Merge pull request #1194 from ontodev/repair-merge-annotations

Make repair command more flexible
ontodev · May 13, 2024 · d4105ae · d4105ae
2 parents 1598c45 + 8af165c
commit d4105ae
Show file tree

Hide file tree

Showing 5 changed files with 664 additions and 6 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -22,6 +22,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [`merge`] and 'annotate' operations '--annotate-defined-by' excludes reserved OWL 2 vocabularies [#1171]
 - Handle IRIs that are not entities in export [#1168]
 - Fix integration tests [#1181]
+- `robot repair` is fixed to be more flexible, to enable partial repairs [#1194]
 - Invalid Xrefs test has been fixed to recognise invalid CURIEs correctly [#1127]
 - Fix issue with correctly determining base entities [#1108]
 

diff --git a/docs/examples/uberon_axiom_annotation_merged.owl b/docs/examples/uberon_axiom_annotation_merged.owl
@@ -0,0 +1,297 @@
+<?xml version="1.0"?>
+<rdf:RDF xmlns="http://purl.obolibrary.org/obo/uberon.owl#"
+     xml:base="http://purl.obolibrary.org/obo/uberon.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:foaf="http://xmlns.com/foaf/0.1/"
+     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/uberon.owl"/>
+
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Annotation properties
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+
+
+
+    <!-- http://purl.obolibrary.org/obo/IAO_0000115 -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000115"/>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/IAO_0000116 -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000116"/>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/IAO_0000232 -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000232"/>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/RO_0002174 -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002174"/>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/RO_0002175 -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002175"/>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/UBPROP_0000001 -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/UBPROP_0000001"/>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/UBPROP_0000003 -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/UBPROP_0000003"/>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/UBPROP_0000007 -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/UBPROP_0000007"/>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/UBPROP_0000008 -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/UBPROP_0000008"/>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/UBPROP_0000009 -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/UBPROP_0000009"/>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/UBPROP_0000012 -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/UBPROP_0000012"/>
+
+
+
+    <!-- http://www.geneontology.org/formats/oboInOwl#date_retrieved -->
+
+    <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#date_retrieved"/>
+
+
+
+    <!-- http://www.geneontology.org/formats/oboInOwl#external_class -->
+
+    <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#external_class"/>
+
+
+
+    <!-- http://www.geneontology.org/formats/oboInOwl#external_ontology -->
+
+    <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#external_ontology"/>
+
+
+
+    <!-- http://www.geneontology.org/formats/oboInOwl#hasAlternativeId -->
+
+    <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasAlternativeId"/>
+
+
+
+    <!-- http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym -->
+
+    <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym"/>
+
+
+
+    <!-- http://www.geneontology.org/formats/oboInOwl#hasDbXref -->
+
+    <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasDbXref"/>
+
+
+
+    <!-- http://www.geneontology.org/formats/oboInOwl#hasExactSynonym -->
+
+    <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasExactSynonym"/>
+
+
+
+    <!-- http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym -->
+
+    <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym"/>
+
+
+
+    <!-- http://www.geneontology.org/formats/oboInOwl#hasOBONamespace -->
+
+    <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasOBONamespace"/>
+
+
+
+    <!-- http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym -->
+
+    <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym"/>
+
+
+
+    <!-- http://www.geneontology.org/formats/oboInOwl#hasSynonymType -->
+
+    <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasSynonymType"/>
+
+
+
