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[protege-owl] BioPortal Reference Widget

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

Hi Tania,

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


 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
/\#\Stofnaam -classpath "C:\Program Files
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
Protege 3.4.1 Build 537, JVM 1.6.0_14-b08, memory=1908M, Windows XP,
encoding=UTF-8, language=nl, co
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 - TGVizTab
Loaded plugin
Loaded plugin
Loaded plugin
Loaded plugin
Loaded plugin
Loaded plugin - Basic Wizards
Loaded plugin - OWL Wizards
Loading triples from:
    Completed triple loading after 672 ms
Importing from location:
C:\Program Files (x86)\Prot
Loading triples from:
    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
= 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
> 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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