First pass at oboformat and obographs conformance suite.

See - owlcollab/oboformat#146 - geneontology/obographs#106 Note that that may move from the OAK repo in the longer term.
INCATools · Mar 12, 2024 · e4f8894 · e4f8894
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diff --git a/tests/input/obo-compliance.obo b/tests/input/obo-compliance.obo
diff --git a/tests/input/obo-compliance/alt_id/alt_id.expected.json b/tests/input/obo-compliance/alt_id/alt_id.expected.json
@@ -0,0 +1,42 @@
+{
+  "graphs" : [ {
+    "id" : "http://purl.obolibrary.org/obo/alt_id.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" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "X:2"
+        } ]
+      }
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/X_2",
+      "type" : "CLASS",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/X_1"
+        } ],
+        "deprecated" : true
+      }
+    }, {
+      "id" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+      "lbl" : "has_alternative_id",
+      "type" : "PROPERTY"
+    }, {
+      "id" : "http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion",
+      "lbl" : "has_obo_format_version",
+      "type" : "PROPERTY"
+    } ]
+  } ]
+}
diff --git a/tests/input/obo-compliance/alt_id/alt_id.expected.obo b/tests/input/obo-compliance/alt_id/alt_id.expected.obo
@@ -0,0 +1,7 @@
+format-version: 1.2
+ontology: alt_id
+
+[Term]
+id: X:1
+alt_id: X:2
+
diff --git a/tests/input/obo-compliance/alt_id/alt_id.expected.ofn b/tests/input/obo-compliance/alt_id/alt_id.expected.ofn
@@ -0,0 +1,49 @@
+Prefix(:=<http://purl.obolibrary.org/obo/alt_id.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#>)
+
+
+Ontology(<http://purl.obolibrary.org/obo/alt_id.owl>
+Annotation(<http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion> "1.4")
+
+Declaration(Class(<http://purl.obolibrary.org/obo/X_1>))
+Declaration(Class(<http://purl.obolibrary.org/obo/X_2>))
+Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000231>))
+Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0100001>))
+Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#hasAlternativeId>))
+Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion>))
+Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#id>))
+############################
+#   Annotation Properties
+############################
+
+# Annotation Property: <http://www.geneontology.org/formats/oboInOwl#hasAlternativeId> (has_alternative_id)
+
+AnnotationAssertion(rdfs:label <http://www.geneontology.org/formats/oboInOwl#hasAlternativeId> "has_alternative_id")
+
+# 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")
+
+
+
+############################
+#   Classes
+############################
+
+# Class: <http://purl.obolibrary.org/obo/X_1> (<http://purl.obolibrary.org/obo/X_1>)
+
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasAlternativeId> <http://purl.obolibrary.org/obo/X_1> "X:2")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/X_1> "X:1")
+
+# Class: <http://purl.obolibrary.org/obo/X_2> (<http://purl.obolibrary.org/obo/X_2>)
+
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000231> <http://purl.obolibrary.org/obo/X_2> <http://purl.obolibrary.org/obo/IAO_0000227>)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0100001> <http://purl.obolibrary.org/obo/X_2> <http://purl.obolibrary.org/obo/X_1>)
+AnnotationAssertion(owl:deprecated <http://purl.obolibrary.org/obo/X_2> "true"^^xsd:boolean)
+
+
+)
diff --git a/tests/input/obo-compliance/alt_id/alt_id.expected.owl b/tests/input/obo-compliance/alt_id/alt_id.expected.owl
@@ -0,0 +1,94 @@
+<?xml version="1.0"?>
+<rdf:RDF xmlns="http://purl.obolibrary.org/obo/alt_id.owl#"
+     xml:base="http://purl.obolibrary.org/obo/alt_id.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/alt_id.owl">
+        <oboInOwl:hasOBOFormatVersion>1.4</oboInOwl:hasOBOFormatVersion>
+    </owl:Ontology>
+
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Annotation properties
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+
+
+
+    <!-- http://purl.obolibrary.org/obo/IAO_0000231 -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000231"/>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/IAO_0100001 -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0100001"/>
+
+
+
+    <!-- http://www.geneontology.org/formats/oboInOwl#hasAlternativeId -->
+
+    <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasAlternativeId">
+        <rdfs:label>has_alternative_id</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"/>
+
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Classes
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+
+
+
+    <!-- http://purl.obolibrary.org/obo/X_1 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/X_1">
+        <oboInOwl:hasAlternativeId>X:2</oboInOwl:hasAlternativeId>
+        <oboInOwl:id>X:1</oboInOwl:id>
+    </owl:Class>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/X_2 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/X_2">
+        <obo:IAO_0000231 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000227"/>
+        <obo:IAO_0100001 rdf:resource="http://purl.obolibrary.org/obo/X_1"/>
+        <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
+    </owl:Class>
+</rdf:RDF>
+
+
+
