:49:25 [CoModIDE:SchemaDiagram] Adding OWL Classhttp://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#xsd:double
INFO 12:49:25 [CoModIDE:SchemaDiagram] Adding OWL Classhttp://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#xsd:string
INFO 12:49:25 [CoModIDE:SchemaDiagram] Adding OWL Classhttp://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#Fire
INFO 12:49:25 [CoModIDE:SchemaDiagram] Adding OWL Classhttp://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#xsd:double
INFO 12:49:25 [CoModIDE:SchemaDiagram] Adding OWL Property http://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#hasCalculatedAcres
INFO 12:49:25 [CoModIDE:SchemaDiagram] Adding OWL Classhttp://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#Fire
INFO 12:49:25 [CoModIDE:SchemaDiagram] Adding OWL Classhttp://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#Wildfire%20OR%20Prescribed%20Fire%20OR%20Incident%20Complex
INFO 12:49:25 [CoModIDE:SchemaDiagram] Adding OWL Property http://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#hasFireCause
INFO 12:49:25 [CoModIDE:SchemaDiagram] Adding OWL Classhttp://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#Fire
INFO 12:49:25 [CoModIDE:SchemaDiagram] Adding OWL Classhttp://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#xsd:datetime
INFO 12:49:25 [CoModIDE:SchemaDiagram] Adding OWL Property http://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#hasFireDiscoveryDateTime
INFO 12:49:25 [CoModIDE:SchemaDiagram] Adding OWL Classhttp://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#Fire
INFO 12:49:25 [CoModIDE:SchemaDiagram] Adding OWL Classhttp://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#xsd:datetime
INFO 12:49:25 [CoModIDE:SchemaDiagram] Adding OWL Property http://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#hasFireOutDateTime
INFO 12:49:25 [CoModIDE:SchemaDiagram] Adding OWL Classhttp://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#Fire
INFO 12:49:25 [CoModIDE:SchemaDiagram] Adding OWL Classhttp://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#xsd:string
INFO 12:49:25 [CoModIDE:SchemaDiagram] Adding OWL Property http://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#hasIncidentName
WARN 12:49:25 [CoModIDE:UFOH] Unsupported AddAxiom: ObjectPropertyDomain(http://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#hasCalculatedAcres http://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#Fire)
WARN 12:49:25 [CoModIDE:UFOH] Unsupported AddAxiom: ObjectPropertyDomain(http://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#hasFireCause http://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#Fire)
WARN 12:49:25 [CoModIDE:UFOH] Unsupported AddAxiom: ObjectPropertyDomain(http://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#hasFireDiscoveryDateTime http://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#Fire)
WARN 12:49:25 [CoModIDE:UFOH] Unsupported AddAxiom: ObjectPropertyDomain(http://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#hasFireOutDateTime http://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#Fire)
WARN 12:49:25 [CoModIDE:UFOH] Unsupported AddAxiom: ObjectPropertyDomain(http://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#hasIncidentName http://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#Fire)
WARN 12:49:25 [CoModIDE:UFOH] Unsupported AddAxiom: ObjectPropertyRange(http://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#hasCalculatedAcres http://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#xsd:double)
WARN 12:49:25 [CoModIDE:UFOH] Unsupported AddAxiom: ObjectPropertyRange(http://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#hasFireCause http://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#Wildfire%20OR%20Prescribed%20Fire%20OR%20Incident%20Complex)
WARN 12:49:25 [CoModIDE:UFOH] Unsupported AddAxiom: ObjectPropertyRange(http://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#hasFireDiscoveryDateTime http://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#xsd:datetime)
WARN 12:49:25 [CoModIDE:UFOH] Unsupported AddAxiom: ObjectPropertyRange(http://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#hasFireOutDateTime http://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#xsd:datetime)
WARN 12:49:25 [CoModIDE:UFOH] Unsupported AddAxiom: ObjectPropertyRange(http://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#hasIncidentName http://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#xsd:string)
INFO 12:49:25 [CoModIDE:SDConnectionHandler] SDConnectionHandler Initialized.
INFO 12:49:25 [CoModIDE:SchemaDiagramComponent] succesfully initialized.
