repair example #214

ontodev · Dec 11, 2017 · 5160356 · 5160356
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diff --git a/examples/README.md b/examples/README.md
@@ -248,6 +248,14 @@ OWL 2 has a number of [profiles](https://www.w3.org/TR/owl2-profiles/) that stri
       --input merged.owl \
       --output results/merged-validation.txt
 
+## Repairing Ontologies
+
+ROBOT can repair certain problems encountered in ontologies. So far this is limited to updating axioms pointing to deprecated classes with their replacement class
+
+    robot repair \
+      --input need-of-repair.owl \
+      --output results/repaired.owl
+
 
 ## Chaining
 

diff --git a/examples/need-of-repair.owl b/examples/need-of-repair.owl
@@ -0,0 +1,57 @@
+<?xml version="1.0"?>
+<rdf:RDF xmlns="http://purl.obolibrary.org/obo/need-of-repair.owl#"
+     xml:base="http://purl.obolibrary.org/obo/need-of-repair.owl"
+     xmlns:obo="http://purl.obolibrary.org/obo/"
+     xmlns:owl="http://www.w3.org/2002/07/owl#"
+     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+     xmlns:xml="http://www.w3.org/XML/1998/namespace"
+     xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
+     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
+     xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
+    <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/need-of-repair.owl"/>
+
+
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Classes
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+
+
+
+    <!-- http://purl.obolibrary.org/obo/GO_1 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_1">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_2"/>
+        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">leaf node</rdfs:label>
+    </owl:Class>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/GO_2 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_2">
+        <obo:IAO_0100001 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GO:3</obo:IAO_0100001>
+        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">original parent</rdfs:label>
+        <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
+    </owl:Class>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/GO_3 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_3">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_3"/>
+        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">replacement parent</rdfs:label>
+    </owl:Class>
+</rdf:RDF>
+
+
+
+<!-- Generated by the OWL API (version 4.5.0) https://github.com/owlcs/owlapi -->
+
diff --git a/examples/repaired.owl b/examples/repaired.owl
@@ -0,0 +1,72 @@
+<?xml version="1.0"?>
+<rdf:RDF xmlns="http://purl.obolibrary.org/obo/need-of-repair.owl#"
+     xml:base="http://purl.obolibrary.org/obo/need-of-repair.owl"
+     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+     xmlns:owl="http://www.w3.org/2002/07/owl#"
+     xmlns:xml="http://www.w3.org/XML/1998/namespace"
+     xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
+     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
+     xmlns:obo="http://purl.obolibrary.org/obo/">
+    <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/need-of-repair.owl"/>
+
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Annotation properties
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+
+
+
+    <!-- http://purl.obolibrary.org/obo/IAO_0100001 -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0100001"/>
+
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Classes
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+
+
+
+    <!-- http://purl.obolibrary.org/obo/GO_1 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_1">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_3"/>
+        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">leaf node</rdfs:label>
+    </owl:Class>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/GO_2 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_2">
+        <obo:IAO_0100001 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GO:3</obo:IAO_0100001>
+        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">original parent</rdfs:label>
+        <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
+    </owl:Class>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/GO_3 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_3">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_3"/>
+        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">replacement parent</rdfs:label>
+    </owl:Class>
+</rdf:RDF>
+
+
+
+<!-- Generated by the OWL API (version 4.2.6) https://github.com/owlcs/owlapi -->
+