Mercurial > repos > mikel-egana-aranguren > oppl

annotate OPPL/src/GalaxyOWLAPI.java @ 13:7e6604a5ee55

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New query tool added
author Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
date Thu, 29 Mar 2012 14:49:22 +0200
parents 6ca67b155e32
children 622cde484f4c
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1 /**
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2 *
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3 */
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4 package es.upm.fi.dia.oeg.oppl.galaxy;
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5
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6 import java.io.BufferedWriter;
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7 import java.io.File;
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8 import java.io.IOException;
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9 import java.io.OutputStreamWriter;
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10 import java.util.ArrayList;
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11 import java.util.List;
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12 import java.util.Scanner;
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13 import java.util.Set;
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14
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15 import org.coode.owlapi.manchesterowlsyntax.ManchesterOWLSyntaxEditorParser;
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16 import org.coode.owlapi.obo.parser.OBOOntologyFormat;
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17 import org.coode.parsers.BidirectionalShortFormProviderAdapter;
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18 import org.semanticweb.HermiT.Reasoner;
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19 import org.semanticweb.owlapi.apibinding.OWLManager;
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20 import org.semanticweb.owlapi.expression.OWLEntityChecker;
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21 import org.semanticweb.owlapi.expression.ParserException;
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22 import org.semanticweb.owlapi.expression.ShortFormEntityChecker;
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23 import org.semanticweb.owlapi.io.RDFXMLOntologyFormat;
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24 import org.semanticweb.owlapi.io.SystemOutDocumentTarget;
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25 import org.semanticweb.owlapi.model.AddAxiom;
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26 import org.semanticweb.owlapi.model.IRI;
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27 import org.semanticweb.owlapi.model.OWLAnnotation;
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28 import org.semanticweb.owlapi.model.OWLAnnotationProperty;
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29 import org.semanticweb.owlapi.model.OWLAxiom;
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30 import org.semanticweb.owlapi.model.OWLClass;
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31 import org.semanticweb.owlapi.model.OWLClassExpression;
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32 import org.semanticweb.owlapi.model.OWLDataFactory;
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33 import org.semanticweb.owlapi.model.OWLLiteral;
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34 import org.semanticweb.owlapi.model.OWLNamedIndividual;
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35 import org.semanticweb.owlapi.model.OWLOntology;
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36 import org.semanticweb.owlapi.model.OWLOntologyChange;
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37 import org.semanticweb.owlapi.model.OWLOntologyCreationException;
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38 import org.semanticweb.owlapi.model.OWLOntologyManager;
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39 import org.semanticweb.owlapi.model.OWLOntologyStorageException;
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40 import org.semanticweb.owlapi.reasoner.InferenceType;
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41 import org.semanticweb.owlapi.reasoner.NodeSet;
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42 import org.semanticweb.owlapi.reasoner.OWLReasoner;
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43 import org.semanticweb.owlapi.reasoner.OWLReasonerFactory;
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44 import org.semanticweb.owlapi.util.BidirectionalShortFormProvider;
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45 import org.semanticweb.owlapi.util.InferredAxiomGenerator;
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46 import org.semanticweb.owlapi.util.InferredClassAssertionAxiomGenerator;
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47 import org.semanticweb.owlapi.util.InferredDisjointClassesAxiomGenerator;
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48 import org.semanticweb.owlapi.util.InferredOntologyGenerator;
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49 import org.semanticweb.owlapi.util.InferredSubClassAxiomGenerator;
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50 import org.semanticweb.owlapi.util.InferredSubDataPropertyAxiomGenerator;
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51 import org.semanticweb.owlapi.util.InferredSubObjectPropertyAxiomGenerator;
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52 import org.semanticweb.owlapi.util.OWLEntityRenamer;
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53 import org.semanticweb.owlapi.util.OWLOntologyMerger;
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54 import org.semanticweb.owlapi.util.SimpleShortFormProvider;
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55 import org.semanticweb.owlapi.vocab.OWL2Datatype;
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56 import org.semanticweb.owlapi.vocab.OWLRDFVocabulary;
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57 import org.semanticweb.owlapi.reasoner.Node;
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58
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59 import uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasonerFactory;
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60
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61 import com.clarkparsia.pellet.owlapiv3.PelletReasonerFactory;
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62
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63 /**
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64 * A wrapper of the OWL API
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65 *
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66 * @author Mikel Egaña Aranguren
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67 */
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68 public class GalaxyOWLAPI {
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69 private OWLOntologyManager manager;
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70 private OWLOntology ontology;
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71 private OWLReasonerFactory reasonerFactory;
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72 private OWLReasoner reasoner;
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73
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74 public GalaxyOWLAPI (){
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75 manager = OWLManager.createOWLOntologyManager();
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76 }
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77 public OWLOntologyManager getOWLManager(){
