Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

[protege-owl] BioPortal Reference Widget

Bo De Lange bodelange at gmail.com
Tue Aug 18 00:09:25 PDT 2009


Hi Tania,

On Mon, Aug 17, 2009 at 6:01 PM, Tania Tudorache <tudorache at stanford.edu>wrote:

>  Hi Bo,
>
> Are you sure it is not there? It usually shows up as the last one in the
> list of widgets. I've just made a test with an object annotation property as
> you had in your project and it worked fine.
>

Yep I'm sure. I've openede the pizza tutorial file, made a new annotation
property hasBioPortalReference and when I want to add it in the form of the
owl:Class class as described, it does not appear in the widget dropdown
list. See two screengrabs attached.

>
>
> Did you unzip the zip file in your plugins folder? The archive contains two
> plugins: the BP reference widget and a modified version of the
> standard-extensions. Check that the standard-extension.jar is dated July 28,
> 2009.
>

Checked all that, everything is correct.

>
>
> If you still have problems, please send me the text from the Protege
> console.
>

Below is the text from the console to show it has been loaded at startup.

Bo

 cwd: C:\Program Files (x86)\Protege_3.4.1\
cmd: "C:\Program Files\Java\jdk1.6.0_14\bin\java.exe" -Xms262144000
-Xmx2146500000 -Dserver.client.p
reload0\=http://www.owl-ontologies.com/unnamed.owl
\#\VoorgeschrevenSNK;-Dserver.client.preload1\=htt
p://www.owl-ontologies.com/unnamed.owl
\#\VoorgeschrevenGPK;-Dserver.client.preload2\=http://www.owl-
ontologies.com/unnamed.owl
\#\ObservedNeurotransmitterAndHormoneRelease;-Dserver.client.preload3\=htt
p://www.owl-ontologies.com/unnamed.owl
\#\GivenFinalDiagnoses;-Dserver.client.preload4\=http://www.ow
l-ontologies.com/unnamed.owl
\#\GivenIntermediateDiagnoses;-Dserver.client.preload5\=http://www.owl-o
ntologies.com/unnamed.owl
\#\ObservedBehaviourAndStimuli;-Dserver.client.preload6\=http://www.owl-ont
ologies.com/unnamed.owl
\#\ObservedDesireAndArousal;-Dserver.client.preload7\=
http://www.owl-ontologi
es.com/unnamed.owl\#\ObservedSymptomsGeneral;-Dserver.client.preload8\=
http://www.owl-ontologies.com
/unnamed.owl\#\Diagnosis;-Dserver.client.preload9\=
http://www.owl-ontologies.com/unnamed.owl\#\Gener
iekNiveauGPK;-Dserver.client.preload10\=
http://www.owl-ontologies.com/unnamed.owl\#\HandelsNiveauHPK
;-Dserver.client.preload11\=http://www.owl-ontologies.com/unnamed.owl
\#\VoorschrijfNiveauPRK;-Dserve
r.client.preload12\=http://www.owl-ontologies.com/unnamed.owl
\#\SuperProduktNiveauSPK;-Dserver.clien
t.preload13\=http://www.owl-ontologies.com/unnamed.owl
\#\StoftoedieningsNiveauSSK;-Dserver.client.pr
eload14\=http://www.owl-ontologies.com/unnamed.owl
\#\StofNiveauSNK;-Dserver.client.preload15\=http:/
/www.owl-ontologies.com/unnamed.owl\#\Stofnaam -classpath "C:\Program Files
(x86)\Protege_3.4.1\prot
ege.jar;C:\Program Files (x86)\Protege_3.4.1\looks-2.1.3.jar;C:\Program
Files (x86)\Protege_3.4.1\un
icode_panel.jar;C:\Program Files (x86)\Protege_3.4.1\driver.jar;C:\Program
Files (x86)\Protege_3.4.1
\driver0.jar;C:\Program Files (x86)\Protege_3.4.1\driver1.jar;C:\Program
Files (x86)\Protege_3.4.1\d
river2.jar$;C:\Program Files (x86)\Protege_3.4.1\lax.jar;" com.zerog.lax.LAX
"C:/Program Files (x86)
/Protege_3.4.1/Protege.lax" "C:/Documents and Settings/Bo/Local
Settings/Temp/laxF47.tmp"
Protege 3.4.1 Build 537, JVM 1.6.0_14-b08, memory=1908M, Windows XP,
encoding=UTF-8, language=nl, co
untry=NL
Loaded plugin bioPortalReferencePlugin
Loaded plugin edu.stanford.smi.protegex.owl - OWL Plugin
Loaded plugin ca.uvic.cs.chisel.jambalaya - Jambalaya
Loaded plugin dfki.protege.ontoviz
Loaded plugin edu.stanford.smi.protegex.rdf_backend - RDF Backend
Loaded plugin edu.stanford.smi.protegex.changes - Changes tab
Loaded plugin edu.stanford.smi.protegex.standard_extensions - Graph Widget,
Table Widget
Loaded plugin edu.stanford.smi.protegex.chatPlugin - Chat
Loaded plugin edu.stanford.smi.protege.collab - Collaborative Protege
Loaded plugin edu.stanford.smi.protege.script - Script Plugin
Loaded plugin edu.stanford.smi.protege.stringsearch - String Search Tab
Loaded plugin edu.stanford.smi.protegex.datamaster - DataMaster Tab
Loaded plugin edu.stanford.smi.protegex.pal_tabs - PAL Tabs
Loaded plugin edu.stanford.smi.protegex.ezpal - EZPal Tab
Loaded plugin edu.stanford.smi.protegex.facets_tab
Loaded plugin edu.stanford.smi.protegex.instance_tree
Loaded plugin edu.stanford.smi.protegex.prompt - PROMPT Tab
Loaded plugin edu.stanford.smi.protegex.metaanalysis - MetaAnalysis Tab
Loaded plugin edu.stanford.smi.protegex.owl.inference.pellet - Protege
Pellet Reasoner
Loaded plugin edu.stanford.smi.protegex.umls_tab - UMLS Tab
Loaded plugin edu.stanford.smi.protegex.wordnet - WordNet Tab
Loaded plugin edu.stanford.smi.protegex.xml_tab - XML Tab
Loaded plugin org.algernon - Algernon
Loaded plugin se.liu.ida.JessTab - JessTab Plugin
Loaded plugin uk.ac.iam.soton.akt.tgviztab - TGVizTab
Loaded plugin uk.ac.man.cs.mig.coode.debugger
Loaded plugin uk.ac.man.cs.mig.coode.manchesterowlsyntaxeditor
Loaded plugin uk.ac.man.cs.mig.coode.owldoc
Loaded plugin uk.ac.man.cs.mig.coode.owlindividualstab
Loaded plugin uk.ac.man.cs.mig.coode.owlviz
Loaded plugin uk.ac.man.cs.mig.coode.protege.wizard - Basic Wizards
Loaded plugin uk.ac.man.cs.mig.coode.protege.wizard.owl - OWL Wizards
Loading triples from:
file:/C:/Program%20Files%20(x86)/Protege_3.4.1/examples/pizza/pizza.owl
    Completed triple loading after 672 ms
Importing http://protege.stanford.edu/plugins/owl/protege from location:
C:\Program Files (x86)\Prot
ege_3.4.1\plugins\edu.stanford.smi.protegex.owl\protege.owl
Loading triples from: http://protege.stanford.edu/plugins/owl/protege
    Completed triple loading after 16 ms
Postprocess: Process entities with incorrect Java type (0 entities) ... 0 ms
Postprocess: Process metaclasses (3 metaclasses) ... 0 ms
Postprocess: Process subclasses of rdf:List (1 classes) ... 0 ms
Postprocess: Instances with multiple types (122 instances) ... 15 ms
Postprocess: Add inferred superclasses ... 0 ms
Postprocess: Process orphan classes (97 classes) ... 0 ms
Postprocess: Generalized Concept Inclusion (0 axioms) ... 0 ms
Postprocess: Abstract classes... 16 ms
Postprocess: Domain and range of properties... 0 ms
Postprocess: Possibly typed entities (0 resources) ... 0 ms
Updating underlying frames model in 0 ms
Protege Wizards v1.0 beta build 15
Loaded OWL wizards library
Load time for
file:\C:\Program%20Files%20(x86)\Protege_3.4.1\examples\pizza\pizza.owl.pprj
= 2 sec (
project) + 3 sec (ui)




