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annotate OPPL/src/GalaxyOWLAPI.java @ 11:6ca67b155e32

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Imports simplified, new tool for inference added
author Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
date Fri, 09 Mar 2012 16:15:27 +0100
parents
children 7e6604a5ee55
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11
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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
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14 import org.coode.owlapi.obo.parser.OBOOntologyFormat;
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15 import org.semanticweb.HermiT.Reasoner;
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16 import org.semanticweb.owlapi.apibinding.OWLManager;
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17 import org.semanticweb.owlapi.io.RDFXMLOntologyFormat;
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18 import org.semanticweb.owlapi.io.SystemOutDocumentTarget;
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19 import org.semanticweb.owlapi.model.AddAxiom;
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20 import org.semanticweb.owlapi.model.IRI;
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21 import org.semanticweb.owlapi.model.OWLAnnotation;
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22 import org.semanticweb.owlapi.model.OWLAnnotationProperty;
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23 import org.semanticweb.owlapi.model.OWLAxiom;
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24 import org.semanticweb.owlapi.model.OWLClass;
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25 import org.semanticweb.owlapi.model.OWLDataFactory;
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26 import org.semanticweb.owlapi.model.OWLLiteral;
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27 import org.semanticweb.owlapi.model.OWLOntology;
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28 import org.semanticweb.owlapi.model.OWLOntologyChange;
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29 import org.semanticweb.owlapi.model.OWLOntologyCreationException;
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30 import org.semanticweb.owlapi.model.OWLOntologyManager;
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31 import org.semanticweb.owlapi.model.OWLOntologyStorageException;
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32 import org.semanticweb.owlapi.reasoner.InferenceType;
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33 import org.semanticweb.owlapi.reasoner.OWLReasoner;
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34 import org.semanticweb.owlapi.reasoner.OWLReasonerFactory;
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35 import org.semanticweb.owlapi.util.InferredAxiomGenerator;
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36 import org.semanticweb.owlapi.util.InferredClassAssertionAxiomGenerator;
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37 import org.semanticweb.owlapi.util.InferredDisjointClassesAxiomGenerator;
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38 import org.semanticweb.owlapi.util.InferredOntologyGenerator;
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39 import org.semanticweb.owlapi.util.InferredSubClassAxiomGenerator;
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40 import org.semanticweb.owlapi.util.InferredSubDataPropertyAxiomGenerator;
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41 import org.semanticweb.owlapi.util.InferredSubObjectPropertyAxiomGenerator;
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42 import org.semanticweb.owlapi.util.OWLEntityRenamer;
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43 import org.semanticweb.owlapi.util.OWLOntologyMerger;
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44 import org.semanticweb.owlapi.vocab.OWL2Datatype;
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45 import org.semanticweb.owlapi.vocab.OWLRDFVocabulary;
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46
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47 import uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasonerFactory;
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48
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49 import com.clarkparsia.pellet.owlapiv3.PelletReasonerFactory;
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50
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51 /**
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52 * A wrapper of the OWL API
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53 *
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54 * @author Mikel Egaña Aranguren
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55 */
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56 public class GalaxyOWLAPI {
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57 private OWLOntologyManager manager;
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58 private OWLOntology ontology;
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59 private OWLReasonerFactory reasonerFactory;
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60 private OWLReasoner reasoner;
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61
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62 public GalaxyOWLAPI (){
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63 manager = OWLManager.createOWLOntologyManager();
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64 }
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65 public OWLOntologyManager getOWLManager(){
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66 return manager;
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67 }
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68 public OWLOntology getMainOntology(){
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69 return ontology;
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70 }
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71 public OWLReasoner getReasoner(){
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72 return reasoner;
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73 }
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74
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75 public void loadMainOntology(String OWLFilePath) throws OWLOntologyCreationException{
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76 File owl_file = new File(OWLFilePath);
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77 ontology = manager.loadOntologyFromOntologyDocument(owl_file);
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78 }
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79
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80 // public void loadImportedOntology(IRI importedOntologyIRI) throws OWLOntologyCreationException{
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81 // manager.loadOntologyFromOntologyDocument(importedOntologyIRI);
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82 // }
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83
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84 // OWLLink: The problem is that Racer, for example, listens in 8080, the same port as Galaxy
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85 // I have to change Racer settings and OWLLink settings
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86 // OWLlinkHTTPXMLReasonerFactory factory = new OWLlinkHTTPXMLReasonerFactory();
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87 // reasoner = factory.createReasoner(OWL_ontology);
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88
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89 public void setReasonerPellet (){
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90 reasonerFactory = new PelletReasonerFactory();
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91 reasoner = reasonerFactory.createReasoner(ontology);
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92 }
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93 public void setReasonerFaCT (){
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94 reasonerFactory = new FaCTPlusPlusReasonerFactory();
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95 reasoner = reasonerFactory.createReasoner(ontology);
