[Pellet-users] OutOfMemoryException

[Veronika Grandl]

Hi, 

I'm working on an ontology database for clinical patients and before importing new data for one patient into the knowledge base I want to reason over the data and check if it is consistent. 
Using Pellet in the code always stops with a java.lang.OutOfMemoryError exception. If I reason on the commandline it returns consistent and Owl DL. 
I'm using Pellet 1.4-RC2 and Jena 2.5.2

An example patient data rdf file is attached. 

The link to the ontologies: 
http://bioinfo.icapture.ubc.ca/subversion/SIRS/researchdata.owl
http://bioinfo.icapture.ubc.ca/subversion/SIRS/clinicalphenotype.owl

The code: 	
private static void isModelValidPelletOntModel() {
		


	    // ontology that will be used
	    String ont = "http://bioinfo.icapture.ubc.ca/subversion/SIRS/clinicalphenotype.owl";
	       
	    // create an empty ontology model using Pellet spec
	    OntModel model = ModelFactory.createOntologyModel( PelletReasonerFactory.THE_SPEC );

	    // read the file
	    model.read(ont);

	    try {
			model.read(new FileInputStream("/home/vgrandl/eclipse/workspace3/SIRS/backup/yes/test7.rdf"), null);
		} catch (FileNotFoundException e) {
			// TODO Auto-generated catch block
			e.printStackTrace();
		}


	    // print validation report
	    ValidityReport report = model.validate();

	    System.out.println("Validity Report:"+ report.isValid());    
	}

I don't know where the problem is. I tried to use the inference Model but the problem is the same. 

Thanks for your help, Veronika

***CONFIDENTIALITY NOTICE***
This electronic message is intended only for the use of the addressee and may contain information that is privileged and confidential.  Any dissemination, distribution or copying of this communication by unauthorized individuals is strictly prohibited. If you have received this communication in error, please notify the sender immediately by reply e-mail and delete the original and all copies from your system.
-------------- next part --------------
A non-text attachment was scrubbed...
Name: sampleData.rdf
Type: application/octet-stream
Size: 166230 bytes
Desc: not available
Url : http://lists.owldl.com/pipermail/pellet-users/attachments/20070305/354482df/attachment-0001.obj