INFO 12:49:25 [CoModIDE:RenderingView] Successfully initialized
INFO 12:49:25 Pattern Selector view initialized
INFO 12:49:25 Configuration view initialized
ERROR 12:51:09 Uncaught Exception in thread 'AWT-EventQueue-0'
java.lang.IllegalArgumentException: URI has an authority component
at java.io.File.(File.java:423) ~[na:1.8.0_121]
at org.protege.editor.owl.model.io.OntologySourcesManager.getTimestampOfUri(OntologySourcesManager.java:111) ~[na:na]
at org.protege.editor.owl.model.io.OntologySourcesManager.getChangedOntologies(OntologySourcesManager.java:71) ~[na:na]
at org.protege.editor.owl.model.io.OntologySourcesManager.checkSources(OntologySourcesManager.java:54) ~[na:na]
at org.protege.editor.owl.ui.ontology.OntologySourcesChangedHandlerUI.handleWindowActivated(OntologySourcesChangedHandlerUI.java:170) ~[na:na]
at org.protege.editor.owl.ui.ontology.OntologySourcesChangedHandlerUI$1$1.windowActivated(OntologySourcesChangedHandlerUI.java:62) ~[na:na]
at java.awt.AWTEventMulticaster.windowActivated(AWTEventMulticaster.java:390) ~[na:1.8.0_121]
at java.awt.Window.processWindowEvent(Window.java:2066) ~[na:1.8.0_121]
at javax.swing.JFrame.processWindowEvent(JFrame.java:305) ~[na:1.8.0_121]
at java.awt.Window.processEvent(Window.java:2013) ~[na:1.8.0_121]
at java.awt.Component.dispatchEventImpl(Component.java:4889) ~[na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2294) ~[na:1.8.0_121]
at java.awt.Window.dispatchEventImpl(Window.java:2746) ~[na:1.8.0_121]
at java.awt.Component.dispatchEvent(Component.java:4711) ~[na:1.8.0_121]
at java.awt.KeyboardFocusManager.redispatchEvent(KeyboardFocusManager.java:1954) ~[na:1.8.0_121]
at java.awt.DefaultKeyboardFocusManager.typeAheadAssertions(DefaultKeyboardFocusManager.java:995) ~[na:1.8.0_121]
at java.awt.DefaultKeyboardFocusManager.dispatchEvent(DefaultKeyboardFocusManager.java:488) ~[na:1.8.0_121]
at java.awt.Component.dispatchEventImpl(Component.java:4760) ~[na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2294) ~[na:1.8.0_121]
at java.awt.Window.dispatchEventImpl(Window.java:2746) ~[na:1.8.0_121]
at java.awt.Component.dispatchEvent(Component.java:4711) ~[na:1.8.0_121]
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) ~[na:1.8.0_121]
at java.awt.EventQueue.access$500(EventQueue.java:97) ~[na:1.8.0_121]
at java.awt.EventQueue$3.run(EventQueue.java:709) ~[na:1.8.0_121]
at java.awt.EventQueue$3.run(EventQueue.java:703) ~[na:1.8.0_121]
at java.security.AccessController.doPrivileged(Native Method) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) ~[na:1.8.0_121]
at java.awt.EventQueue$4.run(EventQueue.java:731) ~[na:1.8.0_121]
at java.awt.EventQueue$4.run(EventQueue.java:729) ~[na:1.8.0_121]
at java.security.AccessController.doPrivileged(Native Method) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) ~[na:1.8.0_121]
at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) ~[na:1.8.0_121]
at java.awt.SentEvent.dispatch(SentEvent.java:70) ~[na:1.8.0_121]
at java.awt.DefaultKeyboardFocusManager$DefaultKeyboardFocusManagerSentEvent.dispatch(DefaultKeyboardFocusManager.java:217) ~[na:1.8.0_121]
at java.awt.DefaultKeyboardFocusManager.sendMessage(DefaultKeyboardFocusManager.java:244) ~[na:1.8.0_121]
at java.awt.DefaultKeyboardFocusManager.dispatchEvent(DefaultKeyboardFocusManager.java:366) ~[na:1.8.0_121]
at java.awt.Component.dispatchEventImpl(Component.java:4760) ~[na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2294) ~[na:1.8.0_121]
at java.awt.Window.dispatchEventImpl(Window.java:2746) ~[na:1.8.0_121]
at java.awt.Component.dispatchEvent(Component.java:4711) ~[na:1.8.0_121]
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) ~[na:1.8.0_121]
at java.awt.EventQueue.access$500(EventQueue.java:97) ~[na:1.8.0_121]
at java.awt.EventQueue$3.run(EventQueue.java:709) ~[na:1.8.0_121]
