[Pellet-users] Reasoning problem

[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. 
I can reason over the ontology and the rdf file individually. But adding these two files into one model and reasoning over this model always stops with a java.lang.OutOfMemoryError exception. 

I'm using Pellet 1.4 and Jena 2.5.2 . The links to all files and the java code are attached.

Thanks a lot for your help!
Veronika



The link to an example patient data rdf file:
 http://bioinfo.icapture.ubc.ca/subversion/SIRSKB/utils/phcImport/sampleData.rdf

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());    
	}




The error message:
 INFO [main] (PelletOptions.java:51) - Reading Pellet configuration file jar:file:/usr/local/pellet-1.4/lib/pellet.jar!/pellet.properties
 INFO [main] (KnowledgeBase.java:869) - Expressivity: SHOIF(D), Classes: 529 Properties: 105 Individuals: 542, GCIs: 0 (55 absorbed) Strategy: SHOIQStrategy
 INFO [main] (ABox.java:1476) - ABox consistency for 0 individuals
Exception in thread "main" java.lang.OutOfMemoryError: Java heap space


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