+    <!-- http://www.geneontology.org/formats/oboInOwl#id -->
+
+    <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#id"/>
+
+
+
+    <!-- http://www.geneontology.org/formats/oboInOwl#inSubset -->
+
+    <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#inSubset"/>
+
+
+
+    <!-- http://www.geneontology.org/formats/oboInOwl#notes -->
+
+    <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#notes"/>
+
+
+
+    <!-- http://www.geneontology.org/formats/oboInOwl#ontology -->
+
+    <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#ontology"/>
+
+
+
+    <!-- http://www.geneontology.org/formats/oboInOwl#shorthand -->
+
+    <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#shorthand"/>
+
+
+
+    <!-- http://www.geneontology.org/formats/oboInOwl#source -->
+
+    <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#source"/>
+
+
+
+    <!-- http://xmlns.com/foaf/0.1/depicted_by -->
+
+    <owl:AnnotationProperty rdf:about="http://xmlns.com/foaf/0.1/depicted_by"/>
+
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Object Properties
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+
+
+
+    <!-- http://purl.obolibrary.org/obo/BFO_0000050 -->
+
+    <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000050">
+        <owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
+        <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
+        <oboInOwl:hasDbXref>BFO:0000050</oboInOwl:hasDbXref>
+        <oboInOwl:hasOBONamespace>uberon</oboInOwl:hasOBONamespace>
+        <oboInOwl:id>part_of</oboInOwl:id>
+        <oboInOwl:shorthand>part_of</oboInOwl:shorthand>
+        <rdfs:label>part_of</rdfs:label>
+    </owl:ObjectProperty>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/BFO_0000051 -->
+
+    <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000051">
+        <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
+        <oboInOwl:hasDbXref>BFO:0000051</oboInOwl:hasDbXref>
+        <oboInOwl:hasOBONamespace>uberon</oboInOwl:hasOBONamespace>
+        <oboInOwl:id>has_part</oboInOwl:id>
+        <oboInOwl:shorthand>has_part</oboInOwl:shorthand>
+        <rdfs:label>has_part</rdfs:label>
+    </owl:ObjectProperty>
+
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Classes
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+
+
+
+    <!-- http://purl.obolibrary.org/obo/UBERON_0000062 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0000062">
+        <rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
+                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000467"/>
+            </owl:Restriction>
+        </rdfs:subClassOf>
+        <obo:IAO_0000115>Anatomical structure that performs a specific function or group of functions [WP].</obo:IAO_0000115>
+        <oboInOwl:hasDbXref rdf:resource="http://en.wikipedia.org/wiki/page1"/>
+        <oboInOwl:hasDbXref rdf:resource="http://en.wikipedia.org/wiki/page2"/>
+        <oboInOwl:hasDbXref rdf:resource="http://linkedlifedata.com/resource/umls/id/C0178784"/>
+        <oboInOwl:hasDbXref rdf:resource="http://ncicb.nci.nih.gov/xml/owl/EVS/Organ"/>
+        <oboInOwl:hasDbXref>WBbt:0003760</oboInOwl:hasDbXref>
+        <oboInOwl:hasRelatedSynonym>anatomical unit</oboInOwl:hasRelatedSynonym>
+        <oboInOwl:hasRelatedSynonym>body organ</oboInOwl:hasRelatedSynonym>
+        <oboInOwl:hasRelatedSynonym>element</oboInOwl:hasRelatedSynonym>
+        <oboInOwl:id>UBERON:0000062</oboInOwl:id>
+        <rdfs:label>organ</rdfs:label>
+    </owl:Class>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000062"/>
+        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
+        <owl:annotatedTarget>Anatomical structure that performs a specific function or group of functions [WP].</owl:annotatedTarget>
+        <oboInOwl:hasDbXref rdf:resource="http://en.wikipedia.org/wiki/page1"/>
+        <oboInOwl:hasDbXref rdf:resource="http://en.wikipedia.org/wiki/page2"/>
+    </owl:Axiom>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000062"/>
+        <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym"/>
+        <owl:annotatedTarget>body organ</owl:annotatedTarget>
+        <oboInOwl:hasDbXref rdf:resource="UBERON:123"/>
+        <oboInOwl:source rdf:resource="http://en.wikipedia.org/wiki/page1"/>
+        <oboInOwl:source rdf:resource="http://en.wikipedia.org/wiki/page2"/>
+    </owl:Axiom>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/UBERON_0000467 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0000467"/>
+</rdf:RDF>
+
+
+
+<!-- Generated by the OWL API (version 4.5.26) https://github.com/owlcs/owlapi -->
+