From c7c641bbdd387124f5e9de97b40893e7fc0795a6 Mon Sep 17 00:00:00 2001
From: Chris Mungall <cjm@berkeleybop.org>
Date: Thu, 9 May 2024 09:33:12 -0700
Subject: [PATCH] Adding skos-xref-duplicate to obo compliance suite (#752)

* Adding skos-xref-duplicate to obo compliance suite

See https://github.com/geneontology/obographs/issues/102

* derived files
---
 tests/input/obo-compliance.obo                | 15 ++++
 .../skos-xref-duplicate.expected.json         | 45 ++++++++++
 .../skos-xref-duplicate.expected.obo          | 13 +++
 .../skos-xref-duplicate.expected.ofn          | 53 +++++++++++
 .../skos-xref-duplicate.expected.owl          | 90 +++++++++++++++++++
 .../skos-xref-duplicate.meta.yaml             |  5 ++
 .../skos-xref-duplicate.obo                   | 13 +++
 7 files changed, 234 insertions(+)
 create mode 100644 tests/input/obo-compliance/skos-xref-duplicate/skos-xref-duplicate.expected.json
 create mode 100644 tests/input/obo-compliance/skos-xref-duplicate/skos-xref-duplicate.expected.obo
 create mode 100644 tests/input/obo-compliance/skos-xref-duplicate/skos-xref-duplicate.expected.ofn
 create mode 100644 tests/input/obo-compliance/skos-xref-duplicate/skos-xref-duplicate.expected.owl
 create mode 100644 tests/input/obo-compliance/skos-xref-duplicate/skos-xref-duplicate.meta.yaml
 create mode 100644 tests/input/obo-compliance/skos-xref-duplicate/skos-xref-duplicate.obo

diff --git a/tests/input/obo-compliance.obo b/tests/input/obo-compliance.obo
index a0ca211cf..f70afd914 100644
--- a/tests/input/obo-compliance.obo
+++ b/tests/input/obo-compliance.obo
@@ -268,6 +268,21 @@ relationship: skos:exactMatch Y:1
 id: skos:exactMatch
 is_metadata_tag: true
 
+!! name: skos-xref-duplicate
+!! description: Using both xref and skos relationship (annotation) to communicate the same mapping
+!! seeAlso: https://github.com/geneontology/obographs/issues/102
+!! unstable: true
+idspace: skos http://www.w3.org/2004/02/skos/core#
+
+[Term]
+id: X:1
+relationship: skos:exactMatch Y:1
+xref: Y:1
+
+[Typedef]
+id: skos:exactMatch
+is_metadata_tag: true
+
 !! name: alt_id
 !! description: Alternative ID for the term
 
