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balhoffbalhoff
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Added obsoletion menu.
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‎README.md‎

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# OBO annotations editor #
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A plug-in for Protege that provides entry fields for standard OBO annotation properties.
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A plug-in for Protege that provides entry fields for standard OBO annotation properties, as well as menu actions such as term obsoletion.

‎pom.xml‎

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<groupId>org.geneontology</groupId>
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<artifactId>obo-annotations-plugin</artifactId>
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<version>0.3.0</version>
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<version>0.4.0</version>
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<packaging>bundle</packaging>
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<name>OBO Annotations Editor</name>
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<developer>
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<id>balhoff</id>
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<name>Jim Balhoff</name>
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<email>jim@balhoff.org</email>
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<email>balhoff@renci.org</email>
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</developer>
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</developers>
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‎src/main/java/org/protege/oboeditor/menu/ObsoleteEntityMenuAction.java‎

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package org.protege.oboeditor.menu;
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import java.util.Set;
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import org.protege.editor.owl.ui.action.SelectedOWLEntityAction;
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import org.semanticweb.owlapi.model.OWLAnnotation;
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import org.semanticweb.owlapi.model.OWLAnnotationAssertionAxiom;
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import org.semanticweb.owlapi.model.OWLAnnotationProperty;
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import org.semanticweb.owlapi.model.OWLClass;
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import org.semanticweb.owlapi.model.OWLClassExpression;
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import org.semanticweb.owlapi.model.OWLDataFactory;
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import org.semanticweb.owlapi.model.OWLDisjointClassesAxiom;
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import org.semanticweb.owlapi.model.OWLEntity;
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import org.semanticweb.owlapi.model.OWLEquivalentClassesAxiom;
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import org.semanticweb.owlapi.model.OWLHasKeyAxiom;
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import org.semanticweb.owlapi.model.OWLLiteral;
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import org.semanticweb.owlapi.model.OWLOntology;
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import org.semanticweb.owlapi.model.OWLOntologyManager;
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import org.semanticweb.owlapi.model.OWLSubClassOfAxiom;
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import org.semanticweb.owlapi.vocab.OWLRDFVocabulary;
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public class ObsoleteEntityMenuAction extends SelectedOWLEntityAction {
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private static final long serialVersionUID = -1431847694761565949L;
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@Override
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protected void actionPerformed(OWLEntity entity) {
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final OWLOntologyManager manager = this.getOWLModelManager().getOWLOntologyManager();
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final OWLDataFactory factory = this.getOWLDataFactory();
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final OWLOntology ontology = this.getOWLModelManager().getActiveOntology();
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this.relabel(entity);
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manager.addAxiom(ontology, factory.getDeprecatedOWLAnnotationAssertionAxiom(entity.getIRI()));
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if (entity.isOWLClass()) {
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final OWLClass ontClass = entity.asOWLClass();
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for (OWLEquivalentClassesAxiom axiom : ontology.getEquivalentClassesAxioms(ontClass)) {
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manager.removeAxiom(ontology, axiom);
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final Set<OWLClassExpression> otherClasses = axiom.getClassExpressionsMinus(ontClass);
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final Set<OWLAnnotation> annotations = axiom.getAnnotations();
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if (otherClasses.size() > 1) {
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final OWLEquivalentClassesAxiom newAxiom = factory.getOWLEquivalentClassesAxiom(otherClasses, annotations);
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manager.addAxiom(ontology, newAxiom);
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}
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}
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for (OWLSubClassOfAxiom axiom : ontology.getSubClassAxiomsForSubClass(ontClass)) {
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manager.removeAxiom(ontology, axiom);
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}
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for (OWLSubClassOfAxiom axiom : ontology.getSubClassAxiomsForSuperClass(ontClass)) {
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manager.removeAxiom(ontology, axiom);
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}
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for (OWLHasKeyAxiom axiom : ontology.getHasKeyAxioms(ontClass)) {
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manager.removeAxiom(ontology, axiom);
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}
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for (OWLDisjointClassesAxiom axiom : ontology.getDisjointClassesAxioms(ontClass)) {
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manager.removeAxiom(ontology, axiom);
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final Set<OWLClassExpression> otherClasses = axiom.getClassExpressionsMinus(ontClass);
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final Set<OWLAnnotation> annotations = axiom.getAnnotations();
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if (otherClasses.size() > 1) {
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final OWLDisjointClassesAxiom newAxiom = factory.getOWLDisjointClassesAxiom(otherClasses, annotations);
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manager.addAxiom(ontology, newAxiom);
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}
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}
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}
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if (entity.isOWLNamedIndividual()) {
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//TODO
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}
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if (entity.isOWLObjectProperty()) {
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//TODO
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}
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}
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@Override
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protected void disposeAction() throws Exception {}
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private void relabel(OWLEntity entity) {
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final OWLOntologyManager manager = this.getOWLModelManager().getOWLOntologyManager();
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final OWLDataFactory factory = this.getOWLDataFactory();
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final OWLAnnotationProperty rdfsLabel = factory.getOWLAnnotationProperty(OWLRDFVocabulary.RDFS_LABEL.getIRI());
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final OWLOntology ontology = this.getOWLModelManager().getActiveOntology();
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for (OWLAnnotationAssertionAxiom annotation : ontology.getAnnotationAssertionAxioms(entity.getIRI())) {
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if (annotation.getProperty().equals(rdfsLabel)) {
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if (annotation.getValue() instanceof OWLLiteral) {
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final Set<OWLAnnotation> annotationAnnotations = annotation.getAnnotations();
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final OWLLiteral literal = (OWLLiteral)(annotation.getValue());
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final String newLabel = "obsolete " + literal.getLiteral();
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final OWLLiteral newLiteral = factory.getOWLLiteral(newLabel);
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final OWLAnnotationAssertionAxiom newAxiom = factory.getOWLAnnotationAssertionAxiom(rdfsLabel, entity.getIRI(), newLiteral, annotationAnnotations);
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manager.removeAxiom(ontology, annotation);
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manager.addAxiom(ontology, newAxiom);
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}
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}
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}
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}
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}

‎src/main/resources/plugin.xml‎

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<headerColor value="B1CAF6"/>
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<category value="OBO"/>
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</extension>
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<extension id="menu.ObsoleteEntity" name="Make entity obsolete" point="org.protege.editor.core.application.EditorKitMenuAction">
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<class value="org.protege.oboeditor.menu.ObsoleteEntityMenuAction"/>
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<name value="Make entity obsolete"/>
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<toolTip value="Deprecates the selected entity and removes its defining axioms."/>
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<path value="org.protege.editor.core.application.menu.EditMenu/SlotOBO-Z"/>
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<editorKitId value="OWLEditorKit"/>
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</extension>
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</plugin>

‎update.properties‎

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id=org.protege.oboeditor
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version=0.3.0
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download=https://github.com/owlcollab/protege-obo-plugin/releases/download/v0.3.0/obo-annotations-plugin-0.3.0.jar
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version=0.4.0
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download=https://github.com/owlcollab/protege-obo-plugin/releases/download/v0.4.0/obo-annotations-plugin-0.4.0.jar
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name=OBO Annotations Editor
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readme=https://raw.githubusercontent.com/owlcollab/protege-obo-plugin/master/README.md
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license=https://opensource.org/licenses/BSD-3-Clause

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