OWLDoc

classic Classic list List threaded Threaded
3 messages Options
Reply | Threaded
Open this post in threaded view
|

OWLDoc

Daniel Schober
Dear OWLDoc developers,

I am using Protege 4.1 beta and trying to create an OWL doc HTML
serialisation, but a get the error below. I could not find any manual
for this plugin. Is there any?  Why doesn't it work?
The ontologies are attached.

Kind regards,
Daniel Schober
--


Error 1 Logged at Fri Feb 18 15:46:55 CET 2011
NullPointerException: null
     java.lang.String.lastIndexOf(
String.java:1823)
     java.lang.String.lastIndexOf(String.java:1805)
     
org.coode.html.renderer.OWLHTMLVisitor.writeIRIWithBoldFragment(OWLHTMLVisitor.java:775)
     org.coode.html.renderer.OWLHTMLVisitor.visit(OWLHTMLVisitor.java:191)
     org.semanticweb.owlapi.model.IRI$IRIImpl.accept(IRI.java:253)
     org.coode.html.renderer.OWLHTMLRenderer.render(OWLHTMLRenderer.java:41)
     org.coode.html.renderer.OWLHTMLRenderer.render(OWLHTMLRenderer.java:23)
     
org.coode.html.doclet.ElementsDoclet.renderHeader(ElementsDoclet.java:67)
     
org.coode.html.doclet.AbstractHTMLDoclet.renderAll(AbstractHTMLDoclet.java:42)
     
org.coode.html.doclet.AbstractHTMLDoclet.renderContent(AbstractHTMLDoclet.java:37)
     
org.coode.html.doclet.AbstractHTMLDoclet.renderAll(AbstractHTMLDoclet.java:43)
     
org.coode.html.OntologyExporter.exportOntology(OntologyExporter.java:197)
     org.coode.html.OntologyExporter.export(OntologyExporter.java:159)
     
org.coode.browser.protege.ExportOWLDocAction$1.run(ExportOWLDocAction.java:76)
     java.lang.Thread.run(Thread.java:662)


--

-------------------------------------------------------------
   Dr. Daniel Schober
   Universitätsklinikum
   Institut für Medizinische Biometrie und Medizinische Informatik
   Stefan-Meier-Strasse  26 Raum 6
   D-79104 Freiburg Germany
   Tel: +49 (0)761 2036807 FAX: +49 (0)761 2036711


Freiburg   ...     wo die Babys mit Fahrradhelm zur Welt kommen.












_______________________________________________
protege-owl mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-owl

Instructions for unsubscribing: http://protege.stanford.edu/doc/faq.html#01a.03

dco.owl (840K) Download Attachment
biotop.owl (454K) Download Attachment
Reply | Threaded
Open this post in threaded view
|

Re: OWLDoc

Timothy Redmond

Sorry for the delayed response.  I just installed the latest owldoc
(File->Check for plugins) in the latest version of Protege (released
today).  I was able to run owl doc on both of the ontologies that you
sent (dco.owl and biotop.owl).  At one time there was a problem with
ontologies that had #'s instead of /'s. I am not sure what happened with
this.

Unfortunately the OWLDoc plugin is part of the co-ode project which is
no longer active.  On the positive side, I do on occasion try to support
a subset of the co-ode plugins and keep them working.

-Timothy



On 02/18/2011 07:17 AM, Dr. Daniel Schober wrote:

> Dear OWLDoc developers,
>
> I am using Protege 4.1 beta and trying to create an OWL doc HTML
> serialisation, but a get the error below. I could not find any manual
> for this plugin. Is there any?  Why doesn't it work?
> The ontologies are attached.
>
> Kind regards,
> Daniel Schober
> --
>
>
> Error 1 Logged at Fri Feb 18 15:46:55 CET 2011
> NullPointerException: null
>     java.lang.String.lastIndexOf(
> String.java:1823)
>     java.lang.String.lastIndexOf(String.java:1805)
>    
> org.coode.html.renderer.OWLHTMLVisitor.writeIRIWithBoldFragment(OWLHTMLVisitor.java:775)
>     org.coode.html.renderer.OWLHTMLVisitor.visit(OWLHTMLVisitor.java:191)
>     org.semanticweb.owlapi.model.IRI$IRIImpl.accept(IRI.java:253)
>    
> org.coode.html.renderer.OWLHTMLRenderer.render(OWLHTMLRenderer.java:41)
>    
> org.coode.html.renderer.OWLHTMLRenderer.render(OWLHTMLRenderer.java:23)
>    
> org.coode.html.doclet.ElementsDoclet.renderHeader(ElementsDoclet.java:67)
>    
> org.coode.html.doclet.AbstractHTMLDoclet.renderAll(AbstractHTMLDoclet.java:42)
>    
> org.coode.html.doclet.AbstractHTMLDoclet.renderContent(AbstractHTMLDoclet.java:37)
>    
> org.coode.html.doclet.AbstractHTMLDoclet.renderAll(AbstractHTMLDoclet.java:43)
>    
> org.coode.html.OntologyExporter.exportOntology(OntologyExporter.java:197)
>     org.coode.html.OntologyExporter.export(OntologyExporter.java:159)
>    
> org.coode.browser.protege.ExportOWLDocAction$1.run(ExportOWLDocAction.java:76)
>     java.lang.Thread.run(Thread.java:662)
>
>

_______________________________________________
protege-owl mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-owl

Instructions for unsubscribing: http://protege.stanford.edu/doc/faq.html#01a.03
Reply | Threaded
Open this post in threaded view
|

Re: OWLDoc

NCBO
In reply to this post by Daniel Schober
Hi Daniel,

I gather that dco.owl is the DebugIT Core Ontology. If so, based on it's biomedical related content this fits the scope of BioPortal ( http://bioportal.bioontology.org/ ) if you would like to upload dco.owl. Once an ontology is loaded into BioPortal, there are many options to provide a web display of the content from using the graph view and tree view widgets (http://www.bioontology.org/wiki/index.php/NCBO_Widgets) to customizing displays using the BioPortal web services http://www.bioontology.org/wiki/index.php/NCBO_REST_services ).

Cheers,
Trish


Date: Fri, 18 Feb 2011 17:23:10 -0800
From: Timothy Redmond <[hidden email]>
To: [hidden email]
Cc: Ilinca Tudose <[hidden email]>,    protege-owl
       <[hidden email]>
Subject: Re: [protege-owl] OWLDoc
Message-ID: <[hidden email]
>
Content-Type: text/plain; charset=ISO-8859-15; format=flowed


Sorry for the delayed response.  I just installed the latest owldoc
(File->Check for plugins) in the latest version of Protege (released
today).  I was able to run owl doc on both of the ontologies that you
sent (dco.owl and biotop.owl).  At one time there was a problem with
ontologies that had #'s instead of /'s. I am not sure what happened with
this.

Unfortunately the OWLDoc plugin is part of the co-ode project which is
no longer active.  On the positive side, I do on occasion try to support
a subset of the co-ode plugins and keep them working.

-Timothy



On 02/18/2011 07:17 AM, Dr. Daniel Schober wrote:
> Dear OWLDoc developers,
>
> I am using Protege 4.1 beta and trying to create an OWL doc HTML
> serialisation, but a get the error below. I could not find any manual
> for this plugin. Is there any?  Why doesn't it work?
> The ontologies are attached.
>
> Kind regards,
> Daniel Schober

_______________________________________________
protege-owl mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-owl

Instructions for unsubscribing: http://protege.stanford.edu/doc/faq.html#01a.03