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78 return manager;
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79 }
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80 public OWLOntology getMainOntology(){
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81 return ontology;
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82 }
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83 public OWLReasoner getReasoner(){
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84 return reasoner;
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85 }
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86
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87 public void loadMainOntology(String OWLFilePath) throws OWLOntologyCreationException{
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88 File owl_file = new File(OWLFilePath);
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89 ontology = manager.loadOntologyFromOntologyDocument(owl_file);
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90 }
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91
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92 // public void loadImportedOntology(IRI importedOntologyIRI) throws OWLOntologyCreationException{
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93 // manager.loadOntologyFromOntologyDocument(importedOntologyIRI);
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94 // }
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95
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96 // OWLLink: The problem is that Racer, for example, listens in 8080, the same port as Galaxy
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97 // I have to change Racer settings and OWLLink settings
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98 // OWLlinkHTTPXMLReasonerFactory factory = new OWLlinkHTTPXMLReasonerFactory();
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99 // reasoner = factory.createReasoner(OWL_ontology);
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100
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101 public void setReasonerPellet (){
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102 reasonerFactory = new PelletReasonerFactory();
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103 reasoner = reasonerFactory.createReasoner(ontology);
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104 }
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105 public void setReasonerFaCT (){
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106 reasonerFactory = new FaCTPlusPlusReasonerFactory();
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107 reasoner = reasonerFactory.createReasoner(ontology);
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108 }
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109 public void setReasonerHermit (){
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110 reasonerFactory = new Reasoner.ReasonerFactory();
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111 reasoner = reasonerFactory.createReasoner(ontology);
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112 }
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113 public void merge () throws OWLOntologyCreationException{
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114 OWLOntologyMerger merger = new OWLOntologyMerger(manager);
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115 IRI mergedOntologyIRI = IRI.create("http://oeg-upm.net/oppl_galaxy/merged.owl");
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116 ontology = merger.createMergedOntology(manager, mergedOntologyIRI);
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117 }
13
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118
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119 public OWLClassExpression parseMOSClassExpression (String expr) throws ParserException{
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120 Set<OWLOntology> importsClosure = ontology.getImportsClosure();
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121 BidirectionalShortFormProvider bidiShortFormProvider = new BidirectionalShortFormProviderAdapter(manager, importsClosure, new SimpleShortFormProvider());
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122 OWLEntityChecker entityChecker = new ShortFormEntityChecker(bidiShortFormProvider);
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123 ManchesterOWLSyntaxEditorParser MOSparser = new ManchesterOWLSyntaxEditorParser(manager.getOWLDataFactory(), expr);
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124 MOSparser.setOWLEntityChecker(entityChecker);
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125 return MOSparser.parseClassExpression();
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126 }
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127
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128 public Set<OWLNamedIndividual> getIndividuals (OWLClassExpression expr){
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129 return (reasoner.getInstances(expr, false)).getFlattened();
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130 }
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131 public Set<OWLClass> getEquivalentClasses (OWLClassExpression expr){
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132 Node<OWLClass> equivalentClasses = reasoner.getEquivalentClasses(expr);
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133 Set<OWLClass> result;
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134 if (expr.isAnonymous()) {
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135 result = equivalentClasses.getEntities();
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136 }
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137 else {
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138 result = equivalentClasses.getEntitiesMinus(expr.asOWLClass());
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139 }
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140 return result;
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141 }
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142
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143 public Set<OWLClass> getDirectSuperClasses (OWLClassExpression expr){
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144 return (reasoner.getSuperClasses(expr, true)).getFlattened();
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145 }
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146
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147 public Set<OWLClass> getAncestors (OWLClassExpression expr){
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148 return (reasoner.getSuperClasses(expr, false)).getFlattened();
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149 }
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150
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151 public Set<OWLClass> getDirectSubClasses (OWLClassExpression expr){
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152 return (reasoner.getSubClasses(expr, true)).getFlattened();
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153 }
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154
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155 public Set<OWLClass> getDescendants (OWLClassExpression expr){
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156 return (reasoner.getSubClasses(expr, false)).getFlattened();
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157 }
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158
11
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159 // CLASS_ASSERTIONS Denotes the computation of the direct types of individuals for each individual in the signature of the imports closure of the root ontology.