at java.awt.EventQueue$3.run(EventQueue.java:703) ~[na:1.8.0_121]
at java.security.AccessController.doPrivileged(Native Method) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) ~[na:1.8.0_121]
at java.awt.EventQueue$4.run(EventQueue.java:731) ~[na:1.8.0_121]
at java.awt.EventQueue$4.run(EventQueue.java:729) ~[na:1.8.0_121]
at java.security.AccessController.doPrivileged(Native Method) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) ~[na:1.8.0_121]
at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) ~[na:1.8.0_121]
at java.awt.SequencedEvent.dispatch(SequencedEvent.java:128) ~[na:1.8.0_121]
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756) ~[na:1.8.0_121]
at java.awt.EventQueue.access$500(EventQueue.java:97) ~[na:1.8.0_121]
at java.awt.EventQueue$3.run(EventQueue.java:709) ~[na:1.8.0_121]
at java.awt.EventQueue$3.run(EventQueue.java:703) ~[na:1.8.0_121]
at java.security.AccessController.doPrivileged(Native Method) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) ~[na:1.8.0_121]
at java.awt.EventQueue$4.run(EventQueue.java:731) ~[na:1.8.0_121]
at java.awt.EventQueue$4.run(EventQueue.java:729) ~[na:1.8.0_121]
at java.security.AccessController.doPrivileged(Native Method) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) ~[na:1.8.0_121]
at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) ~[na:1.8.0_121]
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) [na:1.8.0_121]
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) [na:1.8.0_121]
I opened Protege and immediately created an ontology in the CoModIDE tab, without doing anything else first, and saved it (File > Save As) as both a ttl and an RDF/XML file. After I close and reopen Protege and try to open the ttl file, I get an error box saying "could not parse the ontology." Under "Turtle Syntax" it says the error is
org.semanticweb.owlapi.rdf.turtle.parser.ParseException: Encountered " <PNAME_LN> ":double "" at line 35, column 36.
Was expecting:
"." ...
When I open the RDF/XML file it opens without errors, but the diagram doesn't look like how I left it. Some boxes are in different places and any classes that had whitespace or special characters in the name are truncated - e.g., xsd:string becomes string.
(For interpreting the log- Wildfire2 was the ttl file, Wildfire3 was the RDF/XML.)
INFO 12:48:49 ------------------------------------ Protege -----------------------------------
INFO 12:48:49 Protege Desktop
INFO 12:48:49 Version 5.5.0, Build
INFO 12:48:49
INFO 12:48:49
INFO 12:48:49 ----------------------------------- Platform -----------------------------------
INFO 12:48:49 Java: JVM 1.8.0_121-b13 Memory: 466M
INFO 12:48:49 Language: en, Country: US
INFO 12:48:49 Framework: Apache Software Foundation (1.8)
INFO 12:48:49 OS: windows8 (6.3)
INFO 12:48:49 Processor: x86-64
INFO 12:48:49
INFO 12:48:49 ------------------------------------ Plugins -----------------------------------
INFO 12:48:49 Plugin: Cellfie Protege 5.0+ Plugin (2.1.0)
INFO 12:48:49 Plugin: OWL Code Generation Plug-in (2.0.0)
INFO 12:48:49 Plugin: CoModIDE (1.1.1)
INFO 12:48:49 Plugin: Existential Query (2.0.0)
INFO 12:48:49 Plugin: Explanation Workbench (3.0.0)
INFO 12:48:49 Plugin: OntoGraf (2.0.3)
INFO 12:48:49 Plugin: OPLa Annotator Protege 5.0+ Plugin (1.0.0)
INFO 12:48:49 Plugin: DL Query (4.0.1)
INFO 12:48:49 Plugin: HermiT Reasoner (1.4.3.456)
INFO 12:48:49 Plugin: OWLAx Protege 5.0+ Plugin (1.2.0)
INFO 12:48:49 Plugin: Browser View (OWLDoc) (3.0.3)
INFO 12:48:49 Plugin: OWLViz (5.0.3)
INFO 12:48:49 Plugin: OWLAPI RDF Library (3.0.0)
INFO 12:48:49 Plugin: SPARQL Query Plugin (3.0.0)
INFO 12:48:49 Plugin: SWRLTab Protege 5.0+ Plugin (2.0.6)
INFO 12:48:49
INFO 12:48:51 Creating and setting up empty (default) editor kit
INFO 12:48:51 OWL API Version: 4.5.9.2019-02-01T07:24:44Z
INFO 12:48:52 [OplaController] Starting Update.
