OWL 2 completeness (#644)

* Fix missing class on qualified restrictions (#566) * Update issue templates Removed "outdated ontology" tag from Bug report. * Update issue templates Template for documentation related issues. * - Update build widget script * - Add README.md * - Update package version * - Update README.md * Add routing support for ebi-lookup service (#631) * - Add routing for ebi lookup service * - Fix URL routing with env variable * - Add console log - Try diff caddy config * - REVERT - Add console log - REVERT - Try diff caddy config * Add biolink (#632) * Add biolink * fix typo * Owl2 completeness (#635) * Union of constructors were not rendered on frontend. * Self references should not be bold or a link. Fixed inconsistent ontology. * UnionOf only applies to classes. Aligned examples with OWL2 Primer. * implement datatypes --------- Co-authored-by: James McLaughlin <james@mclgh.net> * Add DCAT * Testcases for stackoverflow and nesting issue introduced by efe665c. Main failing ontology on dev is genepio with minimal-genepio as example. This causes stackoverflow which causes nesting-error for subsequent ontologies processed. * Recognise datatype leaf nodes to fix stackoverflow. * Changed check for leaf node to just check for any builtin XML data type. * Alignment of dev branch with stable branch. --------- Co-authored-by: James McLaughlin <james@mclgh.net> Co-authored-by: haider <haideriqbal1@hotmail.com> Co-authored-by: Haider Iqbal <haideri@ebi.ac.uk>
EBISPOT · Apr 10, 2024 · 3ce8a64 · 3ce8a64
1 parent 7e1b1d3
commit 3ce8a64
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diff --git a/dataload/json2neo/src/main/java/OntologyScanner.java b/dataload/json2neo/src/main/java/OntologyScanner.java
@@ -207,6 +207,8 @@ private static void visitValue(String predicate, Object value, Set<String> outPr
 
                 visitValue(predicate, mapValue.get("value"), outProps, outEdgeProps);
 
+            } else if(types.contains("datatype")) {
+
             } else {
 		throw new RuntimeException("???");
             }

diff --git a/dataload/json2solr/src/main/java/JSON2Solr.java b/dataload/json2solr/src/main/java/JSON2Solr.java
@@ -276,6 +276,8 @@ public static Object discardMetadata(Object obj) {
 		// (4) reification
                 return discardMetadata(dict.get("value"));
 
+	    } else if(types.contains("datatype")) {
+            return null;
 	    } else {
 		    throw new RuntimeException("???");
 	    }

diff --git a/dataload/rdf2json/src/main/java/uk/ac/ebi/rdf2json/OntologyGraph.java b/dataload/rdf2json/src/main/java/uk/ac/ebi/rdf2json/OntologyGraph.java
@@ -476,6 +476,9 @@ public void writePropertyValue(JsonWriter writer, PropertyValue value, Set<Strin
 
     }
 
+    private boolean isXMLBuiltinDatatype(String uri) {
+        return uri.startsWith("http://www.w3.org/2001/XMLSchema#");
+    }
     public void writeValue(JsonWriter writer, PropertyValue value) throws IOException {
         assert (value.axioms == null);
 
@@ -511,7 +514,14 @@ public void writeValue(JsonWriter writer, PropertyValue value) throws IOExceptio
                 writer.endObject();
                 break;
             case URI:
-                writer.value(((PropertyValueURI) value).getUri());
+                String uri = ((PropertyValueURI) value).getUri();
+                OntologyNode uriNode = nodes.get(uri);
+                if(uriNode != null && !isXMLBuiltinDatatype(uri) && uriNode.types.contains(OntologyNode.NodeType.DATATYPE)) {
+                    // special case for rdfs:Datatype; nest it as with a bnode instead of referencing
+                    writeNode(writer, uriNode, Set.of("datatype"));
+                } else {
+                    writer.value(uri);
+                }
                 break;
             case RELATED:
                 writer.beginObject();
@@ -694,6 +704,10 @@ public void handleType(OntologyNode subjNode, Node type) {
             case "http://www.w3.org/2002/07/owl#NegativePropertyAssertion":
                 subjNode.types.add(OntologyNode.NodeType.NEGATIVE_PROPERTY_ASSERTION);
                 break;
+
+            case "http://www.w3.org/2000/01/rdf-schema#Datatype":
+                subjNode.types.add(OntologyNode.NodeType.DATATYPE);
+                break;
         }
     }
 