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160
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161 public void addCLASS_ASSERTIONS(){
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162 reasoner.precomputeInferences(InferenceType.CLASS_ASSERTIONS);
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163 List<InferredAxiomGenerator<? extends OWLAxiom>> gens = new ArrayList<InferredAxiomGenerator<? extends OWLAxiom>>();
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164 gens.add(new InferredClassAssertionAxiomGenerator());
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165 InferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner, gens);
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166 iog.fillOntology(manager, ontology);
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167 }
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168
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169 // CLASS_HIERARCHY Denotes the computation of the class hierarchy.
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170
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171 public void addCLASS_HIERARCHY(){
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172 reasoner.precomputeInferences(InferenceType.CLASS_HIERARCHY);
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173 List<InferredAxiomGenerator<? extends OWLAxiom>> gens = new ArrayList<InferredAxiomGenerator<? extends OWLAxiom>>();
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174 gens.add(new InferredSubClassAxiomGenerator());
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175 InferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner, gens);
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176 iog.fillOntology(manager, ontology);
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177 }
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178
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179 // DATA_PROPERTY_ASSERTIONS Denotes the computation of relationships between individuals and data property values for each individual in the signature of the imports closure of the root ontology.
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180 // public void addDATA_PROPERTY_ASSERTIONS(){
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181 // reasoner.precomputeInferences(InferenceType.DATA_PROPERTY_ASSERTIONS);
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182 // List<InferredAxiomGenerator<? extends OWLAxiom>> gens = new ArrayList<InferredAxiomGenerator<? extends OWLAxiom>>();
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183 // gens.add(new InferredDataPropertyAxiomGenerator());
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184 // InferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner, gens);
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185 // iog.fillOntology(manager, ontology);
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186 // }
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187
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188 // DATA_PROPERTY_HIERARCHY Denotes the computation of the data property hierarchy.
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189
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190 public void addDATA_PROPERTY_HIERARCHY(){
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191 reasoner.precomputeInferences(InferenceType.DATA_PROPERTY_HIERARCHY);
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192 List<InferredAxiomGenerator<? extends OWLAxiom>> gens = new ArrayList<InferredAxiomGenerator<? extends OWLAxiom>>();
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193 gens.add(new InferredSubDataPropertyAxiomGenerator());
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194 InferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner, gens);
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195 iog.fillOntology(manager, ontology);
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196 }
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197
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198 // DIFFERENT_INDIVIDUALS Denotes the computation of sets of individuals that are different from each individual in the signature of the imports closure of the root ontology.
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199
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200 // public void addDIFFERENT_INDIVIDUALS(){
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201 // reasoner.precomputeInferences(InferenceType.DIFFERENT_INDIVIDUALS);
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202 // List<InferredAxiomGenerator<? extends OWLAxiom>> gens = new ArrayList<InferredAxiomGenerator<? extends OWLAxiom>>();
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203 // gens.add(new Inferred);
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204 // InferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner, gens);
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205 // iog.fillOntology(manager, ontology);
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206 // }
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207
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208 // DISJOINT_CLASSES Denotes the computation of sets of classes that are disjoint for each class in the signature of the imports closure of the root ontology.
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209
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210 public void addDISJOINT_CLASSES(){
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211 reasoner.precomputeInferences(InferenceType.DISJOINT_CLASSES);
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212 List<InferredAxiomGenerator<? extends OWLAxiom>> gens = new ArrayList<InferredAxiomGenerator<? extends OWLAxiom>>();
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213 gens.add(new InferredDisjointClassesAxiomGenerator());
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214 InferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner, gens);
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215 iog.fillOntology(manager, ontology);
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216 }
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217
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218 // OBJECT_PROPERTY_ASSERTIONS Denotes the computation of relationships between individuals in the signature of the imports closure of the root ontology.
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219
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220 // public void addOBJECT_PROPERTY_ASSERTIONS(){
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221 // reasoner.precomputeInferences(InferenceType.OBJECT_PROPERTY_ASSERTIONS);
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222 // List<InferredAxiomGenerator<? extends OWLAxiom>> gens = new ArrayList<InferredAxiomGenerator<? extends OWLAxiom>>();
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223 // gens.add(new InferredObjectPropertyAxiomGenerator<OWLAxiom>() {
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224 // };());
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225 // InferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner, gens);
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226 // iog.fillOntology(manager, ontology);
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227 // }
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228
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229 // OBJECT_PROPERTY_HIERARCHY Denotes the computation of the object property hierarchy.