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96 }
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97 public void setReasonerHermit (){
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98 reasonerFactory = new Reasoner.ReasonerFactory();
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99 reasoner = reasonerFactory.createReasoner(ontology);
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100 }
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101 public void merge () throws OWLOntologyCreationException{
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102 OWLOntologyMerger merger = new OWLOntologyMerger(manager);
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103 IRI mergedOntologyIRI = IRI.create("http://oeg-upm.net/oppl_galaxy/merged.owl");
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104 ontology = merger.createMergedOntology(manager, mergedOntologyIRI);
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105 }
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106
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107 // 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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108
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109 public void addCLASS_ASSERTIONS(){
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110 reasoner.precomputeInferences(InferenceType.CLASS_ASSERTIONS);
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111 List<InferredAxiomGenerator<? extends OWLAxiom>> gens = new ArrayList<InferredAxiomGenerator<? extends OWLAxiom>>();
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112 gens.add(new InferredClassAssertionAxiomGenerator());
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113 InferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner, gens);
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114 iog.fillOntology(manager, ontology);
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115 }
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116
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117 // CLASS_HIERARCHY Denotes the computation of the class hierarchy.
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118
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119 public void addCLASS_HIERARCHY(){
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120 reasoner.precomputeInferences(InferenceType.CLASS_HIERARCHY);
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121 List<InferredAxiomGenerator<? extends OWLAxiom>> gens = new ArrayList<InferredAxiomGenerator<? extends OWLAxiom>>();
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122 gens.add(new InferredSubClassAxiomGenerator());
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123 InferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner, gens);
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124 iog.fillOntology(manager, ontology);
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125 }
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126
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127 // 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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128 // public void addDATA_PROPERTY_ASSERTIONS(){
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129 // reasoner.precomputeInferences(InferenceType.DATA_PROPERTY_ASSERTIONS);
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130 // List<InferredAxiomGenerator<? extends OWLAxiom>> gens = new ArrayList<InferredAxiomGenerator<? extends OWLAxiom>>();
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131 // gens.add(new InferredDataPropertyAxiomGenerator());
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132 // InferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner, gens);
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133 // iog.fillOntology(manager, ontology);
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134 // }
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135
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136 // DATA_PROPERTY_HIERARCHY Denotes the computation of the data property hierarchy.
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137
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138 public void addDATA_PROPERTY_HIERARCHY(){
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139 reasoner.precomputeInferences(InferenceType.DATA_PROPERTY_HIERARCHY);
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140 List<InferredAxiomGenerator<? extends OWLAxiom>> gens = new ArrayList<InferredAxiomGenerator<? extends OWLAxiom>>();
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141 gens.add(new InferredSubDataPropertyAxiomGenerator());
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142 InferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner, gens);
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143 iog.fillOntology(manager, ontology);
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144 }
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145
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146 // 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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147
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148 // public void addDIFFERENT_INDIVIDUALS(){
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149 // reasoner.precomputeInferences(InferenceType.DIFFERENT_INDIVIDUALS);
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150 // List<InferredAxiomGenerator<? extends OWLAxiom>> gens = new ArrayList<InferredAxiomGenerator<? extends OWLAxiom>>();
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151 // gens.add(new Inferred);
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152 // InferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner, gens);
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153 // iog.fillOntology(manager, ontology);
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154 // }
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155
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156 // 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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157
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158 public void addDISJOINT_CLASSES(){
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159 reasoner.precomputeInferences(InferenceType.DISJOINT_CLASSES);
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160 List<InferredAxiomGenerator<? extends OWLAxiom>> gens = new ArrayList<InferredAxiomGenerator<? extends OWLAxiom>>();
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161 gens.add(new InferredDisjointClassesAxiomGenerator());
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162 InferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner, gens);
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163 iog.fillOntology(manager, ontology);
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164 }
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165
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166 // 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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167
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168 // public void addOBJECT_PROPERTY_ASSERTIONS(){
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169 // reasoner.precomputeInferences(InferenceType.OBJECT_PROPERTY_ASSERTIONS);
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170 // List<InferredAxiomGenerator<? extends OWLAxiom>> gens = new ArrayList<InferredAxiomGenerator<? extends OWLAxiom>>();
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171 // gens.add(new InferredObjectPropertyAxiomGenerator<OWLAxiom>() {
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172 // };());
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173 // InferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner, gens);
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174 // iog.fillOntology(manager, ontology);
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175 // }
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176
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177 // OBJECT_PROPERTY_HIERARCHY Denotes the computation of the object property hierarchy.