INFO 12:48:52 [OplaController] Update Completed.
WARN 12:48:52 [OplaTab] Abort Update: no active ontology.
INFO 12:48:52 Cannot generate ontology catalog for ontology at http://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-50. URI scheme is not "file"
INFO 12:48:52 [OplaController] Starting Update.
INFO 12:48:52 [OplaController] Active Ontology items updated.
INFO 12:48:52 [OplaController] Update Completed.
INFO 12:48:52 [OplaController] Starting Update.
INFO 12:48:52 [OplaController] 'opla' namespace already present.
INFO 12:48:52 [OplaController] Active Ontology items updated.
INFO 12:48:52 [OplaController] Update Completed.
INFO 12:48:53 ------------------------------- Auto-update Check ------------------------------
INFO 12:48:53 Auto-update last performed: Tue Jul 20 12:40:44 CDT 2021
INFO 12:48:53 Auto-update has been performed today. Not performing it again.
INFO 12:48:53
INFO 12:48:58 OWL API Version: 4.5.9.2019-02-01T07:24:44Z
INFO 12:48:58 [OplaController] Starting Update.
INFO 12:48:58 [OplaController] Update Completed.
WARN 12:48:58 [OplaTab] Abort Update: no active ontology.
INFO 12:49:01 ------------------------------- Loading Ontology -------------------------------
INFO 12:49:01 Loading ontology from file:/C:/Users/Joseph/Desktop/Wildfire2.owl
WARN 12:49:02 LINE: 8 Expected white space at pos: 12 LINE:
@base http://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49 .
WARN 12:49:02 LINE: 10 Expected white space at pos: 6 LINE:
http://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49 rdf:type owl:Ontology .
INFO 12:49:02 Finished loading file:/C:/Users/Joseph/Desktop/Wildfire2.owl
INFO 12:49:07 ---------------------------- Disposing of Workspace ----------------------------
INFO 12:49:07 Saved tab state for 'Entities' tab
INFO 12:49:07 Saved tab state for 'Data properties' tab
INFO 12:49:07 Saved tab state for 'CoModIDE' tab
INFO 12:49:07 Saved tab state for 'OWLAx' tab
INFO 12:49:07 Saved tab state for 'Individuals by class' tab
INFO 12:49:07 Saved tab state for 'OPLa' tab
INFO 12:49:07 Saved workspace
INFO 12:49:07 Disposed of 'Entities' tab
INFO 12:49:07 Disposed of 'Data properties' tab
INFO 12:49:07 Disposed of 'CoModIDE' tab
INFO 12:49:07 Disposed of 'OWLAx' tab
INFO 12:49:07 Disposed of 'Individuals by class' tab
INFO 12:49:07 Disposed of 'OPLa' tab
INFO 12:49:07 Disposed of workspace
INFO 12:49:07
INFO 12:49:21 OWL API Version: 4.5.9.2019-02-01T07:24:44Z
INFO 12:49:21 [OplaController] Starting Update.
INFO 12:49:21 [OplaController] Update Completed.
WARN 12:49:21 [OplaTab] Abort Update: no active ontology.
INFO 12:49:23 ------------------------------- Loading Ontology -------------------------------
INFO 12:49:23 Loading ontology from file:/C:/Users/Joseph/Desktop/Wildfire3.owl
INFO 12:49:23 Finished loading file:/C:/Users/Joseph/Desktop/Wildfire3.owl
INFO 12:49:23 [OplaController] Starting Update.
INFO 12:49:23 [OplaController] 'opla' namespace already present.
INFO 12:49:23 [OplaController] Active Ontology items updated.
INFO 12:49:23 [OplaController] Update Completed.
