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[protege-owl] BioPortal Reference Widget

Bo De Lange bodelange at gmail.com
Tue Aug 18 06:56:05 PDT 2009


My mistake for not reading properly..., I had just unzipped and put the
whole folder in the plugins folder as per usual. When I instructed the unzip
to the plugins folder the automatic overwriting of the existing standard
extensions occurred as well as the correct unpacking of the actual BP
reference plugin.  It now works fine. Cheers. Nice work.

Bo

On Tue, Aug 18, 2009 at 9:09 AM, Bo De Lange <bodelange at gmail.com> wrote:

> 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
>>
>> ------------------------------
>>
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>>
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>>
>>
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>
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