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178
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179 public void addOBJECT_PROPERTY_HIERARCHY(){
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180 reasoner.precomputeInferences(InferenceType.OBJECT_PROPERTY_HIERARCHY);
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181 List<InferredAxiomGenerator<? extends OWLAxiom>> gens = new ArrayList<InferredAxiomGenerator<? extends OWLAxiom>>();
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182 gens.add(new InferredSubObjectPropertyAxiomGenerator());
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183 InferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner, gens);
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184 iog.fillOntology(manager, ontology);
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185 }
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186
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187 // 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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188
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189 // public void addSAME_INDIVIDUAL(){
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190 // reasoner.precomputeInferences(InferenceType.SAME_INDIVIDUAL);
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191 // List<InferredAxiomGenerator<? extends OWLAxiom>> gens = new ArrayList<InferredAxiomGenerator<? extends OWLAxiom>>();
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192 // gens.add(new Infer);
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193 // InferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner, gens);
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194 // iog.fillOntology(manager, ontology);
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195 // }
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196
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197 public void saveOntology (boolean OWL) throws OWLOntologyStorageException, IOException, OWLOntologyCreationException{
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198 // OWL format
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199 if(OWL){
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200 manager.saveOntology(ontology, new RDFXMLOntologyFormat(), new SystemOutDocumentTarget());
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201 }
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202 // OBO format
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203 else{
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204 // 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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205 // Very inefficient but no time for another solution
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206
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207 OWLDataFactory factory = manager.getOWLDataFactory();
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208 OWLEntityRenamer renamer = new OWLEntityRenamer (manager, manager.getOntologies());
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209 OWLAnnotationProperty label = factory.getOWLAnnotationProperty(OWLRDFVocabulary.RDFS_LABEL.getIRI());
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210 for(OWLClass cls : ontology.getClassesInSignature()){
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211 // Remove annotations (OWL API generates bad OBO annotations)
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212
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213 // Keep rdfs:label
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214 String class_name = null;
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215 for (OWLAnnotation annotation : cls.getAnnotations(ontology, label)){
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216 if (annotation.getValue() instanceof OWLLiteral) {
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217 OWLLiteral val = (OWLLiteral) annotation.getValue();
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218 class_name = val.getLiteral();
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219 }
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220 }
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221
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222 // I have to remove all the annotations cause I don't know which ones are rendered properly
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223 manager.removeAxioms(ontology,ontology.getAnnotationAssertionAxioms(cls.getIRI()));
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224
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225 // Add rdfs:label again
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226 OWLAnnotation labelAnno = factory.getOWLAnnotation(factory.getOWLAnnotationProperty(
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227 OWLRDFVocabulary.RDFS_LABEL.getIRI()),factory.getOWLLiteral(class_name,OWL2Datatype.XSD_STRING));
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228 OWLAxiom ax = factory.getOWLAnnotationAssertionAxiom(cls.getIRI(), labelAnno);
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229 manager.applyChange(new AddAxiom(ontology, ax));
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230
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231 // Rename entities
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232 String cls_IRI = cls.getIRI().toString();
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233 String cls_proper_IRI = cls_IRI.replace("_", ":");
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234 List<OWLOntologyChange> changes = renamer.changeIRI(cls, IRI.create(cls_proper_IRI));
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235 manager.applyChanges(changes);
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236 }
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237
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238 File file = new File("tmp.obo");
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239 manager.saveOntology(ontology, new OBOOntologyFormat(), IRI.create(file.toURI()));
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240 BufferedWriter bw = new BufferedWriter(new OutputStreamWriter(System.out));
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241 Scanner input = new Scanner(file);
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242 String buffer = "";
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243
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244 while(input.hasNext()){
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245 String nextLine = input.nextLine();
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246 if(nextLine.contains("[Term]") || nextLine.contains("[Typedef]")){
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247 if(buffer.isEmpty()){
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248 bw.write(buffer);
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249 bw.newLine();
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250 }
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251 }
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252 if(!nextLine.contains("is_a: Thing") && !nextLine.contains("auto-generated-by:") && !nextLine.contains("id_space:") && !nextLine.contains("! ----")){
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253 if(!nextLine.isEmpty() && !buffer.contains("relationship:")){
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254 bw.write(nextLine);
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255 bw.newLine();
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256 }
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257 }
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258 buffer = nextLine;
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259 }
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260 input.close();
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261 bw.close();
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262 file.delete();
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263 }
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264 }
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265 }