diff --git a/dataload/rdf2json/src/main/java/uk/ac/ebi/rdf2json/OntologyNode.java b/dataload/rdf2json/src/main/java/uk/ac/ebi/rdf2json/OntologyNode.java
@@ -23,7 +23,8 @@ public enum NodeType {
         ALL_DISJOINT_CLASSES("allDisjointClasses"),
         ALL_DIFFERENT("allDifferent"),
         ALL_DISJOINT_PROPERTIES("allDisjointProperties"),
-        NEGATIVE_PROPERTY_ASSERTION("negativePropertyAssertion");
+        NEGATIVE_PROPERTY_ASSERTION("negativePropertyAssertion"),
+        DATATYPE("datatype");
 
         public final String name;
 

diff --git a/dataload/rdf2json/src/main/java/uk/ac/ebi/rdf2json/annotators/ShortFormAnnotator.java b/dataload/rdf2json/src/main/java/uk/ac/ebi/rdf2json/annotators/ShortFormAnnotator.java
@@ -20,7 +20,9 @@ public static void annotateShortForms(OntologyGraph graph) {
 		    OntologyNode c = graph.nodes.get(id);
 		    if (c.types.contains(OntologyNode.NodeType.CLASS) ||
 				c.types.contains(OntologyNode.NodeType.PROPERTY) ||
-				c.types.contains(OntologyNode.NodeType.INDIVIDUAL)) {
+				c.types.contains(OntologyNode.NodeType.INDIVIDUAL) ||
+				c.types.contains(OntologyNode.NodeType.DATATYPE)
+				) {
 
 			// skip bnodes
 			if(c.uri == null)

diff --git a/ebi_ontologies.json b/ebi_ontologies.json
@@ -1,5 +1,9 @@
 {
   "ontologies": [
+	  {
+		  "id": "dcat",
+		  "ontology_purl": "https://www.w3.org/ns/dcat.ttl"
+	  },
 	  {
 		  "id": "biolink",
 		  "ontology_purl": "https://github.com/biolink/biolink-model/raw/master/project/owl/biolink_model.owl.ttl",

diff --git a/frontend/src/components/ClassExpression.tsx b/frontend/src/components/ClassExpression.tsx
@@ -26,6 +26,20 @@ export default function ClassExpression({
 
   linkedEntities = linkedEntities.mergeWith(expr.linkedEntities)
 
+  const types = asArray(expr['type'])
+
+  if(types && types.indexOf('datatype') !== -1) {
+    // rdfs:Datatype
+    let equivClass = expr['http://www.w3.org/2002/07/owl#equivalentClass'];
+    if(equivClass) {
+      return <Fragment>
+        { expr['label'] && <span>{expr['label']} </span> }
+        <ClassExpression currentEntity={currentEntity}   ontologyId={ontologyId} entityType={'properties'} expr={equivClass} linkedEntities={linkedEntities} />
+        </Fragment>
+    }
+  }
+
+
   ///
   /// 1. owl:Class expressions
   ///
@@ -312,43 +326,6 @@ export default function ClassExpression({
       </span>
     );
   }
-
-  let minQualifiedCardinality = asArray(
-    expr["http://www.w3.org/2002/07/owl#minQualifiedCardinality"]
-  )[0];
-  if (minQualifiedCardinality) {
-    return (
-      <span>
-        <ClassExpression  ontologyId={ontologyId} currentEntity={currentEntity} entityType={'properties'} expr={onProperty} linkedEntities={linkedEntities} />
-        <span className="px-1 text-embl-purple-default italic">min</span>
-        <ClassExpression
-	currentEntity={currentEntity} 
-	 ontologyId={ontologyId} entityType={'classes'}
-          expr={minQualifiedCardinality}
-          linkedEntities={linkedEntities}
-        />
-      </span>
-    );
-  }
-
-  let maxQualifiedCardinality = asArray(
-    expr["http://www.w3.org/2002/07/owl#maxQualifiedCardinality"]
-  )[0];
-  if (maxQualifiedCardinality) {
-    return (
-      <span>
-        <ClassExpression  ontologyId={ontologyId} currentEntity={currentEntity} entityType={'properties'} expr={onProperty} linkedEntities={linkedEntities} />
-        <span className="px-1 text-embl-purple-default italic">max</span>
-        <ClassExpression
-	currentEntity={currentEntity} 
-	 ontologyId={ontologyId} entityType={'classes'}
-          expr={maxQualifiedCardinality}
-          linkedEntities={linkedEntities}
-        />
-      </span>
-    );
-  }
-
   let exactCardinality = asArray(
     expr["http://www.w3.org/2002/07/owl#cardinality"]
   )[0];
@@ -362,24 +339,6 @@ export default function ClassExpression({
     );
   }
 