+<!-- Generated by the OWL API (version 4.5.25) https://github.com/owlcs/owlapi -->
+
diff --git a/tests/input/obo-compliance/alt_id/alt_id.meta.yaml b/tests/input/obo-compliance/alt_id/alt_id.meta.yaml
@@ -0,0 +1,3 @@
+name: alt_id
+name: alt_id
+description: Alternative ID for the term
diff --git a/tests/input/obo-compliance/alt_id/alt_id.obo b/tests/input/obo-compliance/alt_id/alt_id.obo
@@ -0,0 +1,7 @@
+format-version: 1.4
+ontology: alt_id
+
+[Term]
+id: X:1
+alt_id: X:2
+
diff --git a/tests/input/obo-compliance/broad_synonym/broad_synonym.expected.json b/tests/input/obo-compliance/broad_synonym/broad_synonym.expected.json
@@ -0,0 +1,30 @@
+{
+  "graphs" : [ {
+    "id" : "http://purl.obolibrary.org/obo/broad_synonym.owl",
+    "meta" : {
+      "basicPropertyValues" : [ {
+        "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion",
+        "val" : "1.4"
+      } ]
+    },
+    "nodes" : [ {
+      "id" : "http://purl.obolibrary.org/obo/X_1",
+      "lbl" : "example term",
+      "type" : "CLASS",
+      "meta" : {
+        "synonyms" : [ {
+          "pred" : "hasBroadSynonym",
+          "val" : "broad synonym"
+        } ]
+      }
+    }, {
+      "id" : "http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym",
+      "lbl" : "has_broad_synonym",
+      "type" : "PROPERTY"
+    }, {
+      "id" : "http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion",
+      "lbl" : "has_obo_format_version",
+      "type" : "PROPERTY"
+    } ]
+  } ]
+}
diff --git a/tests/input/obo-compliance/broad_synonym/broad_synonym.expected.obo b/tests/input/obo-compliance/broad_synonym/broad_synonym.expected.obo
@@ -0,0 +1,8 @@
+format-version: 1.2
+ontology: broad_synonym
+
+[Term]
+id: X:1
+name: example term
+synonym: "broad synonym" BROAD []
+
diff --git a/tests/input/obo-compliance/broad_synonym/broad_synonym.expected.ofn b/tests/input/obo-compliance/broad_synonym/broad_synonym.expected.ofn
@@ -0,0 +1,42 @@
+Prefix(:=<http://purl.obolibrary.org/obo/broad_synonym.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#>)
+
+
+Ontology(<http://purl.obolibrary.org/obo/broad_synonym.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#hasBroadSynonym>))
+Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion>))
+Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#id>))
+Declaration(AnnotationProperty(rdfs:label))
+############################
+#   Annotation Properties
+############################
+
+# Annotation Property: <http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym> (has_broad_synonym)
+
+AnnotationAssertion(rdfs:label <http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym> "has_broad_synonym")
+
+# 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")
+
+
+
+############################
+#   Classes
+############################
+
+# Class: <http://purl.obolibrary.org/obo/X_1> (example term)
+
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym> <http://purl.obolibrary.org/obo/X_1> "broad synonym")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/X_1> "X:1")
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/X_1> "example term")
+
+
+)
diff --git a/tests/input/obo-compliance/broad_synonym/broad_synonym.expected.owl b/tests/input/obo-compliance/broad_synonym/broad_synonym.expected.owl
@@ -0,0 +1,78 @@
+<?xml version="1.0"?>
+<rdf:RDF xmlns="http://purl.obolibrary.org/obo/broad_synonym.owl#"
+     xml:base="http://purl.obolibrary.org/obo/broad_synonym.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:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
+    <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/broad_synonym.owl">
+        <oboInOwl:hasOBOFormatVersion>1.4</oboInOwl:hasOBOFormatVersion>
+    </owl:Ontology>
+
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Annotation properties
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+
+
+
+    <!-- http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym -->
+
+    <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym">
+        <rdfs:label>has_broad_synonym</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"/>
+
+
+
+    <!-- http://www.w3.org/2000/01/rdf-schema#label -->
+
+    <owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#label"/>
+
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Classes
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+
+
+
+    <!-- http://purl.obolibrary.org/obo/X_1 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/X_1">
+        <oboInOwl:hasBroadSynonym>broad synonym</oboInOwl:hasBroadSynonym>
+        <oboInOwl:id>X:1</oboInOwl:id>
+        <rdfs:label>example term</rdfs:label>
+    </owl:Class>
+</rdf:RDF>
+
+
+
+<!-- Generated by the OWL API (version 4.5.25) https://github.com/owlcs/owlapi -->
+
diff --git a/tests/input/obo-compliance/broad_synonym/broad_synonym.meta.yaml b/tests/input/obo-compliance/broad_synonym/broad_synonym.meta.yaml
@@ -0,0 +1,3 @@
+name: broad_synonym
+name: broad_synonym
+description: Test for broad synonym type
diff --git a/tests/input/obo-compliance/broad_synonym/broad_synonym.obo b/tests/input/obo-compliance/broad_synonym/broad_synonym.obo
@@ -0,0 +1,8 @@
+format-version: 1.4
+ontology: broad_synonym
+
+[Term]
+id: X:1
+name: example term
+synonym: "broad synonym" BROAD []
+