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/**
* Copyright CSIRO Australian e-Health Research Centre (http://aehrc.com).
* All rights reserved. Use is subject to license terms and conditions.
*/
package au.csiro.snorocket.examples;
import java.util.HashSet;
import java.util.Set;
import au.csiro.ontology.Factory;
import au.csiro.ontology.Ontology;
import au.csiro.ontology.Node;
import au.csiro.ontology.model.Axiom;
import au.csiro.ontology.classification.IReasoner;
import au.csiro.ontology.model.Concept;
import au.csiro.ontology.model.NamedRole;
import au.csiro.ontology.model.Role;
import au.csiro.snorocket.core.SnorocketReasoner;
/**
* This class shows how to use Snorocket's classification API.
*
* @author Alejandro Metke
*
*/
public class APIExample {
/**
* @param args
*/
public static void main(String[] args) {
System.out.println("Running Snorocket API Example");
// Create the reasoner instance - the parametrised type refers to the
// type of the external identifiers
IReasoner reasoner = new SnorocketReasoner();
// This set will contain the base axioms
Set baseAxioms = new HashSet();
// The factory returns IConcepts - in this case the actual type is
// INamedConcept
Concept endocardium = Factory.createNamedConcept("Endocardium");
Concept tissue = Factory.createNamedConcept("Tissue");
Concept heartWall = Factory.createNamedConcept("HeartWall");
Concept heartValve = Factory.createNamedConcept("HeartValve");
Concept bodyWall = Factory.createNamedConcept("BodyWall");
Concept heart = Factory.createNamedConcept("Heart");
Concept bodyValve = Factory.createNamedConcept("BodyValve");
Concept endocarditis = Factory.createNamedConcept("Endocarditis");
Concept inflammation = Factory.createNamedConcept("Inflammation");
Concept disease = Factory.createNamedConcept("Disease");
Concept heartDisease = Factory.createNamedConcept("HeartDisease");
Concept criticalDisease = Factory.createNamedConcept("CriticalDisease");
// The factory can also be used to create roles
Role actsOn = Factory.createNamedRole("acts-on");
Role partOf = Factory.createNamedRole("part-of");
Role contIn = Factory.createNamedRole("cont-in");
Role hasLoc = Factory.createNamedRole("has-loc");
// Finally, the factory can be used to create axioms
Concept lhs = endocardium;
Concept rhs = Factory.createConjunction(
tissue,
Factory.createExistential((NamedRole) contIn, heartWall),
Factory.createExistential((NamedRole) contIn, heartValve)
);
baseAxioms.add(Factory.createConceptInclusion(lhs, rhs));
lhs = heartWall;
rhs = Factory.createConjunction(
bodyWall,
Factory.createExistential((NamedRole) partOf, heart)
);
baseAxioms.add(Factory.createConceptInclusion(lhs, rhs));
lhs = heartValve;
rhs = Factory.createConjunction(
bodyValve,
Factory.createExistential((NamedRole) partOf, heart)
);
baseAxioms.add(Factory.createConceptInclusion(lhs, rhs));
lhs = endocarditis;
rhs = Factory.createConjunction(
inflammation,
Factory.createExistential((NamedRole) hasLoc, endocardium)
);
baseAxioms.add(Factory.createConceptInclusion(lhs, rhs));
lhs = inflammation;
rhs = Factory.createConjunction(
disease,
Factory.createExistential(actsOn, tissue)
);
baseAxioms.add(Factory.createConceptInclusion(lhs, rhs));
lhs = Factory.createConjunction(
heartDisease,
Factory.createExistential(hasLoc, heartValve)
);
rhs = criticalDisease;
baseAxioms.add(Factory.createConceptInclusion(lhs, rhs));
// There is no direct support in the API to create an equivalence axiom
// so it has to be created using two concept inclusion axioms
lhs = heartDisease;
rhs = Factory.createConjunction(
disease,
Factory.createExistential(hasLoc, heart)
);
baseAxioms.add(Factory.createConceptInclusion(lhs, rhs));
baseAxioms.add(Factory.createConceptInclusion(rhs, lhs));
Role[] rlhs = new Role[]{partOf, partOf};
Role rrhs = partOf;
baseAxioms.add(Factory.createRoleInclusion(rlhs, rrhs));
rlhs = new Role[]{partOf};
rrhs = contIn;
baseAxioms.add(Factory.createRoleInclusion(rlhs, rrhs));
rlhs = new Role[]{hasLoc, contIn};
rrhs = hasLoc;
baseAxioms.add(Factory.createRoleInclusion(rlhs, rrhs));
// The first time the classify method is called it runs a full
// classification
reasoner.loadAxioms(baseAxioms);
reasoner.classify();
// If classification worked properly then Endocarditis should be
// classified not only as an Inflammation but also as a HeartDisease
// and a CriticalDisease
Ontology t = reasoner.getClassifiedOntology();
// We use the same id that was used to create the concept to look for
// the corresponding node in the taxonomy
Node endocarditisNode = t.getNode("Endocarditis");
System.out.println("Node for endocarditis:\n "+
endocarditisNode.getEquivalentConcepts());
// We can now print the equivalent concepts in the node and the parent
// nodes
Set parentNodes = endocarditisNode.getParents();
System.out.println("Parents of endocarditis:");
for(Node parentNode : parentNodes) {
System.out.println(" "+parentNode.getEquivalentConcepts());
}
// We can now add more axioms to the ontology and re-run the
// classification
Set additionalAxioms = new HashSet();
Concept heartInflammation = Factory.createNamedConcept("HeartInflammation");
lhs = heartInflammation;
rhs = inflammation;
additionalAxioms.add(Factory.createConceptInclusion(lhs, rhs));
lhs = endocarditis;
rhs = Factory.createConjunction(
heartInflammation,
Factory.createExistential(hasLoc, endocardium)
);
additionalAxioms.add(Factory.createConceptInclusion(lhs, rhs));
// Subsequent invocations will trigger an incremental classification
System.out.println("Running incremental classification:");
reasoner.loadAxioms(additionalAxioms);
reasoner.classify();
// Now Endocarditis should be a HeartInflammation instead of an
// Inflammation
t = reasoner.getClassifiedOntology();
endocarditisNode = t.getNode("Endocarditis");
System.out.println("Node for endocarditis:\n "+
endocarditisNode.getEquivalentConcepts());
parentNodes = endocarditisNode.getParents();
System.out.println("Parents of endocarditis:");
for(Node parentNode : parentNodes) {
System.out.println(" "+parentNode.getEquivalentConcepts());
}
}
}