diff --git a/tests/input/obo-compliance/skos-xref-duplicate/skos-xref-duplicate.expected.json b/tests/input/obo-compliance/skos-xref-duplicate/skos-xref-duplicate.expected.json
new file mode 100644
index 000000000..60132f7e3
--- /dev/null
+++ b/tests/input/obo-compliance/skos-xref-duplicate/skos-xref-duplicate.expected.json
@@ -0,0 +1,45 @@
+{
+  "graphs" : [ {
+    "id" : "http://purl.obolibrary.org/obo/skos-xref-duplicate.owl",
+    "meta" : {
+      "basicPropertyValues" : [ {
+        "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion",
+        "val" : "1.4"
+      } ]
+    },
+    "nodes" : [ {
+      "id" : "http://purl.obolibrary.org/obo/X_1",
+      "type" : "CLASS",
+      "meta" : {
+        "xrefs" : [ {
+          "val" : "Y:1"
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.w3.org/2004/02/skos/core#exactMatch",
+          "val" : "http://purl.obolibrary.org/obo/Y_1"
+        } ]
+      }
+    }, {
+      "id" : "http://www.geneontology.org/formats/oboInOwl#hasDbXref",
+      "lbl" : "database_cross_reference",
+      "type" : "PROPERTY"
+    }, {
+      "id" : "http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion",
+      "lbl" : "has_obo_format_version",
+      "type" : "PROPERTY"
+    }, {
+      "id" : "http://www.geneontology.org/formats/oboInOwl#id",
+      "lbl" : "id",
+      "type" : "PROPERTY"
+    }, {
+      "id" : "http://www.w3.org/2004/02/skos/core#exactMatch",
+      "type" : "PROPERTY",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag",
+          "val" : "true"
+        } ]
+      }
+    } ]
+  } ]
+}
\ No newline at end of file
diff --git a/tests/input/obo-compliance/skos-xref-duplicate/skos-xref-duplicate.expected.obo b/tests/input/obo-compliance/skos-xref-duplicate/skos-xref-duplicate.expected.obo
new file mode 100644
index 000000000..e669b8eac
--- /dev/null
+++ b/tests/input/obo-compliance/skos-xref-duplicate/skos-xref-duplicate.expected.obo
@@ -0,0 +1,13 @@
+format-version: 1.2
+idspace: skos http://www.w3.org/2004/02/skos/core# 
+ontology: skos-xref-duplicate
+
+[Term]
+id: X:1
+xref: Y:1
+relationship: skos:exactMatch Y:1
+
+[Typedef]
+id: skos:exactMatch
+is_metadata_tag: true
+
diff --git a/tests/input/obo-compliance/skos-xref-duplicate/skos-xref-duplicate.expected.ofn b/tests/input/obo-compliance/skos-xref-duplicate/skos-xref-duplicate.expected.ofn
new file mode 100644
index 000000000..76d3f55a2
--- /dev/null
+++ b/tests/input/obo-compliance/skos-xref-duplicate/skos-xref-duplicate.expected.ofn
@@ -0,0 +1,53 @@
+Prefix(:=<http://purl.obolibrary.org/obo/skos-xref-duplicate.owl#>)
+Prefix(owl:=<http://www.w3.org/2002/07/owl#>)
+Prefix(rdf:=<http://www.w3.org/1999/02/22-rdf-syntax-ns#>)
+Prefix(xml:=<http://www.w3.org/XML/1998/namespace>)
+Prefix(xsd:=<http://www.w3.org/2001/XMLSchema#>)
+Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
+Prefix(skos:=<http://www.w3.org/2004/02/skos/core#>)
+
+
+Ontology(<http://purl.obolibrary.org/obo/skos-xref-duplicate.owl>
+Annotation(<http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion> "1.4")
+
+Declaration(Class(<http://purl.obolibrary.org/obo/X_1>))
+Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#hasDbXref>))
+Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion>))
+Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#id>))
+Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#is_metadata_tag>))
+Declaration(AnnotationProperty(skos:exactMatch))
+############################
+#   Annotation Properties
+############################
+
+# Annotation Property: <http://www.geneontology.org/formats/oboInOwl#hasDbXref> (database_cross_reference)
+
+AnnotationAssertion(rdfs:label <http://www.geneontology.org/formats/oboInOwl#hasDbXref> "database_cross_reference")
+
+# Annotation Property: <http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion> (has_obo_format_version)
+
+AnnotationAssertion(rdfs:label <http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion> "has_obo_format_version")
+
+# Annotation Property: <http://www.geneontology.org/formats/oboInOwl#id> (id)
+
+AnnotationAssertion(rdfs:label <http://www.geneontology.org/formats/oboInOwl#id> "id")
+
+# Annotation Property: skos:exactMatch (skos:exactMatch)
+
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> skos:exactMatch "skos:exactMatch")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#is_metadata_tag> skos:exactMatch "true"^^xsd:boolean)
