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[p4-feedback] OBO loading error

Timothy Redmond tredmond at stanford.edu
Sat Apr 17 09:23:07 PDT 2010


I didn't replicate this.  I did download a couple of the SO ontologies 
from the sequence ontology website and they loaded without error.  I 
attached them so that we can find out if the problem is in the download 
somehow.  I was also able to load the ontology from uri using [1].

There is an issue with viewing obo ontologies in Protege.  The OBO tools 
present a hierarchy of OBO concepts that is not the class hierarchy.  
This means that Protege, which displays the class hierarchy of concepts, 
will not look right to OBO people.  I don't know much about this but it 
is my intention that sometime I will write an OBO hierarchy view for 
Protege 4.1 to make this easier.

-Timothy

[1] http://song.cvs.sourceforge.net/viewvc/*checkout*/song/ontology/sofa.obo?revision=1.208


On 04/16/2010 12:50 PM, Alexander Garcia Castro wrote:
> I have P4 4.1, I am trying to open an OBO file, the SO ontology 
> -downloaded from the Sequence Ontology website. I am getting :
>
> Server returned HTTP response code: 503 for URL: 
> http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd
>
>
> Full Stack Trace
> -----------------------------------------------------------------------------------------
>
> org.semanticweb.owlapi.io.OWLOntologyCreationIOException: Server 
> returned HTTP response code: 503 for URL: 
> http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd
>     at 
> uk.ac.manchester.cs.owl.owlapi.ParsableOWLOntologyFactory.loadOWLOntology(ParsableOWLOntologyFactory.java:173)
>     at 
> uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:632)
>     at 
> uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:590)
>     at 
> org.protege.editor.owl.model.OWLModelManagerImpl.loadOntologyFromPhysicalURI(OWLModelManagerImpl.java:313)
>     at 
> org.protege.editor.owl.OWLEditorKit.handleLoadFrom(OWLEditorKit.java:152)
>     at 
> org.protege.editor.owl.OWLEditorKit.handleLoadRequest(OWLEditorKit.java:146)
>     at 
> org.protege.editor.core.ui.action.OpenAction.openInCurrentWorkspace(OpenAction.java:65)
>     at org.protege.editor.core.ui.util.UIUtil.openRequest(UIUtil.java:223)
>     at 
> org.protege.editor.core.ui.action.OpenAction.actionPerformed(OpenAction.java:33)
>     at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
>     at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
>     at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
>     at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
>     at javax.swing.AbstractButton.doClick(Unknown Source)
>     at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source)
>     at 
> javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknown 
> Source)
>     at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
>     at java.awt.Component.processMouseEvent(Unknown Source)
>     at javax.swing.JComponent.processMouseEvent(Unknown Source)
>     at java.awt.Component.processEvent(Unknown Source)
>     at java.awt.Container.processEvent(Unknown Source)
>     at java.awt.Component.dispatchEventImpl(Unknown Source)
>     at java.awt.Container.dispatchEventImpl(Unknown Source)
>     at java.awt.Component.dispatchEvent(Unknown Source)
>     at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
>     at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
>     at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
>     at java.awt.Container.dispatchEventImpl(Unknown Source)
>     at java.awt.Window.dispatchEventImpl(Unknown Source)
>     at java.awt.Component.dispatchEvent(Unknown Source)
>     at java.awt.EventQueue.dispatchEvent(Unknown Source)
>     at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
>     at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
>     at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
>     at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
>     at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
>     at java.awt.EventDispatchThread.run(Unknown Source)
> Caused by: java.io.IOException: Server returned HTTP response code: 
> 503 for URL: http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd
>     at 
> sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source)
>     at 
> com.sun.org.apache.xerces.internal.impl.XMLEntityManager.setupCurrentEntity(Unknown 
> Source)
>     at 
> com.sun.org.apache.xerces.internal.impl.XMLEntityManager.startEntity(Unknown 
> Source)
>     at 
> com.sun.org.apache.xerces.internal.impl.XMLEntityManager.startDTDEntity(Unknown 
> Source)
>     at 
> com.sun.org.apache.xerces.internal.impl.XMLDTDScannerImpl.setInputSource(Unknown 
> Source)
>     at 
> com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$DTDDriver.dispatch(Unknown 
> Source)
>     at 
> com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$DTDDriver.next(Unknown 
> Source)
>     at 
> com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$PrologDriver.next(Unknown 
> Source)
>     at 
> com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(Unknown 
> Source)
>     at 
> com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.next(Unknown 
> Source)
>     at 
> com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown 
> Source)
>     at 
> com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(Unknown 
> Source)
>     at 
> com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(Unknown 
> Source)
>     at 
> com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(Unknown Source)
>     at 
> com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(Unknown 
> Source)
>     at 
> com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown 
> Source)
>     at javax.xml.parsers.SAXParser.parse(Unknown Source)
>     at 
> org.semanticweb.owlapi.rdf.syntax.RDFParser.parse(RDFParser.java:139)
>     at 
> org.coode.owlapi.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:88)
>     at 
> uk.ac.manchester.cs.owl.owlapi.ParsableOWLOntologyFactory.loadOWLOntology(ParsableOWLOntologyFactory.java:165)
>     ... 36 more
>
>
> Why? how can I open OBO files in P4.1 ?
>
> -- 
> Alexander Garcia
> http://www.alexandergarcia.name/
> http://www.usefilm.com/photographer/75943.html
> http://www.linkedin.com/in/alexgarciac
> Postal address:
> Alexander Garcia, Tel.: +49 421 218 64211
> Universität Bremen
> Enrique-Schmidt-Str. 5
> D-28359 Bremen
>
>
> _______________________________________________
> p4-feedback mailing list
> p4-feedback at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/p4-feedback
>    

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