Add append contributor shortcut

src/pyobo/sources/geonames/utils.py

@@ -8,8 +8,7 @@
 from tqdm import tqdm
 
 from pyobo import Reference, Term, TypeDef, default_reference
-from pyobo.struct.struct import CHARLIE_TERM, HUMAN_TERM
-from pyobo.struct.vocabulary import has_contributor
+from pyobo.struct.struct import CHARLIE_TERM, HUMAN_TERM, PYOBO_INJECTED
 from pyobo.utils.path import ensure_df
 
 PREFIX = "geonames"
@@ -108,8 +107,8 @@ def get_feature_terms(
         yield (
             Term(reference=cat)
             .append_parent(FEATURE_TERM)
-            .annotate_object(has_contributor, CHARLIE_TERM)
-            .append_comment("injected by PyOBO source")
+            .append_contributor(CHARLIE_TERM)
+            .append_comment(PYOBO_INJECTED)
         )
     if features is None:
         features = get_features(force=force)

src/pyobo/sources/ncbi/ncbi_gc.py

@@ -6,7 +6,7 @@
 from collections.abc import Iterable
 
 from pyobo import default_reference
-from pyobo.struct import CHARLIE_TERM, HUMAN_TERM, Obo, Reference, Term, TypeDef
+from pyobo.struct import CHARLIE_TERM, HUMAN_TERM, PYOBO_INJECTED, Obo, Reference, Term, TypeDef
 from pyobo.struct.typedef import comment, has_contributor, see_also, term_replaced_by
 from pyobo.utils.path import ensure_path
 
@@ -29,7 +29,7 @@
     definition="Connects a taxonomy term to a genetic code translation table",
     domain=NCBITAXON_ROOT,
     range=GC_ROOT,
-).annotate_object(has_contributor, CHARLIE_TERM)
+).append_contributor(CHARLIE_TERM)
 
 NUCLEAR_GENETIC_CODE = default_reference(
     prefix=PREFIX, identifier="nuclear-genetic-code", name="nuclear genetic code translation table"
@@ -120,15 +120,15 @@ def get_terms() -> Iterable[Term]:
             definition="A table for translating codons into amino acids. This can change for "
             "different taxa, or be different in different organelles that include genetic information.",
         )
-        .annotate_object(has_contributor, CHARLIE_TERM)
-        .append_comment("injected by PyOBO")
+        .append_contributor(CHARLIE_TERM)
+        .append_comment(PYOBO_INJECTED)
     )
 
     for reference in CATEGORY_TO_TABLES:
         term = Term(reference=reference)
         term.append_parent(GC_ROOT)
-        term.annotate_object(has_contributor, CHARLIE_TERM)
-        term.append_comment("injected by PyOBO")
+        term.append_contributor(CHARLIE_TERM)
+        term.append_comment(PYOBO_INJECTED)
         if substructure := CATEGORY_TO_CELLULAR_COMPONENT.get(reference):
             term.append_see_also(substructure)
         yield term

src/pyobo/sources/nlm/utils.py

@@ -6,8 +6,8 @@
 from tqdm import tqdm
 
 from pyobo import Reference, Term, TypeDef, default_reference, ensure_path
-from pyobo.struct.struct import CHARLIE_TERM
-from pyobo.struct.typedef import has_contributor, has_end_date, has_start_date
+from pyobo.struct.struct import CHARLIE_TERM, PYOBO_INJECTED
+from pyobo.struct.typedef import has_end_date, has_start_date
 from pyobo.utils.path import ensure_df
 
 PREFIX_CATALOG = "nlm"
@@ -29,16 +29,16 @@
     .append_exact_match(Reference(prefix="MI", identifier="0885"))
     .append_exact_match(Reference(prefix="bibo", identifier="Journal"))
     .append_exact_match(Reference(prefix="uniprot.core", identifier="Journal"))
-    .annotate_object(has_contributor, CHARLIE_TERM)
-    .append_comment("injected by PyOBO source")
+    .append_contributor(CHARLIE_TERM)
+    .append_comment(PYOBO_INJECTED)
 )
 PUBLISHER_TERM = (
     Term(reference=default_reference(PREFIX_CATALOG, "publisher", name="publisher"))
     .append_exact_match(Reference(prefix="biolink", identifier="publisher"))
     .append_exact_match(Reference(prefix="schema", identifier="publisher"))
     .append_exact_match(Reference(prefix="uniprot.core", identifier="publisher"))
-    .annotate_object(has_contributor, CHARLIE_TERM)
-    .append_comment("injected by PyOBO source")
+    .append_contributor(CHARLIE_TERM)
+    .append_comment(PYOBO_INJECTED)
 )
 
 

src/pyobo/sources/signor/signor_complexes.py

@@ -7,7 +7,7 @@
 from pyobo import Obo, Reference, Term, default_reference
 from pyobo.sources.signor.download import DownloadKey, get_signor_df
 from pyobo.struct import CHARLIE_TERM, HUMAN_TERM, PYOBO_INJECTED
-from pyobo.struct.typedef import exact_match, has_component, has_contributor, has_member
+from pyobo.struct.typedef import exact_match, has_component, has_member
 
 __all__ = [
     "SignorGetter",
@@ -17,22 +17,22 @@
 
 PROTEIN_FAMILY = (
     Term(reference=default_reference(PREFIX, "protein-family"))
-    .annotate_object(has_contributor, CHARLIE_TERM)
+    .append_contributor(CHARLIE_TERM)
     .append_comment(PYOBO_INJECTED)
 )
 PROTEIN_COMPLEX = (
     Term(reference=default_reference(PREFIX, "protein-complex"))
-    .annotate_object(has_contributor, CHARLIE_TERM)
+    .append_contributor(CHARLIE_TERM)
     .append_comment(PYOBO_INJECTED)
 )
 PHENOTYPE = (
     Term(reference=default_reference(PREFIX, "phenotype"))
-    .annotate_object(has_contributor, CHARLIE_TERM)
+    .append_contributor(CHARLIE_TERM)
     .append_comment(PYOBO_INJECTED)
 )
 STIMULUS = (
     Term(reference=default_reference(PREFIX, "stimulus"))
-    .annotate_object(has_contributor, CHARLIE_TERM)
+    .append_contributor(CHARLIE_TERM)
     .append_comment(PYOBO_INJECTED)
 )
 ROOT_TERMS = (PROTEIN_FAMILY, PROTEIN_COMPLEX, PHENOTYPE, STIMULUS)

src/pyobo/struct/struct_utils.py

@@ -387,6 +387,10 @@ def annotate_object(
         self._extend_annotations(typedef, value, annotations)
         return self
 
+    def append_contributor(self, reference: ReferenceHint) -> Self:
+        """Append contributor."""
+        return self.annotate_object(v.has_contributor, reference)
+
     def get_see_also(self) -> list[Reference]:
         """Get all see also objects."""
         return self.get_property_objects(v.see_also)