+
+
+
+############################
+#   Classes
+############################
+
+# Class: <http://purl.obolibrary.org/obo/X_1> (<http://purl.obolibrary.org/obo/X_1>)
+
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/X_1> "Y:1")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/X_1> "X:1")
+AnnotationAssertion(skos:exactMatch <http://purl.obolibrary.org/obo/X_1> <http://purl.obolibrary.org/obo/Y_1>)
+
+
+)
\ No newline at end of file
diff --git a/tests/input/obo-compliance/skos-xref-duplicate/skos-xref-duplicate.expected.owl b/tests/input/obo-compliance/skos-xref-duplicate/skos-xref-duplicate.expected.owl
new file mode 100644
index 000000000..497358778
--- /dev/null
+++ b/tests/input/obo-compliance/skos-xref-duplicate/skos-xref-duplicate.expected.owl
@@ -0,0 +1,90 @@
+<?xml version="1.0"?>
+<rdf:RDF xmlns="http://purl.obolibrary.org/obo/skos-xref-duplicate.owl#"
+     xml:base="http://purl.obolibrary.org/obo/skos-xref-duplicate.owl"
+     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:skos="http://www.w3.org/2004/02/skos/core#"
+     xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
+    <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/skos-xref-duplicate.owl">
+        <oboInOwl:hasOBOFormatVersion>1.4</oboInOwl:hasOBOFormatVersion>
+    </owl:Ontology>
+    
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Annotation properties
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+    
+
+
+    <!-- http://www.geneontology.org/formats/oboInOwl#hasDbXref -->
+
+    <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasDbXref">
+        <rdfs:label>database_cross_reference</rdfs:label>
+    </owl:AnnotationProperty>
+    
+
+
+    <!-- http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion -->
+
+    <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion">
+        <rdfs:label>has_obo_format_version</rdfs:label>
+    </owl:AnnotationProperty>
+    
+
+
+    <!-- http://www.geneontology.org/formats/oboInOwl#id -->
+
+    <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#id">
+        <rdfs:label>id</rdfs:label>
+    </owl:AnnotationProperty>
+    
+
+
+    <!-- http://www.geneontology.org/formats/oboInOwl#is_metadata_tag -->
+
+    <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#is_metadata_tag"/>
+    
+
+
+    <!-- http://www.w3.org/2004/02/skos/core#exactMatch -->
+
+    <owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#exactMatch">
+        <oboInOwl:id>skos:exactMatch</oboInOwl:id>
+        <oboInOwl:is_metadata_tag rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</oboInOwl:is_metadata_tag>
+    </owl:AnnotationProperty>
+    
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Classes
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+    
+
+
+    <!-- http://purl.obolibrary.org/obo/X_1 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/X_1">
+        <oboInOwl:hasDbXref>Y:1</oboInOwl:hasDbXref>
+        <oboInOwl:id>X:1</oboInOwl:id>
+        <skos:exactMatch rdf:resource="http://purl.obolibrary.org/obo/Y_1"/>
+    </owl:Class>
+</rdf:RDF>
+
+
+
+<!-- Generated by the OWL API (version 4.5.26) https://github.com/owlcs/owlapi -->
+
diff --git a/tests/input/obo-compliance/skos-xref-duplicate/skos-xref-duplicate.meta.yaml b/tests/input/obo-compliance/skos-xref-duplicate/skos-xref-duplicate.meta.yaml
new file mode 100644
index 000000000..602cf905a
--- /dev/null
+++ b/tests/input/obo-compliance/skos-xref-duplicate/skos-xref-duplicate.meta.yaml
@@ -0,0 +1,5 @@
+name: skos-xref-duplicate
+name: skos-xref-duplicate
+description: Using both xref and skos relationship (annotation) to communicate the same mapping
+seeAlso: https://github.com/geneontology/obographs/issues/102
+unstable: true
\ No newline at end of file
diff --git a/tests/input/obo-compliance/skos-xref-duplicate/skos-xref-duplicate.obo b/tests/input/obo-compliance/skos-xref-duplicate/skos-xref-duplicate.obo
new file mode 100644
index 000000000..cac3ecaa4
--- /dev/null
+++ b/tests/input/obo-compliance/skos-xref-duplicate/skos-xref-duplicate.obo
@@ -0,0 +1,13 @@
+format-version: 1.4
+ontology: skos-xref-duplicate
+idspace: skos http://www.w3.org/2004/02/skos/core#
+
+[Term]
+id: X:1
+relationship: skos:exactMatch Y:1
+xref: Y:1
+
+[Typedef]
+id: skos:exactMatch
+is_metadata_tag: true
+