-  let exactQualifiedCardinality = asArray(
-    expr["http://www.w3.org/2002/07/owl#qualifiedCardinality"]
-  )[0];
-  if (exactQualifiedCardinality) {
-    return (
-      <span>
-        <ClassExpression  ontologyId={ontologyId} currentEntity={currentEntity} entityType={'properties'} expr={onProperty} linkedEntities={linkedEntities} />
-        <span className="px-1 text-embl-purple-default italic">exactly</span>
-        <ClassExpression
-	 ontologyId={ontologyId} entityType={'classes'}
-	 currentEntity={currentEntity} 
-          expr={exactQualifiedCardinality}
-          linkedEntities={linkedEntities}
-        />
-      </span>
-    );
-  }
-
   let hasSelf = asArray(expr["http://www.w3.org/2002/07/owl#hasSelf"])[0];
   if (hasSelf) {
     return (
@@ -391,6 +350,89 @@ export default function ClassExpression({
   }
 
 
+  ///
+  /// 4. owl:Restriction qualified cardinalities (property and class)
+  ///
+  const onClass = expr["http://www.w3.org/2002/07/owl#onClass"];
+
+  if(onClass) {
+    let minQualifiedCardinality = asArray(
+      expr["http://www.w3.org/2002/07/owl#minQualifiedCardinality"]
+    )[0];
+    if (minQualifiedCardinality) {
+      return (
+        <span>
+          <ClassExpression  ontologyId={ontologyId} currentEntity={currentEntity} entityType={'properties'} expr={onProperty} linkedEntities={linkedEntities} />
+          <span className="px-1 text-embl-purple-default italic">min</span>
+          <ClassExpression
+    currentEntity={currentEntity} 
+    ontologyId={ontologyId} entityType={'classes'}
+            expr={minQualifiedCardinality}
+            linkedEntities={linkedEntities}
+          />
+          &nbsp;
+          <ClassExpression
+    currentEntity={currentEntity} 
+    ontologyId={ontologyId} entityType={'classes'}
+            expr={onClass}
+            linkedEntities={linkedEntities}
+          />
+        </span>
+      );
+    }
+
+    let maxQualifiedCardinality = asArray(
+      expr["http://www.w3.org/2002/07/owl#maxQualifiedCardinality"]
+    )[0];
+    if (maxQualifiedCardinality) {
+      return (
+        <span>
+          <ClassExpression  ontologyId={ontologyId} currentEntity={currentEntity} entityType={'properties'} expr={onProperty} linkedEntities={linkedEntities} />
+          <span className="px-1 text-embl-purple-default italic">max</span>
+          <ClassExpression
+    currentEntity={currentEntity} 
+    ontologyId={ontologyId} entityType={'classes'}
+            expr={maxQualifiedCardinality}
+            linkedEntities={linkedEntities}
+          />
+          &nbsp;
+          <ClassExpression
+    currentEntity={currentEntity} 
+    ontologyId={ontologyId} entityType={'classes'}
+            expr={onClass}
+            linkedEntities={linkedEntities}
+          />
+        </span>
+      );
+    }
+
+    let exactQualifiedCardinality = asArray(
+      expr["http://www.w3.org/2002/07/owl#qualifiedCardinality"]
+    )[0];
+    if (exactQualifiedCardinality) {
+      return (
+        <span>
+          <ClassExpression  ontologyId={ontologyId} currentEntity={currentEntity} entityType={'properties'} expr={onProperty} linkedEntities={linkedEntities} />
+          <span className="px-1 text-embl-purple-default italic">exactly</span>
+          <ClassExpression
+    ontologyId={ontologyId} entityType={'classes'}
+    currentEntity={currentEntity} 
+            expr={exactQualifiedCardinality}
+            linkedEntities={linkedEntities}
+          />
+          &nbsp;
+          <ClassExpression
+    currentEntity={currentEntity} 
+    ontologyId={ontologyId} entityType={'classes'}
+            expr={onClass}
+            linkedEntities={linkedEntities}
+          />
+        </span>
+      );
+    }
+  }
+
+
     return (
       <span className="text-embl-red-default italic">
         unknown class expression

diff --git a/frontend/src/components/EntityLink.tsx b/frontend/src/components/EntityLink.tsx
@@ -27,7 +27,7 @@ export default function EntityLink({
 
   // reference to self; just display label bc we are already on that page
   if (currentEntity && iri === currentEntity.getIri()) {
-    return <b>{currentEntity.getName()}</b>;
+    return <span>{currentEntity.getName()}</span>;
   }
 
   const label =

diff --git a/frontend/src/model/Class.ts b/frontend/src/model/Class.ts
@@ -23,6 +23,10 @@ export default class Class extends Entity {
 	return asArray(this.properties['http://www.w3.org/2002/07/owl#disjointWith'])
   }
 