INFO 12:49:23 [OplaController] Starting Update.
INFO 12:49:23 [OplaController] 'opla' namespace already present.
INFO 12:49:23 [OplaController] Active Ontology items updated.
INFO 12:49:23 [OplaController] Update Completed.
INFO 12:49:23 Loading for ontology and imports closure successfully completed in 104 ms
INFO 12:49:23
INFO 12:49:23 [OplaController] Starting Update.
INFO 12:49:23 [OplaController] 'opla' namespace already present.
INFO 12:49:23 [OplaController] Active Ontology items updated.
INFO 12:49:23 [OplaController] Update Completed.
INFO 12:49:23 ---------------------------- Disposing of Workspace ----------------------------
INFO 12:49:23 Saved tab state for 'Data properties' tab
INFO 12:49:23 Saved tab state for 'CoModIDE' tab
INFO 12:49:23 Saved tab state for 'Individuals by class' tab
INFO 12:49:23 Saved tab state for 'OWLAx' tab
INFO 12:49:23 Saved tab state for 'Entities' tab
INFO 12:49:23 Saved tab state for 'OPLa' tab
INFO 12:49:23 Saved workspace
INFO 12:49:23 Disposed of 'Data properties' tab
INFO 12:49:23 Disposed of 'CoModIDE' tab
INFO 12:49:23 Disposed of 'Individuals by class' tab
INFO 12:49:23 Disposed of 'OWLAx' tab
INFO 12:49:23 Disposed of 'Entities' tab
INFO 12:49:23 Disposed of 'OPLa' tab
INFO 12:49:23 Disposed of workspace
INFO 12:49:23
INFO 12:49:25 Cannot generate ontology catalog for ontology at file://null/C:/Users/Joseph/Desktop/Wildfire3-comodide-metadata.owl. URI has an authority component
INFO 12:49:25 [CoModIDE:OPLaAnnotationManager] successfully initialized.
INFO 12:49:25 [CoModIDE:SchemaDiagram] Successfully initialized.
INFO 12:49:25 [CoModIDE:SchemaDiagram] Adding OWL Classhttp://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#Fire
INFO 12:49:25 [CoModIDE:SchemaDiagram] Adding OWL Classhttp://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#Wildfire%20OR%20Prescribed%20Fire%20OR%20Incident%20Complex
INFO 12:49:25 [CoModIDE:SchemaDiagram] Adding OWL Classhttp://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#xsd:datetime
INFO 12:49:25 [CoModIDE:SchemaDiagram] Adding OWL Classhttp://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#xsd:double
INFO 12:49:25 [CoModIDE:SchemaDiagram] Adding OWL Classhttp://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#xsd:string
INFO 12:49:25 [CoModIDE:SchemaDiagram] Adding OWL Classhttp://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#Fire
INFO 12:49:25 [CoModIDE:SchemaDiagram] Adding OWL Classhttp://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#xsd:double
INFO 12:49:25 [CoModIDE:SchemaDiagram] Adding OWL Property http://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#hasCalculatedAcres
INFO 12:49:25 [CoModIDE:SchemaDiagram] Adding OWL Classhttp://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#Fire
INFO 12:49:25 [CoModIDE:SchemaDiagram] Adding OWL Classhttp://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#Wildfire%20OR%20Prescribed%20Fire%20OR%20Incident%20Complex
INFO 12:49:25 [CoModIDE:SchemaDiagram] Adding OWL Property http://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#hasFireCause
INFO 12:49:25 [CoModIDE:SchemaDiagram] Adding OWL Classhttp://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#Fire
INFO 12:49:25 [CoModIDE:SchemaDiagram] Adding OWL Classhttp://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#xsd:datetime
INFO 12:49:25 [CoModIDE:SchemaDiagram] Adding OWL Property http://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#hasFireDiscoveryDateTime
INFO 12:49:25 [CoModIDE:SchemaDiagram] Adding OWL Classhttp://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#Fire
INFO 12:49:25 [CoModIDE:SchemaDiagram] Adding OWL Classhttp://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#xsd:datetime
INFO 12:49:25 [CoModIDE:SchemaDiagram] Adding OWL Property http://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#hasFireOutDateTime
INFO 12:49:25 [CoModIDE:SchemaDiagram] Adding OWL Classhttp://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#Fire
