Use None for default specificity (#275)

biopragmatics · Jan 5, 2025 · 16e27f8 · 16e27f8
1 parent 57001c5
commit 16e27f8
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Showing 6 changed files with 13 additions and 17 deletions.
diff --git a/src/pyobo/obographs.py b/src/pyobo/obographs.py
@@ -94,7 +94,7 @@ def _get_class_node(term: Term) -> Node:
     synonyms = [
         Synonym.from_parsed(
             name=synonym.name,
-            predicate=OIO_TO_REFERENCE[OBO_SYNONYM_TO_OIO[synonym.specificity]],
+            predicate=OIO_TO_REFERENCE[OBO_SYNONYM_TO_OIO[synonym.specificity or "EXACT"]],
             synonym_type=_rewire(synonym.type) if synonym.type else None,
             references=[_rewire(x) for x in synonym.provenance],
         )

diff --git a/src/pyobo/reader.py b/src/pyobo/reader.py
@@ -539,7 +539,7 @@ def _extract_synonym(
 
     return Synonym(
         name=name,
-        specificity=specificity or "EXACT",
+        specificity=specificity,
         type=synonym_typedef.reference if synonym_typedef else DEFAULT_SYNONYM_TYPE.reference,
         provenance=provenance,
         annotations=annotations,

diff --git a/src/pyobo/sources/conso.py b/src/pyobo/sources/conso.py
@@ -44,17 +44,13 @@ def iter_terms() -> Iterable[Term]:
     synonyms_df["reference"] = synonyms_df["reference"].map(
         lambda s: [Reference.from_curie_or_uri(s)] if pd.notna(s) and s != "?" else [],
     )
-    synonyms_df["specificity"] = synonyms_df["specificity"].map(
-        lambda s: "EXACT" if pd.isna(s) or s == "?" else s
-    )
-
     synonyms = multidict(
         (
             identifier,
             Synonym(
                 name=synonym,
                 provenance=provenance,
-                specificity=specificity,
+                specificity=None if pd.isna(specificity) or specificity == "?" else specificity,
             ),
         )
         for identifier, synonym, provenance, specificity in synonyms_df.values

diff --git a/src/pyobo/struct/struct.py b/src/pyobo/struct/struct.py
@@ -111,7 +111,7 @@ class Synonym:
     name: str
 
     #: The specificity of the synonym
-    specificity: SynonymSpecificity = "EXACT"
+    specificity: SynonymSpecificity | None = None
 
     #: The type of synonym. Must be defined in OBO document!
     type: Reference = field(
@@ -129,7 +129,7 @@ def __lt__(self, other: Synonym) -> bool:
         return self._sort_key() < other._sort_key()
 
     def _sort_key(self) -> tuple[str, str, Reference]:
-        return self.name, self.specificity, self.type
+        return self.name, self.specificity or "EXACT", self.type
 
     def to_obo(
         self,
@@ -149,7 +149,7 @@ def _fp(
         _synonym_typedef_warn(ontology_prefix, self.type, synonym_typedefs)
         # TODO inherit specificity from typedef?
         # TODO validation of specificity against typedef
-        x = f'"{self._escape(self.name)}" {self.specificity}'
+        x = f'"{self._escape(self.name)}" {self.specificity or "EXACT"}'
         if self.type and self.type.pair != DEFAULT_SYNONYM_TYPE.pair:
             x = f"{x} {reference_escape(self.type, ontology_prefix=ontology_prefix)}"
         return f"{x} [{comma_separate_references(self.provenance)}]"
@@ -367,7 +367,7 @@ def append_synonym(
             synonym = Synonym(
                 synonym,
                 type=type,
-                specificity=specificity or "EXACT",
+                specificity=specificity,
                 provenance=provenance or [],
             )
         self.synonyms.append(synonym)

diff --git a/tests/test_get.py b/tests/test_get.py
@@ -138,13 +138,13 @@ def test_extract_synonym(self):
             (
                 Synonym(
                     name="LTEC I",
-                    specificity="EXACT",
+                    specificity=None,
                     provenance=[Reference(prefix="orphanet", identifier="93938")],
                 ),
                 '"LTEC I" [Orphanet:93938]',
             ),
             (
-                Synonym(name="LTEC I", specificity="EXACT"),
+                Synonym(name="LTEC I", specificity=None),
                 '"LTEC I" []',
             ),
             (
@@ -156,11 +156,11 @@ def test_extract_synonym(self):
                 '"HAdV-A" BROAD omo:0003012 []',
             ),
             (
-                Synonym(name="HAdV-A", specificity="EXACT", type=acronym.reference),
+                Synonym(name="HAdV-A", specificity=None, type=acronym.reference),
                 '"HAdV-A" OMO:0003012 []',
             ),
             (
-                Synonym(name="HAdV-A", specificity="EXACT", type=acronym.reference),
+                Synonym(name="HAdV-A", specificity=None, type=acronym.reference),
                 '"HAdV-A" omo:0003012 []',
             ),
         ]:

diff --git a/tests/test_reader.py b/tests/test_reader.py
@@ -608,7 +608,7 @@ def test_synonym_minimal(self) -> None:
         self.assertEqual(1, len(term.synonyms))
         synonym = term.synonyms[0]
         self.assertEqual("LTEC I", synonym.name)
-        self.assertEqual("EXACT", synonym.specificity)
+        self.assertIsNone(synonym.specificity)
         self.assertEqual(DEFAULT_SYNONYM_TYPE.reference, synonym.type)
         self.assertEqual([], synonym.provenance)
 
@@ -658,7 +658,7 @@ def test_synonym_with_type(self) -> None:
         self.assertEqual(1, len(term.synonyms))
         synonym = term.synonyms[0]
         self.assertEqual("LTEC I", synonym.name)
-        self.assertEqual("EXACT", synonym.specificity)
+        self.assertIsNone(synonym.specificity)
         self.assertEqual(Reference(prefix="omo", identifier="1234567"), synonym.type)
         self.assertEqual([], synonym.provenance)