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[protege-discussion] Reasoning Errors

Jones, Josette F. jofjones at
Wed Nov 5 07:57:51 PST 2008

Greetings we keep running into some errors. Please advise on how we can correct. Thanks.  
The errors are described below and in attached files.
System Configuration:

Windows Vista Home Basic sp1 32 bit
Dell Vostro 1400 Intel Core2 Duo 1.4GHz 2Gb RAM
Java(TM) 6 Update 10 (11/3/2008)

Protege v3.4 beta with following tabs enabled: Classes, Slots, Forms, Instances, Queries, UMLS, Jambalaya, Knowledge Tree, Prompt, Changes, DataMaster v1.3.1, String Search, XML Tab.

Issue 1: Converting project to OWL using "File -> Export to Format -> OWL" fails with the following message in a pop -up window:

"Export Failed: edu.stanford.smi.protege.util.MessageError at f16070"

The following exception is seen in the console (please check the attachment Export_Console.txt for complete log):

SEVERE: Failed to save file file:/C:/Users/bugsnspikes/Documents/IUPU/RA/Ontolog
y/scans_oct30_1.owl using Protege2Jena. -- com.hp.hpl.jena.shared.BadURIExceptio
n: Only well-formed absolute URIrefs can be included in RDF/XML output: <E> Code
: 58/REQUIRED_COMPONENT_MISSING in SCHEME: A component that is required by the 
scheme is missing.

Disabled all tabs except Classes, Instances, Slots and tried again. But the error persists.

Issue 2: Converting project using "File -> Convert Project to Format .." turns non-responsive (has been running for about 10 minutes) with numerous plugin exceptions, out of memory exceptions after running high CPU (100% on one of my Dual core) and java.exe consuming > 268,000k memory. Please check Convert_Console.txt for complete log.

Resolution: The logs indicated problem with Jambalaya, UMLS. Disabled all the tabs except Classes, Instances, Slots and the conversion worked fine.

Issue 3: Enabling SWRL tab after resolving issue#3 does not converge. Runs on high CPU(100%) and memory (> 271,000k) for several minutes. Then the Protege display goes blank and CPU usage falls to zero for the process. Please check SWRLTab_Console.txt for the complete log.

NOTE: This problem is not seen while working with a OWL project. Its only seen after converting to OWL from RDF format.

Josette Jones, RN, PhD
Phone:  (317) 274-8059
Fax:      (317) 278-7669
Email: jofjones at

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