Simplify construction of synonyms in PyOBO sources (#247)

src/pyobo/obographs.py

@@ -91,12 +91,11 @@ def _get_class_node(term: Term) -> Node:
         )
         for xref, xref_type in zip(term.xrefs, term.xref_types, strict=False)
     ]
-    default_st = Reference(prefix="oboInOwl", identifier="SynonymType")
     synonyms = [
         Synonym.from_parsed(
             name=synonym.name,
             predicate=OIO_TO_REFERENCE[OBO_SYNONYM_TO_OIO[synonym.specificity]],
-            synonym_type=_rewire(synonym.type.reference) if synonym.type else default_st,
+            synonym_type=_rewire(synonym.type) if synonym.type else None,
             references=[_rewire(x) for x in synonym.provenance],
         )
         for synonym in term.synonyms

src/pyobo/sources/dictybase_gene.py

@@ -9,7 +9,7 @@
 import pandas as pd
 from tqdm.auto import tqdm
 
-from pyobo.struct import Obo, Synonym, Term, from_species, has_gene_product
+from pyobo.struct import Obo, Term, from_species, has_gene_product
 from pyobo.utils.path import ensure_df
 
 __all__ = [
@@ -67,7 +67,7 @@ def get_terms(force: bool = False) -> Iterable[Term]:
                 term.append_synonym(synonym.strip())
         if synonyms and pd.notna(synonyms):
             for synonym in synonyms.split(","):
-                term.append_synonym(Synonym(synonym.strip()))
+                term.append_synonym(synonym.strip())
         # for uniprot_id in uniprot_mappings.get(identifier, []):
         #     if not uniprot_id or pd.isna(uniprot_id) or uniprot_id in {"unknown", "pseudogene"}:
         #         continue

src/pyobo/sources/hgnc.py

@@ -15,7 +15,6 @@
 from pyobo.struct import (
     Obo,
     Reference,
-    Synonym,
     SynonymTypeDef,
     Term,
     TypeDef,
@@ -412,15 +411,15 @@ def get_terms(version: str | None = None, force: bool = False) -> Iterable[Term]
             )
 
         for alias_symbol in entry.pop("alias_symbol", []):
-            term.append_synonym(Synonym(name=alias_symbol, type=alias_symbol_type))
+            term.append_synonym(alias_symbol, type=alias_symbol_type)
         for alias_name in entry.pop("alias_name", []):
-            term.append_synonym(Synonym(name=alias_name, type=alias_name_type))
+            term.append_synonym(alias_name, type=alias_name_type)
         for previous_symbol in itt.chain(
             entry.pop("previous_symbol", []), entry.pop("prev_symbol", [])
         ):
-            term.append_synonym(Synonym(name=previous_symbol, type=previous_symbol_type))
+            term.append_synonym(previous_symbol, type=previous_symbol_type)
         for previous_name in entry.pop("prev_name", []):
-            term.append_synonym(Synonym(name=previous_name, type=previous_name_type))
+            term.append_synonym(previous_name, type=previous_name_type)
 
         for prop, td in [("location", HAS_LOCATION)]:
             value = entry.pop(prop, None)

src/pyobo/sources/hgncgenefamily.py

@@ -8,7 +8,6 @@
 from ..struct import (
     Obo,
     Reference,
-    Synonym,
     SynonymTypeDef,
     Term,
     enables,
@@ -104,7 +103,7 @@ def _get_terms_helper(force: bool = False) -> Iterable[Term]:
             go_id = desc_go[len("http://purl.uniprot.org/go/") :]
             term.append_relationship(enables, Reference(prefix="GO", identifier=go_id))
         if symbol and pd.notna(symbol):
-            term.append_synonym(Synonym(name=symbol, type=symbol_type))
+            term.append_synonym(symbol, type=symbol_type)
         term.set_species(identifier="9606", name="Homo sapiens")
         yield term
 

src/pyobo/sources/mgi.py

@@ -12,7 +12,6 @@
 from ..struct import (
     Obo,
     Reference,
-    Synonym,
     Term,
     from_species,
     has_gene_product,
@@ -158,7 +157,7 @@ def get_terms(force: bool = False) -> Iterable[Term]:
         )
         if identifier in mgi_to_synonyms:
             for synonym in mgi_to_synonyms[identifier]:
-                term.append_synonym(Synonym(name=synonym))
+                term.append_synonym(synonym)
         if identifier in mgi_to_entrez_id:
             term.append_exact_match(
                 Reference(prefix="ncbigene", identifier=mgi_to_entrez_id[identifier])

src/pyobo/sources/npass.py

@@ -6,7 +6,7 @@
 import pandas as pd
 from tqdm.auto import tqdm
 
-from ..struct import Obo, Reference, Synonym, Term
+from ..struct import Obo, Reference, Term
 from ..utils.path import ensure_df
 
 __all__ = [
@@ -82,7 +82,7 @@ def iter_terms(version: str, force: bool = False) -> Iterable[Term]:
 
         for synonym in [iupac]:
             if pd.notna(synonym):
-                term.append_synonym(Synonym(name=synonym))
+                term.append_synonym(synonym)
 
         yield term
 

src/pyobo/sources/rgd.py

@@ -9,7 +9,6 @@
 from pyobo.struct import (
     Obo,
     Reference,
-    Synonym,
     SynonymTypeDef,
     Term,
     default_reference,
@@ -124,11 +123,11 @@ def get_terms(force: bool = False, version: str | None = None) -> Iterable[Term]
         old_names = row["OLD_NAME"]
         if old_names and pd.notna(old_names):
             for old_name in old_names.split(";"):
-                term.append_synonym(Synonym(name=old_name, type=old_name_type))
+                term.append_synonym(old_name, type=old_name_type)
         old_symbols = row["OLD_SYMBOL"]
         if old_symbols and pd.notna(old_symbols):
             for old_symbol in old_symbols.split(";"):
-                term.append_synonym(Synonym(name=old_symbol, type=old_symbol_type))
+                term.append_synonym(old_symbol, type=old_symbol_type)
         for prefix, key in namespace_to_column:
             xref_ids = str(row[key])
             if xref_ids and pd.notna(xref_ids):