>
> Tania
>
>
> Bo De Lange wrote:
>
> Hi Tania et al.,
>
> Thanks for releasing the BioPortal Reference Plugin that you presented at
> the Protege conference in Amsterdam.
>
> I've followed instructions on
> http://protegewiki.stanford.edu/index.php/BioPortal_Reference_Plugin and
> created an annotation  property 'hasBioPortalReference'. However, the *BioPortalReferenceWidget
> *is not available from the Widget drop-down menu (see attachment).
>
> I'm using Protege 3.4.1 (build 537) on a windows machine. According to the
> protege.exe terminal window the plugin has loaded during startup.
>
> Ideas as to what could be wrong?
>
> Bo
>
> ------------------------------
>
> _______________________________________________
> protege-owl mailing listprotege-owl at lists.stanford.eduhttps://mailman.stanford.edu/mailman/listinfo/protege-owl
>
> Instructions for unsubscribing: http://protege.stanford.edu/doc/faq.html#01a.03
>
>
>
> _______________________________________________
> protege-owl mailing list
> protege-owl at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/protege-owl
>
> Instructions for unsubscribing:
> http://protege.stanford.edu/doc/faq.html#01a.03
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/protege-owl/attachments/20090818/4fef6884/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: widgets1.png
Type: image/png
Size: 21223 bytes
Desc: not available
URL: <http://mailman.stanford.edu/pipermail/protege-owl/attachments/20090818/4fef6884/attachment.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: widgets2.png
Type: image/png
Size: 20204 bytes
Desc: not available
URL: <http://mailman.stanford.edu/pipermail/protege-owl/attachments/20090818/4fef6884/attachment-0001.png>


More information about the protege-owl mailing list