Adding back the placeholders for object, collections and datasets

Changed OWL.Class to OWL.Thing Added descriptions for relationships
BAMresearch · Jan 30, 2025 · 254f2eb · 254f2eb
1 parent a8dcec7
commit 254f2eb
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Showing 2 changed files with 44 additions and 19 deletions.
diff --git a/bam_masterdata/cli/entities_to_rdf.py b/bam_masterdata/cli/entities_to_rdf.py
@@ -80,30 +80,50 @@ def rdf_graph_init(g: "Graph") -> None:
     bam_props_uri = {
         BAM["hasMandatoryProperty"]: [
             (RDF.type, OWL.ObjectProperty),
-            (RDFS.domain, BAM.ObjectType),
+            # (RDFS.domain, OWL.Class),
             (RDFS.range, BAM.PropertyType),
             (RDFS.label, Literal("hasMandatoryProperty", lang="en")),
+            (
+                RDFS.comment,
+                Literal(
+                    "The property must be mandatorily filled when creating the object in openBIS.",
+                    lang="en",
+                ),
+            ),
         ],
         BAM["hasOptionalProperty"]: [
             (RDF.type, OWL.ObjectProperty),
-            (RDFS.domain, BAM.ObjectType),
+            # (RDFS.domain, OWL.Class),
             (RDFS.range, BAM.PropertyType),
             (RDFS.label, Literal("hasOptionalProperty", lang="en")),
+            (
+                RDFS.comment,
+                Literal(
+                    "The property is optionally filled when creating the object in openBIS.",
+                    lang="en",
+                ),
+            ),
         ],
         BAM["referenceTo"]: [
             (RDF.type, OWL.ObjectProperty),
             (RDFS.domain, BAM.PropertyType),  # Restricting domain to PropertyType
-            (RDFS.range, BAM.ObjectType),  # Explicitly setting range to ObjectType
+            # (RDFS.range, OWL.Class),  # Explicitly setting range to ObjectType
             (RDFS.label, Literal("referenceTo", lang="en")),
+            (
+                RDFS.comment,
+                Literal(
+                    "The property is referencing an object existing in openBIS.",
+                    lang="en",
+                ),
+            ),
         ],
     }
     for prop_uri, obj_properties in bam_props_uri.items():
         for prop in obj_properties:  # type: ignore
             g.add((prop_uri, prop[0], prop[1]))  # type: ignore
 
-    # Adding base PropertyType object as a placeholder for all properties
-    prop_uri = BAM.PropertyType
-    g.add((prop_uri, RDF.type, OWL.Class))
+    # Adding base PropertyType and other objects as placeholders
+    # ! add only PropertyType
     prop_type_description = """A conceptual placeholder used to define and organize properties as first-class entities.
         PropertyType is used to place properties and define their metadata, separating properties from the
         entities they describe.
@@ -112,7 +132,12 @@ def rdf_graph_init(g: "Graph") -> None:
         - PropertyType can align with `BFO:Quality` for inherent attributes.
         - PropertyType can represent `BFO:Role` if properties serve functional purposes.
         - PropertyType can be treated as a `prov:Entity` when properties participate in provenance relationships."""
-    g.add((prop_uri, RDFS.comment, Literal(prop_type_description, lang="en")))
+    for entity in ["PropertyType", "ObjectType", "CollectionType", "DatasetType"]:
+        entity_uri = BAM[entity]
+        g.add((entity_uri, RDF.type, OWL.Thing))
+        g.add((entity_uri, RDFS.label, Literal(entity, lang="en")))
+        if entity == "PropertyType":
+            g.add((entity_uri, RDFS.comment, Literal(prop_type_description, lang="en")))
 
 
 def entities_to_rdf(
@@ -136,7 +161,7 @@ def entities_to_rdf(
             prop_uri = BAM[obj.id]
 
             # Define the property as an OWL class inheriting from PropertyType
-            graph.add((prop_uri, RDF.type, OWL.Class))
+            graph.add((prop_uri, RDF.type, OWL.Thing))
             graph.add((prop_uri, RDFS.subClassOf, BAM.PropertyType))
 
             # Add attributes like id, code, description in English and Deutsch, property_label, data_type

diff --git a/bam_masterdata/metadata/entities.py b/bam_masterdata/metadata/entities.py
@@ -96,20 +96,20 @@ def to_rdf(self, namespace: "Namespace", graph: "Graph") -> None:
         entity_uri = namespace[self.defs.id]
 
         # Define the entity as an OWL class inheriting from the specific namespace type
-        graph.add((entity_uri, RDF.type, OWL.Class))
+        graph.add((entity_uri, RDF.type, OWL.Thing))
         parent_classes = self.__class__.__bases__
         for parent_class in parent_classes:
             if issubclass(parent_class, BaseEntity) and parent_class != BaseEntity:
-                if parent_class.__name__ in [
-                    "ObjectType",
-                    "CollectionType",
-                    "DatasetType",
-                ]:
-                    # ! add here logic of subClassOf connecting with PROV-O or BFO
-                    # ! maybe via classes instead of ObjectType/CollectionType/DatasetType?
-                    # ! Example:
-                    # !     graph.add((entity_uri, RDFS.subClassOf, "http://www.w3.org/ns/prov#Entity"))
-                    continue
+                # if parent_class.__name__ in [
+                #     "ObjectType",
+                #     "CollectionType",
+                #     "DatasetType",
+                # ]:
+                #     # ! add here logic of subClassOf connecting with PROV-O or BFO
+                #     # ! maybe via classes instead of ObjectType/CollectionType/DatasetType?
+                #     # ! Example:
+                #     # !     graph.add((entity_uri, RDFS.subClassOf, "http://www.w3.org/ns/prov#Entity"))
+                #     continue
                 parent_uri = namespace[parent_class.__name__]
                 graph.add((entity_uri, RDFS.subClassOf, parent_uri))