Update

src/pyobo/reader.py

@@ -277,6 +277,8 @@ def from_obonet(
         _data_version=data_version,
         _root_terms=root_terms,
         terms=terms,
+        # TODO add subsetdefs
+        # TODO add extra properties
     )
 
 

src/pyobo/struct/reference.py

@@ -246,6 +246,11 @@ class OBOLiteral(NamedTuple):
     value: str
     datatype: Reference
 
+    @classmethod
+    def string(cls, value: str) -> OBOLiteral:
+        """Get a string literal."""
+        return cls(value, Reference(prefix="xsd", identifier="string"))
+
 
 AxiomsHint = Mapping[
     tuple[Reference, Reference | OBOLiteral], Sequence[tuple[Reference, Reference | OBOLiteral]]

src/pyobo/struct/struct.py

@@ -934,6 +934,8 @@ class Obo:
 
     subsetdefs: ClassVar[list[tuple[Reference, str]] | None] = None
 
+    property_values: ClassVar[list[tuple[Reference, Reference | OBOLiteral]] | None] = None
+
     def __post_init__(self):
         """Run post-init checks."""
         if self.ontology is None:
@@ -1135,7 +1137,7 @@ def _iterate_properties(self) -> Iterable[str]:
         for predicate, value in self._iterate_property_pairs():
             match value:
                 case OBOLiteral():
-                    end = f"{obo_escape_slim(value.value)} {reference_escape(value.datatype, ontology_prefix=self.ontology)}"
+                    end = f"\"{obo_escape_slim(value.value)}\" {reference_escape(value.datatype, ontology_prefix=self.ontology)}"
                 case Reference():
                     end = reference_escape(value, ontology_prefix=self.ontology)
             yield f"property_value: {reference_escape(predicate, ontology_prefix=self.ontology)} {end}"
@@ -1168,6 +1170,10 @@ def _iterate_property_pairs(self) -> Iterable[tuple[Reference, Reference | OBOLi
         for root_term in self.root_terms or []:
             yield has_ontology_root_term.reference, root_term
 
+        # Extras
+        if self.property_values:
+            yield from self.property_values
+
     def _index_typedefs(self) -> Mapping[ReferenceTuple, TypeDef]:
         return ChainMap(
             {t.pair: t for t in self.typedefs or []},
@@ -2012,6 +2018,7 @@ def make_ad_hoc_ontology(
     _idspaces: Mapping[str, str] | None = None,
     _root_terms: list[Reference] | None = None,
     _subsetdefs: list[tuple[Reference, str]] | None = None,
+    _property_values: list[tuple[Reference, Reference | OBOLiteral]] | None = None,
     *,
     terms: list[Term] | None = None,
 ) -> Obo:
@@ -2029,6 +2036,7 @@ class AdHocOntology(Obo):
         idspaces = _idspaces
         root_terms = _root_terms
         subsetdefs = _subsetdefs
+        property_values = _property_values
 
         def __post_init__(self):
             self.date = _date

tests/test_struct_obo.py

@@ -5,7 +5,9 @@
 from textwrap import dedent
 
 from pyobo import default_reference
+from pyobo.struct.reference import OBOLiteral
 from pyobo.struct.struct import Obo, make_ad_hoc_ontology
+from pyobo.struct.typedef import has_license
 
 
 class TestOBOHeader(unittest.TestCase):
@@ -148,3 +150,36 @@ def test_18_properties(self) -> None:
             """,
             ontology,
         )
+
+    def test_18_properties_bioregistry(self) -> None:
+        """Test auto-populating."""
+        ontology = make_ad_hoc_ontology(
+            _ontology="go",
+        )
+        self.assert_obo_lines(
+            """\
+            format-version: 1.2
+            ontology: go
+            property_value: dcterms:title "Gene Ontology" xsd:string
+            property_value: dcterms:license "CC-BY-4.0" xsd:string
+            property_value: dcterms:description "The Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism." xsd:string
+            """,
+            ontology,
+        )
+
+    def test_18_properties_external(self) -> None:
+        """Test properties."""
+        ontology = make_ad_hoc_ontology(
+            _ontology="xxx",
+            _property_values=[
+                (has_license.reference, OBOLiteral.string("CC0")),
+            ],
+        )
+        self.assert_obo_lines(
+            """\
+            format-version: 1.2
+            ontology: xxx
+            property_value: dcterms:license "CC0" xsd:string
+            """,
+            ontology,
+        )