INFO 12:49:25 [CoModIDE:SchemaDiagram] Adding OWL Classhttp://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#xsd:string
INFO 12:49:25 [CoModIDE:SchemaDiagram] Adding OWL Property http://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#hasIncidentName
WARN 12:49:25 [CoModIDE:UFOH] Unsupported AddAxiom: ObjectPropertyDomain(http://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#hasCalculatedAcres http://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#Fire)
WARN 12:49:25 [CoModIDE:UFOH] Unsupported AddAxiom: ObjectPropertyDomain(http://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#hasFireCause http://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#Fire)
WARN 12:49:25 [CoModIDE:UFOH] Unsupported AddAxiom: ObjectPropertyDomain(http://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#hasFireDiscoveryDateTime http://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#Fire)
WARN 12:49:25 [CoModIDE:UFOH] Unsupported AddAxiom: ObjectPropertyDomain(http://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#hasFireOutDateTime http://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#Fire)
WARN 12:49:25 [CoModIDE:UFOH] Unsupported AddAxiom: ObjectPropertyDomain(http://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#hasIncidentName http://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#Fire)
WARN 12:49:25 [CoModIDE:UFOH] Unsupported AddAxiom: ObjectPropertyRange(http://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#hasCalculatedAcres http://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#xsd:double)
WARN 12:49:25 [CoModIDE:UFOH] Unsupported AddAxiom: ObjectPropertyRange(http://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#hasFireCause http://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#Wildfire%20OR%20Prescribed%20Fire%20OR%20Incident%20Complex)
WARN 12:49:25 [CoModIDE:UFOH] Unsupported AddAxiom: ObjectPropertyRange(http://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#hasFireDiscoveryDateTime http://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#xsd:datetime)
WARN 12:49:25 [CoModIDE:UFOH] Unsupported AddAxiom: ObjectPropertyRange(http://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#hasFireOutDateTime http://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#xsd:datetime)
WARN 12:49:25 [CoModIDE:UFOH] Unsupported AddAxiom: ObjectPropertyRange(http://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#hasIncidentName http://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-49#xsd:string)
INFO 12:49:25 [CoModIDE:SDConnectionHandler] SDConnectionHandler Initialized.
INFO 12:49:25 [CoModIDE:SchemaDiagramComponent] succesfully initialized.
INFO 12:49:25 [CoModIDE:RenderingView] Successfully initialized
INFO 12:49:25 Pattern Selector view initialized
INFO 12:49:25 Configuration view initialized
ERROR 12:51:09 Uncaught Exception in thread 'AWT-EventQueue-0'
java.lang.IllegalArgumentException: URI has an authority component
at java.io.File.(File.java:423) ~[na:1.8.0_121]
at org.protege.editor.owl.model.io.OntologySourcesManager.getTimestampOfUri(OntologySourcesManager.java:111) ~[na:na]
at org.protege.editor.owl.model.io.OntologySourcesManager.getChangedOntologies(OntologySourcesManager.java:71) ~[na:na]
at org.protege.editor.owl.model.io.OntologySourcesManager.checkSources(OntologySourcesManager.java:54) ~[na:na]
at org.protege.editor.owl.ui.ontology.OntologySourcesChangedHandlerUI.handleWindowActivated(OntologySourcesChangedHandlerUI.java:170) ~[na:na]
at org.protege.editor.owl.ui.ontology.OntologySourcesChangedHandlerUI$1$1.windowActivated(OntologySourcesChangedHandlerUI.java:62) ~[na:na]
at java.awt.AWTEventMulticaster.windowActivated(AWTEventMulticaster.java:390) ~[na:1.8.0_121]
at java.awt.Window.processWindowEvent(Window.java:2066) ~[na:1.8.0_121]
at javax.swing.JFrame.processWindowEvent(JFrame.java:305) ~[na:1.8.0_121]
at java.awt.Window.processEvent(Window.java:2013) ~[na:1.8.0_121]