+  getUnionOf() {
+    return asArray(this.properties['http://www.w3.org/2002/07/owl#unionOf'])
+  }
+
   getHasKey() {
     return asArray(this.properties['http://www.w3.org/2002/07/owl#hasKey'])
   }

diff --git a/frontend/src/pages/ontologies/entities/EntityPage.tsx b/frontend/src/pages/ontologies/entities/EntityPage.tsx
@@ -30,6 +30,7 @@ import DomainSection from "./entityPageSections/DomainSection";
 import EntityAnnotationsSection from "./entityPageSections/EntityAnnotationsSection";
 import EntityDescriptionSection from "./entityPageSections/EntityDescriptionSection";
 import EntityEquivalentsSection from "./entityPageSections/EntityEquivalentsSection";
+import UnionOfSection from "./entityPageSections/UnionOfSection";
 import EntityImagesSection from "./entityPageSections/EntityImagesSection";
 import EntityParentsSection from "./entityPageSections/EntityParentsSection";
 import EntityRelatedFromSection from "./entityPageSections/EntityRelatedFromSection";
@@ -462,6 +463,10 @@ export default function EntityPage({
                       entity={entity}
                       linkedEntities={linkedEntities}
                     />
+                    <UnionOfSection
+                        entity={entity}
+                        linkedEntities={linkedEntities}
+                    />
                     <PropertyInverseOfSection
                       entity={entity}
                       linkedEntities={linkedEntities}

diff --git a/frontend/src/pages/ontologies/entities/entityPageSections/UnionOfSection.tsx b/frontend/src/pages/ontologies/entities/entityPageSections/UnionOfSection.tsx
@@ -0,0 +1,83 @@
+import { Fragment } from "react";
+import { randomString } from "../../../../app/util";
+import ClassExpression from "../../../../components/ClassExpression";
+import EntityLink from "../../../../components/EntityLink";
+import Entity from "../../../../model/Entity";
+import Class from "../../../../model/Class";
+import LinkedEntities from "../../../../model/LinkedEntities";
+import Property from "../../../../model/Property";
+
+export default function UnionOfSection({
+  entity,
+  linkedEntities,
+}: {
+  entity: Entity;
+  linkedEntities: LinkedEntities;
+}) {
+  if (!(entity instanceof Class)) {
+    return <Fragment />;
+  }
+
+  let unionOfs = entity.getUnionOf();
+
+  if (!unionOfs || unionOfs.length === 0) {
+    return <Fragment />;
+  }
+
+  return (
+    <div>
+      <div className="font-bold">Union of</div>
+      {unionOfs.length === 1 ? (
+        <p>
+          {typeof unionOfs[0] === "object" &&
+          !Array.isArray(unionOfs[0]) ? (
+            <ClassExpression
+              ontologyId={entity.getOntologyId()}
+              currentEntity={entity}
+              expr={unionOfs[0]}
+              linkedEntities={linkedEntities}
+            />
+          ) : (
+            <EntityLink
+              ontologyId={entity.getOntologyId()}
+	          currentEntity={entity}
+              entityType={
+                entity.getType() === "property" ? "properties" : "classes"
+              }
+              iri={unionOfs[0]}
+              linkedEntities={linkedEntities}
+            />
+          )}
+        </p>
+      ) : (
+        <ul className="list-disc list-inside">
+          {unionOfs.map((disjointWith) => {
+            return (
+              <li key={randomString()}>
+                {typeof disjointWith === "object" &&
+                !Array.isArray(disjointWith) ? (
+                  <ClassExpression
+                    ontologyId={entity.getOntologyId()}
+                currentEntity={entity}
+                    expr={disjointWith}
+                    linkedEntities={linkedEntities}
+                  />
+                ) : (
+                  <EntityLink
+                    ontologyId={entity.getOntologyId()}
+		    currentEntity={entity}
+                    entityType={
+                      entity.getType() === "property" ? "properties" : "classes"
+                    }
+                    iri={disjointWith}
+                    linkedEntities={linkedEntities}
+                  />
+                )}
+              </li>
+            );
+          })}
+        </ul>
+      )}
+    </div>
+  );
+}
diff --git a/testcases/datatypes/nesting-issue/datatype-enumeration.json b/testcases/datatypes/nesting-issue/datatype-enumeration.json
@@ -0,0 +1,9 @@
+{
+  "ontologies": [
+    {
+      "id": "owl2primer-datatype-enumeration",
+      "preferredPrefix": "owl2primer-datatype-enumeration",
+      "ontology_purl": "./testcases/owl2-primer/datatype-enumeration.owl"
+    }
+  ]
+}