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230
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231 public void addOBJECT_PROPERTY_HIERARCHY(){
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232 reasoner.precomputeInferences(InferenceType.OBJECT_PROPERTY_HIERARCHY);
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233 List<InferredAxiomGenerator<? extends OWLAxiom>> gens = new ArrayList<InferredAxiomGenerator<? extends OWLAxiom>>();
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234 gens.add(new InferredSubObjectPropertyAxiomGenerator());
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235 InferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner, gens);
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236 iog.fillOntology(manager, ontology);
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237 }
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238
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239 // SAME_INDIVIDUAL Denotes the computation of individuals that are interpreted as the same object for each individual in the imports closure of the root ontology.
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240
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241 // public void addSAME_INDIVIDUAL(){
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242 // reasoner.precomputeInferences(InferenceType.SAME_INDIVIDUAL);
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243 // List<InferredAxiomGenerator<? extends OWLAxiom>> gens = new ArrayList<InferredAxiomGenerator<? extends OWLAxiom>>();
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244 // gens.add(new Infer);
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245 // InferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner, gens);
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246 // iog.fillOntology(manager, ontology);
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247 // }
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248
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249 public void saveOntology (boolean OWL) throws OWLOntologyStorageException, IOException, OWLOntologyCreationException{
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250 // OWL format
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251 if(OWL){
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252 manager.saveOntology(ontology, new RDFXMLOntologyFormat(), new SystemOutDocumentTarget());
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253 }
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254 // OBO format
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255 else{
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256 // OWL API generates bad OBO but OBOformat doesn't work either so I correct the OWL API problems (More predictable) in a temporary file
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257 // Very inefficient but no time for another solution
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258
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259 OWLDataFactory factory = manager.getOWLDataFactory();
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260 OWLEntityRenamer renamer = new OWLEntityRenamer (manager, manager.getOntologies());
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261 OWLAnnotationProperty label = factory.getOWLAnnotationProperty(OWLRDFVocabulary.RDFS_LABEL.getIRI());
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262 for(OWLClass cls : ontology.getClassesInSignature()){
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263 // Remove annotations (OWL API generates bad OBO annotations)
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264
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265 // Keep rdfs:label
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266 String class_name = null;
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267 for (OWLAnnotation annotation : cls.getAnnotations(ontology, label)){
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268 if (annotation.getValue() instanceof OWLLiteral) {
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269 OWLLiteral val = (OWLLiteral) annotation.getValue();
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270 class_name = val.getLiteral();
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271 }
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272 }
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273
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274 // I have to remove all the annotations cause I don't know which ones are rendered properly
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275 manager.removeAxioms(ontology,ontology.getAnnotationAssertionAxioms(cls.getIRI()));
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276
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277 // Add rdfs:label again
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278 OWLAnnotation labelAnno = factory.getOWLAnnotation(factory.getOWLAnnotationProperty(
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279 OWLRDFVocabulary.RDFS_LABEL.getIRI()),factory.getOWLLiteral(class_name,OWL2Datatype.XSD_STRING));
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280 OWLAxiom ax = factory.getOWLAnnotationAssertionAxiom(cls.getIRI(), labelAnno);
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281 manager.applyChange(new AddAxiom(ontology, ax));
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282
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283 // Rename entities
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284 String cls_IRI = cls.getIRI().toString();
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285 String cls_proper_IRI = cls_IRI.replace("_", ":");
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286 List<OWLOntologyChange> changes = renamer.changeIRI(cls, IRI.create(cls_proper_IRI));
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287 manager.applyChanges(changes);
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288 }
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289
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290 File file = new File("tmp.obo");
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291 manager.saveOntology(ontology, new OBOOntologyFormat(), IRI.create(file.toURI()));
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292 BufferedWriter bw = new BufferedWriter(new OutputStreamWriter(System.out));
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293 Scanner input = new Scanner(file);
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294 String buffer = "";
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295
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296 while(input.hasNext()){
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297 String nextLine = input.nextLine();
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298 if(nextLine.contains("[Term]") || nextLine.contains("[Typedef]")){
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299 if(buffer.isEmpty()){
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300 bw.write(buffer);
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301 bw.newLine();
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302 }
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303 }
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304 if(!nextLine.contains("is_a: Thing") && !nextLine.contains("auto-generated-by:") && !nextLine.contains("id_space:") && !nextLine.contains("! ----")){
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305 if(!nextLine.isEmpty() && !buffer.contains("relationship:")){
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306 bw.write(nextLine);
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307 bw.newLine();
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308 }
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309 }
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310 buffer = nextLine;
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311 }
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312 input.close();
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313 bw.close();
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314 file.delete();
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315 }
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316 }
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317 }