get_supperClasses.groovy

@Grapes([
	  @Grab(group='org.semanticweb.elk', module='elk-owlapi', version='0.4.2'),
	  @Grab(group='net.sourceforge.owlapi', module='owlapi-api', version='4.1.0'),
	  @Grab(group='net.sourceforge.owlapi', module='owlapi-apibinding', version='4.1.0'),
	  @Grab(group='net.sourceforge.owlapi', module='owlapi-impl', version='4.1.0'),
	  @Grab(group='net.sourceforge.owlapi', module='owlapi-parsers', version='4.1.0'),
	  @GrabConfig(systemClassLoader=true)
	])

import org.semanticweb.owlapi.model.parameters.*
import org.semanticweb.elk.owlapi.ElkReasonerFactory;
import org.semanticweb.elk.owlapi.ElkReasonerConfiguration
import org.semanticweb.elk.reasoner.config.*
import org.semanticweb.owlapi.apibinding.OWLManager;
import org.semanticweb.owlapi.reasoner.*
import org.semanticweb.owlapi.reasoner.structural.StructuralReasoner
import org.semanticweb.owlapi.vocab.OWLRDFVocabulary;
import org.semanticweb.owlapi.model.*;
import org.semanticweb.owlapi.io.*;
import org.semanticweb.owlapi.owllink.*;
import org.semanticweb.owlapi.util.*;
import org.semanticweb.owlapi.search.*;
import org.semanticweb.owlapi.manchestersyntax.renderer.*;
import org.semanticweb.owlapi.reasoner.structural.*

OWLOntologyManager manager = OWLManager.createOWLOntologyManager()
def ont = manager.loadOntologyFromOntologyDocument(new File(args[0]))
OWLDataFactory fac = manager.getOWLDataFactory()
ConsoleProgressMonitor progressMonitor = new ConsoleProgressMonitor()
OWLReasonerConfiguration config = new SimpleConfiguration(progressMonitor)
ElkReasonerFactory f1 = new ElkReasonerFactory()
OWLReasoner reasoner = f1.createReasoner(ont,config)


new File("../../../Documents/smudge_data/phenomNet_super_classes.txt").withWriter { writer ->

	for (OWLClass c: ont.getClassesInSignature(false)){
	    NodeSet superclasses = reasoner.getSuperClasses(c, false);
	    writer.write c.getIRI().getShortForm() + " "
	    for (Node<OWLClass> superc: superclasses){
	    	writer.write superc.getRepresentativeElement().getIRI().getShortForm() + " "
	    }
	    writer.writeLine ""
	}
}