Coerce uncompressible URIs in seeAlso relations to literals

src/pyobo/reader.py

@@ -1146,17 +1146,24 @@ def _handle_prop(
         obj_reference = _parse_identifier(
             value_type, strict=strict, ontology_prefix=ontology_prefix, node=node
         )
-        if obj_reference is None:
-            if not UNHANDLED_PROP_OBJECTS[prop_reference, value_type]:
-                logger.warning(
-                    "[%s - %s] could not parse object: %s",
-                    node.curie,
-                    prop_reference.curie,
-                    value_type,
-                )
-            UNHANDLED_PROP_OBJECTS[prop_reference, value_type] += 1
-            return None
-        return Annotation(prop_reference, obj_reference)
+        if obj_reference is not None:
+            return Annotation(prop_reference, obj_reference)
+
+        # TODO if the predicate is part of a sacred class (e.g., rdfs:seeAlso)
+        #  and the value_type looks like a URL, store it
+        if prop_reference in {v.see_also} and value_type.startswith("http"):
+            return Annotation(prop_reference, OBOLiteral.uri(value_type))
+
+        if not UNHANDLED_PROP_OBJECTS[prop_reference, value_type]:
+            logger.warning(
+                "[%s - %s] could not parse object: %s",
+                node.curie,
+                prop_reference.curie,
+                value_type,
+            )
+        UNHANDLED_PROP_OBJECTS[prop_reference, value_type] += 1
+        return None
+
 
     try:
         value, datatype = value_type.rsplit(" ", 1)  # second entry is the value type

tests/test_obo_reader/test_reader.py

@@ -954,6 +954,25 @@ def test_12_property_literal_object(self) -> None:
         self.assertIn(see_also.reference, term.properties)
         self.assertEqual("hgnc:1234", term.get_property(see_also))
 
+    def test_12_property_convert_uri(self) -> None:
+        """Test that unparsable URIs for seeAlso are stored as literals."""
+        ontology = from_str("""\
+            ontology: chebi
+
+            [Term]
+            id: CHEBI:1234
+            property_value: rdfs:seeAlso https://example.org
+        """)
+        term = self.get_only_term(ontology)
+        self.assertEqual(1, len(list(term.properties)))
+        self.assertIn(see_also.reference, term.properties)
+        properties = term.properties[see_also.reference]
+        self.assertEqual(1, len(properties))
+        prop = properties[0]
+        self.assertIsInstance(prop, OBOLiteral)
+        self.assertEqual("https://example.org", prop.value)
+        self.assertEqual(v.xsd_uri, prop.datatype)
+
     def test_13_parent(self) -> None:
         """Test parsing out a parent."""
         ontology = from_str("""\