Clean up annotations typing

src/pyobo/reader_utils.py

@@ -12,6 +12,7 @@
 
 from pyobo.struct.reference import _parse_identifier
 from pyobo.struct.struct import Reference, SynonymTypeDef, _synonym_typedef_warn
+from pyobo.struct.struct_utils import Annotation
 
 logger = logging.getLogger(__name__)
 
@@ -115,7 +116,5 @@ def _chomp_references(
     return references, rest
 
 
-def _chomp_axioms(
-    s: str, *, strict: bool = True, node: Reference
-) -> list[tuple[Reference, Reference]]:
+def _chomp_axioms(s: str, *, strict: bool = True, node: Reference) -> list[Annotation]:
     return []

src/pyobo/struct/struct.py

@@ -113,7 +113,7 @@ class Synonym:
     provenance: list[Reference] = field(default_factory=list)
 
     #: Extra annotations
-    annotations: list[tuple[Reference, Reference]] = field(default_factory=list)
+    annotations: list[Annotation] = field(default_factory=list)
 
     def __lt__(self, other: Synonym) -> bool:
         """Sort lexically by name."""
@@ -405,11 +405,7 @@ def iterate_obo_lines(
         if emit_annotation_properties:
             yield from self._iterate_obo_properties(
                 ontology_prefix=ontology_prefix,
-                skip_predicates=[
-                    v.term_replaced_by,
-                    v.see_also,
-                    v.alternative_term,
-                ],
+                skip_predicates=v.SKIP_PROPERTY_PREDICATES,
                 typedefs=typedefs,
             )
         # 13
@@ -1848,11 +1844,7 @@ def iterate_obo_lines(
         # 11
         yield from self._iterate_obo_properties(
             ontology_prefix=ontology_prefix,
-            skip_predicates={
-                v.term_replaced_by,
-                v.see_also,
-                v.alternative_term,
-            },
+            skip_predicates=v.SKIP_PROPERTY_PREDICATES,
             typedefs=typedefs,
         )
         # 12

src/pyobo/struct/struct_utils.py

@@ -331,6 +331,10 @@ def annotate_object(
         self._annotate_axioms(typedef, value, axioms)
         return self
 
+    def get_see_also(self) -> list[Reference]:
+        """Get all see also objects."""
+        return self.get_property_objects(v.see_also)
+
     def get_replaced_by(self) -> list[Reference]:
         """Get all replaced by."""
         return self.get_property_objects(v.term_replaced_by)

src/pyobo/struct/vocabulary.py

@@ -14,7 +14,6 @@
     "mapping_has_justification",
 ]
 
-
 RO_PREFIX = "RO"
 BFO_PREFIX = "BFO"
 IAO_PREFIX = "IAO"
@@ -53,7 +52,6 @@ def _c(c: curies.NamedReference) -> Reference:
 see_also = Reference(prefix="rdfs", identifier="seeAlso", name="see also")
 comment = Reference(prefix="rdfs", identifier="comment", name="comment")
 
-
 from_species = Reference(prefix=RO_PREFIX, identifier="0002162", name="in taxon")
 species_specific = Reference(prefix="debio", identifier="0000007", name="species specific")
 has_left_to_right_reaction = Reference(
@@ -96,3 +94,11 @@ def _c(c: curies.NamedReference) -> Reference:
     alternative_term,
     term_replaced_by,
 )
+
+#: These are predicates that have their own dedicated fields
+#: in OBO and FunOWL output
+SKIP_PROPERTY_PREDICATES = [
+    term_replaced_by,
+    see_also,
+    alternative_term,
+]