FW: [Pellet-users] ANN: Pellet 1.5 RC1
Parsa Mirhaji
How we can move forward with this new release of the Pellet, before you
incorporate it in your new TBC compilations?
-----Original Message-----
From: pellet-use...@lists.owldl.com
[mailto:pellet-use...@lists.owldl.com] On Behalf Of Evren Sirin
Sent: Thursday, June 07, 2007 12:57 PM
To: Pellet-Users
Subject: [Pellet-users] ANN: Pellet 1.5 RC1
Pellet users,
We are pleased to announce the first release candidate for Pellet 1.5
which you can download from the following URL:
http://pellet.owldl.com/downloads/pellet-1.5-RC1.zip
Major changes for this release are as follows:
* Optimized classifier: Classifier with a better performance for all
ontologies and also incorporates the CD optimization to handle large
taxonomic ontologies very efficiently, e.g. classification time for NCI
ontology [1] reduced from 45min to 15sec.
* Axiom tracing: Axiom tracing is integrated into this version so a
single justification can be computed for arbitrary inferences, e.g.
subclass relations. It can also be used for debugging unsatisfiable
concepts.
* Incremental reasoning: Some preliminary support for incremental
reasoning with changing ontologies. After an ontology change, the
previous reasoning results are reused to improve the performance of
consistency checking. Currently only ABox additions are supported for
incremental reasoning.
We have added example programs that shows how to use these new features.
In addition, there have been many bug fixes and improvements since the
1.4 release. See [2] for a complete list of changes and check out the
Trac site [3] for detailed information about bug fixes.
We would like to thank National Cancer Institute (NCI) Center for
Bioinformatics and specifically Gilberto Fragoso, Sherri de Coronado,
and Frank Hartel for their support that made the improvements for this
release possible.
As you will realize, we also have a new design for the Pellet web site.
The content of the Web site has been enriched with more information
about Pellet including a more extensive FAQ [4].
Cheers,
Evren
[1] http://www.mindswap.org/2003/CancerOntology/nciOncology.owl
[2]
http://svn.versiondude.net/clark-parsia/pellet-devel/tags/release-1.5-rc
1/CHANGES.txt
[3] http://cvsdude.com/trac/clark-parsia/pellet-devel/report
[4] http://pellet.owldl.com/faq
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Holger Knublauch
the changes to Pellet sound indeed useful. We need to wait for a stable
release though before bundling it in.
In the meantime you should be able to just replace all occurances of
pellet.jar in your ecplipse installation (there is one hidden somewhere
under the configuration folder).
Holger
Parsa Mirhaji
It looks like it is incredibly faster, but I had to check it with Protégé as I couldn't get the TBC to even find its DIG interface. No matter what I do it ends up with the following error.
Here is what I did:
1- I found all pellet.jar files and replaced them with the new version: didn't work, ended up with the error below.
2- I configured inferencing from the menu to use the DIG interface, ran the pellet DIG interface on port 8081: didn't work, ended with the same error
3- I erased all pellet.jar files from the eclipse subdirectories (I could not find any in configuration directory though), stopped the DIG interface: did not work (apparently) but what is interesting is that its error is identically the same.
As protégé works fine with it, and the TBC produces the same error with or without the new version, with DIG interface or integrated interface, I thought I would report it here to see if you have some comments to make it work...
Best regards
Parsa
Error Entries from TBC Error Log:
!ENTRY org.eclipse.ui 4 4 2007-06-07 23:28:06.093
!MESSAGE Unhandled event loop exception
!ENTRY org.eclipse.ui 4 0 2007-06-07 23:28:06.093
!MESSAGE org/mindswap/pellet/taxonomy/ClassifyProgress
!STACK 0
java.lang.NoClassDefFoundError: org/mindswap/pellet/taxonomy/ClassifyProgress
at org.topbraidcomposer.inference.actions.AbstractRunInferencesAction.createChange(AbstractRunInferencesAction.java:27)
at org.topbraidcomposer.inference.actions.AbstractRunInferencesAction.run(AbstractRunInferencesAction.java:51)
at org.eclipse.ui.internal.PluginAction.runWithEvent(PluginAction.java:254)
at org.eclipse.ui.internal.WWinPluginAction.runWithEvent(WWinPluginAction.java:229)
at org.eclipse.jface.action.ActionContributionItem.handleWidgetSelection(ActionContributionItem.java:539)
at org.eclipse.jface.action.ActionContributionItem.access$2(ActionContributionItem.java:488)
at org.eclipse.jface.action.ActionContributionItem$6.handleEvent(ActionContributionItem.java:441)
at org.eclipse.swt.widgets.EventTable.sendEvent(EventTable.java:66)
at org.eclipse.swt.widgets.Widget.sendEvent(Widget.java:928)
at org.eclipse.swt.widgets.Display.runDeferredEvents(Display.java:3348)
at org.eclipse.swt.widgets.Display.readAndDispatch(Display.java:2968)
at org.eclipse.ui.internal.Workbench.runEventLoop(Workbench.java:1930)
at org.eclipse.ui.internal.Workbench.runUI(Workbench.java:1894)
at org.eclipse.ui.internal.Workbench.createAndRunWorkbench(Workbench.java:422)
at org.eclipse.ui.PlatformUI.createAndRunWorkbench(PlatformUI.java:149)
at org.eclipse.ui.internal.ide.IDEApplication.run(IDEApplication.java:95)
at org.eclipse.core.internal.runtime.PlatformActivator$1.run(PlatformActivator.java:78)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:92)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:68)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:400)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:177)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at org.eclipse.core.launcher.Main.invokeFramework(Main.java:336)
at org.eclipse.core.launcher.Main.basicRun(Main.java:280)
at org.eclipse.core.launcher.Main.run(Main.java:977)
at org.eclipse.core.launcher.Main.main(Main.java:952)
Parsa Mirhaji, MD
Director, The Center for Biosecurity and Public Health Informatics Research
The School of Health Information Sciences
The University of Texas Health Science Center at Houston
Tel: (713) 500-3157
Fax: (713) 500-0370
Assistance (Cynthia Castro): (713) 500-3901
Holger Knublauch
been removed (or moved at least). I'd need to check, and I hope they
will quickly proceed with a final Pellet release so that we can
confidently upgrade our libraries as well.
The DIG interface is likely not compatible - there are various DIG
implementations and versions around. We are just using the Jena
implementation and Protege may use some other one.
So there is no short-term solution right now.