at java.awt.Component.dispatchEventImpl(Component.java:4889) ~[na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2294) ~[na:1.8.0_121]
at java.awt.Window.dispatchEventImpl(Window.java:2746) ~[na:1.8.0_121]
at java.awt.Component.dispatchEvent(Component.java:4711) ~[na:1.8.0_121]
at java.awt.KeyboardFocusManager.redispatchEvent(KeyboardFocusManager.java:1954) ~[na:1.8.0_121]
at java.awt.DefaultKeyboardFocusManager.typeAheadAssertions(DefaultKeyboardFocusManager.java:995) ~[na:1.8.0_121]
at java.awt.DefaultKeyboardFocusManager.dispatchEvent(DefaultKeyboardFocusManager.java:488) ~[na:1.8.0_121]
at java.awt.Component.dispatchEventImpl(Component.java:4760) ~[na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2294) ~[na:1.8.0_121]
at java.awt.Window.dispatchEventImpl(Window.java:2746) ~[na:1.8.0_121]
at java.awt.Component.dispatchEvent(Component.java:4711) ~[na:1.8.0_121]
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) ~[na:1.8.0_121]
at java.awt.EventQueue.access$500(EventQueue.java:97) ~[na:1.8.0_121]
at java.awt.EventQueue$3.run(EventQueue.java:709) ~[na:1.8.0_121]
at java.awt.EventQueue$3.run(EventQueue.java:703) ~[na:1.8.0_121]
at java.security.AccessController.doPrivileged(Native Method) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) ~[na:1.8.0_121]
at java.awt.EventQueue$4.run(EventQueue.java:731) ~[na:1.8.0_121]
at java.awt.EventQueue$4.run(EventQueue.java:729) ~[na:1.8.0_121]
at java.security.AccessController.doPrivileged(Native Method) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) ~[na:1.8.0_121]
at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) ~[na:1.8.0_121]
at java.awt.SentEvent.dispatch(SentEvent.java:70) ~[na:1.8.0_121]
at java.awt.DefaultKeyboardFocusManager$DefaultKeyboardFocusManagerSentEvent.dispatch(DefaultKeyboardFocusManager.java:217) ~[na:1.8.0_121]
at java.awt.DefaultKeyboardFocusManager.sendMessage(DefaultKeyboardFocusManager.java:244) ~[na:1.8.0_121]
at java.awt.DefaultKeyboardFocusManager.dispatchEvent(DefaultKeyboardFocusManager.java:366) ~[na:1.8.0_121]
at java.awt.Component.dispatchEventImpl(Component.java:4760) ~[na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2294) ~[na:1.8.0_121]
at java.awt.Window.dispatchEventImpl(Window.java:2746) ~[na:1.8.0_121]
at java.awt.Component.dispatchEvent(Component.java:4711) ~[na:1.8.0_121]
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) ~[na:1.8.0_121]
at java.awt.EventQueue.access$500(EventQueue.java:97) ~[na:1.8.0_121]
at java.awt.EventQueue$3.run(EventQueue.java:709) ~[na:1.8.0_121]
at java.awt.EventQueue$3.run(EventQueue.java:703) ~[na:1.8.0_121]
at java.security.AccessController.doPrivileged(Native Method) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) ~[na:1.8.0_121]
at java.awt.EventQueue$4.run(EventQueue.java:731) ~[na:1.8.0_121]
at java.awt.EventQueue$4.run(EventQueue.java:729) ~[na:1.8.0_121]
at java.security.AccessController.doPrivileged(Native Method) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) ~[na:1.8.0_121]
at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) ~[na:1.8.0_121]
at java.awt.SequencedEvent.dispatch(SequencedEvent.java:128) ~[na:1.8.0_121]
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756) ~[na:1.8.0_121]
at java.awt.EventQueue.access$500(EventQueue.java:97) ~[na:1.8.0_121]
at java.awt.EventQueue$3.run(EventQueue.java:709) ~[na:1.8.0_121]
at java.awt.EventQueue$3.run(EventQueue.java:703) ~[na:1.8.0_121]
at java.security.AccessController.doPrivileged(Native Method) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) ~[na:1.8.0_121]
at java.awt.EventQueue$4.run(EventQueue.java:731) ~[na:1.8.0_121]
at java.awt.EventQueue$4.run(EventQueue.java:729) ~[na:1.8.0_121]
at java.security.AccessController.doPrivileged(Native Method) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) ~[na:1.8.0_121]
at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) ~[na:1.8.0_121]
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) [na:1.8.0_121]
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) [na:1.8.0_121]