Rename scope to predicate

README.md

@@ -62,14 +62,14 @@ columns:
 2. `curie` the compact uniform resource identifier (CURIE) for a biomedical
    entity or concept, standardized using the Bioregistry
 3. `name` the standard name for the concept
-4. `scope` the predicate which encodes the synonym scope, written as a CURIE
-   from the [OBO in OWL (`oio`)](https://bioregistry.io/oio) controlled
-   vocabulary, i.e., one of:
+4. `predicate` the predicate which encodes the synonym scope, written as a CURIE
+   from the [OBO in OWL (`oboInOWL`)](https://bioregistry.io/oio) or RDFS
+   controlled vocabularies, e.g., one of:
+   - `rdfs:label`
    - `oboInOwl:hasExactSynonym`
    - `oboInOwl:hasNarrowSynonym` (i.e., the synonym represents a narrower term)
    - `oboInOwl:hasBroadSynonym` (i.e., the synonym represents a broader term)
-   - `oboInOwl:hasRelatedSynonym`
-   - `oboInOwl:hasSynonym` (use this if the scope is unknown)
+   - `oboInOwl:hasRelatedSynonym` (use this if the scope is unknown)
 5. `type` the (optional) synonym property type, written as a CURIE from the
    [OBO Metadata Ontology (`omo`)](https://bioregistry.io/omo) controlled
    vocabulary, e.g., one of:
@@ -93,17 +93,17 @@ columns:
 
 Here's an example of some rows in the synonyms table (with linkified CURIEs):
 
-| text                            | curie                                             | scope                                                                       | provenance                                                                                                           | contributor                                                                   | language |
-| ------------------------------- | ------------------------------------------------- | --------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------- | ----------------------------------------------------------------------------- | -------- |
-| PI(3,4,5)P3                     | [CHEBI:16618](https://bioregistry.io/CHEBI:16618) | [oboInOwl:hasExactSynonym](https://bioregistry.io/oboInOwl:hasExactSynonym) | [pubmed:29623928](https://bioregistry.io/pubmed:29623928), [pubmed:20817957](https://bioregistry.io/pubmed:20817957) | [orcid:0000-0003-4423-4370](https://bioregistry.io/orcid:0000-0003-4423-4370) | en       |
-| phosphatidylinositol (3,4,5) P3 | [CHEBI:16618](https://bioregistry.io/CHEBI:16618) | [oboInOwl:hasExactSynonym](https://bioregistry.io/oboInOwl:hasExactSynonym) | [pubmed:29695532](https://bioregistry.io/pubmed:29695532)                                                            | [orcid:0000-0003-4423-4370](https://bioregistry.io/orcid:0000-0003-4423-4370) | en       |
+| text            | curie                                               | predicate                                                                   | provenance                                                                                                           | contributor                                                                   | language |
+| --------------- | --------------------------------------------------- | --------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------- | ----------------------------------------------------------------------------- | -------- |
+| alsterpaullone  | [CHEBI:138488](https://bioregistry.io/CHEBI:138488) | [rdfs:label](https://bioregistry.io/rdfs:label)                             | [pubmed:30655881](https://bioregistry.io/pubmed:30655881)                                                            | [orcid:0000-0003-4423-4370](https://bioregistry.io/orcid:0000-0003-4423-4370) | en       |
+| 9-nitropaullone | [CHEBI:138488](https://bioregistry.io/CHEBI:138488) | [oboInOwl:hasExactSynonym](https://bioregistry.io/oboInOwl:hasExactSynonym) | [pubmed:11597333](https://bioregistry.io/pubmed:11597333), [pubmed:10911915](https://bioregistry.io/pubmed:10911915) | [orcid:0000-0003-4423-4370](https://bioregistry.io/orcid:0000-0003-4423-4370) | en       |
 
 ### Incorrect Synonyms
 
 The [`negatives.tsv`](src/biosynonyms/resources/negatives.tsv) has the following
 columns for non-trivial examples of text strings that aren't synonyms. This
 document doesn't address the same issues as context-based disambiguation, but
-rather helps dscribe issues like incorrect sub-string matching:
+rather helps describe issues like incorrect sub-string matching:
 
 1. `text` the non-synonym text itself
 2. `curie` the compact uniform resource identifier (CURIE) for a biomedical

src/biosynonyms/generate_owl.py

@@ -222,7 +222,7 @@ def get_axiom_str(reference: Reference, synonym: Synonym) -> str | None:
 [
     a owl:Axiom ;
     owl:annotatedSource {reference.curie} ;
-    owl:annotatedProperty {synonym.scope.curie} ;
+    owl:annotatedProperty {synonym.predicate.curie} ;
     owl:annotatedTarget {_text_for_turtle(synonym)} ;
 {axiom_parts_str}
 ] .
@@ -255,7 +255,7 @@ def _write_owl_rdf(  # noqa:C901
         mains: list[str] = []
         axiom_strs: list[str] = []
         for synonym in synonyms:
-            mains.append(f"{synonym.scope.curie} {_text_for_turtle(synonym)}")
+            mains.append(f"{synonym.predicate.curie} {_text_for_turtle(synonym)}")
             if axiom_str := get_axiom_str(reference, synonym):
                 axiom_strs.append(axiom_str)
 

src/biosynonyms/model.py

@@ -37,7 +37,7 @@ class SynonymTuple(NamedTuple):
     text: str
     curie: str
     name: str
-    scope: str
+    predicate: str
     type: str | None
     provenance: str | None
     contributor: str | None
@@ -50,6 +50,9 @@ class SynonymTuple(NamedTuple):
 #: The header for the spreadsheet
 HEADER = list(SynonymTuple._fields)
 
+#: A set of permissible predicates
+PREDICATES = [v.has_label, *v.synonym_scopes.values()]
+
 
 class Synonym(BaseModel):
     """A data model for synonyms."""
@@ -61,23 +64,27 @@ class Synonym(BaseModel):
         "assumed to be american english.",
     )
     reference: NamedReference
-    scope: Reference = Field(
-        default=Reference.from_curie("oboInOwl:hasSynonym"),
+    predicate: Reference = Field(
+        default=v.has_related_synonym,
         description="The predicate that connects the term (as subject) "
         "to the textual synonym (as object)",
+        examples=PREDICATES,
     )
     type: Reference | None = Field(
         default=None,
         title="Synonym type",
         description="See the OBO Metadata Ontology for valid values",
+        examples=list(v.synonym_types),
     )
 
     provenance: list[Reference] = Field(
         default_factory=list,
         description="A list of articles (e.g., from PubMed, PMC, arXiv) where this synonym appears",
     )
     contributor: Reference | None = Field(
-        None, description="The contributor, usually given as a reference to ORCID"
+        None,
+        description="The contributor, usually given as a reference to ORCID",
+        examples=[v.charlie],
     )
     comment: str | None = Field(
         None, description="An optional comment on the synonym curation or status"
@@ -89,7 +96,7 @@ class Synonym(BaseModel):
 
     def get_all_references(self) -> set[Reference]:
         """Get all references made by this object."""
-        rv: set[Reference] = {self.reference, self.scope, *self.provenance}
+        rv: set[Reference] = {self.reference, self.predicate, *self.provenance}
         if self.type:
             rv.add(self.type)
         if self.contributor:
@@ -125,10 +132,10 @@ def from_row(
             "reference": NamedReference(
                 prefix=reference.prefix, identifier=reference.identifier, name=name
             ),
-            "scope": (
-                Reference.from_curie(scope_curie.strip())
-                if (scope_curie := row.get("scope"))
-                else Reference.from_curie("oboInOwl:hasSynonym")
+            "predicate": (
+                Reference.from_curie(predicate_curie.strip())
+                if (predicate_curie := row.get("predicate"))
+                else v.has_related_synonym
             ),
             "type": _safe_parse_curie(row["type"]) if "type" in row else None,
             "provenance": [
@@ -154,7 +161,7 @@ def _as_row(self) -> SynonymTuple:
             text=self.text,
             curie=self.curie,
             name=self.name,
-            scope=self.scope.curie,
+            predicate=self.predicate.curie,
             type=self.type.curie if self.type else None,
             provenance=",".join(p.curie for p in self.provenance) if self.provenance else None,
             contributor=self.contributor.curie if self.contributor is not None else None,
@@ -204,7 +211,7 @@ def to_gilda(self, organism: str | None = None) -> gilda.Term:
 
 def _get_gilda_status(synonym: Synonym) -> GildaStatus:
     """Get the Gilda status for a synonym."""
-    if synonym.scope and synonym.scope.pair == v.has_label.pair:
+    if synonym.predicate and synonym.predicate.pair == v.has_label.pair:
         return "name"
     if synonym.type and synonym.type.pair == v.previous_name.pair:
         return "former_name"

src/biosynonyms/resources/__init__.py

@@ -6,7 +6,7 @@
 from pathlib import Path
 from typing import TYPE_CHECKING, cast
 
-from biosynonyms.model import Synonym, grounder_from_synonyms, parse_synonyms
+from biosynonyms.model import PREDICATES, Synonym, grounder_from_synonyms, parse_synonyms
 
 if TYPE_CHECKING:
     import gilda
@@ -25,13 +25,7 @@
 NEGATIVES_PATH = HERE.joinpath("negatives.tsv")
 UNENTITIES_PATH = HERE.joinpath("unentities.tsv")
 
-SYNONYM_SCOPES = {
-    "oboInOwl:hasExactSynonym",
-    "oboInOwl:hasNarrowSynonym",
-    "oboInOwl:hasBroadSynonym",
-    "oboInOwl:hasRelatedSynonym",
-    "oboInOwl:hasSynonym",
-}
+SYNONYM_PREDICATE_CURIES: set[str] = {p.curie for p in PREDICATES}
 
 
 def load_unentities() -> set[str]:

src/biosynonyms/resources/positives.tsv

@@ -1,4 +1,4 @@
-text	curie	name	scope	type	provenance	contributor	date	language	comment	source
+text	curie	name	predicate	type	provenance	contributor	date	language	comment	source
 1,3-dimethylurate	chebi:133726	1,3-dimethylurate anion	oboInOwl:hasExactSynonym			orcid:0000-0003-4423-4370		en		biosynonyms
 abema	mesh:C000590451	abemaciclib	oboInOwl:hasExactSynonym			orcid:0000-0001-9439-5346		en		biosynonyms
 adaptor protein cbl	interpro:IPR024162	Adaptor protein Cbl	oboInOwl:hasExactSynonym			orcid:0000-0003-4423-4370		en		biosynonyms

tests/test_integrity.py

@@ -14,7 +14,7 @@
 from biosynonyms.resources import (
     NEGATIVES_PATH,
     POSITIVES_PATH,
-    SYNONYM_SCOPES,
+    SYNONYM_PREDICATE_CURIES,
     UNENTITIES_PATH,
     _unentities_key,
 )
@@ -51,7 +51,7 @@ def test_positives(self):
                     text,
                     curie,
                     _name,
-                    scope,
+                    predicate,
                     synonym_type,
                     references,
                     contributor_curie,
@@ -62,7 +62,7 @@ def test_positives(self):
                 ) = row
                 self.assertLess(1, len(text), msg="can not have 1 letter synonyms")
                 self.assert_curie(curie)
-                self.assertIn(scope, SYNONYM_SCOPES)
+                self.assertIn(predicate, SYNONYM_PREDICATE_CURIES)
                 if synonym_type:
                     self.assertTrue(synonym_type.startswith("OMO:"))
                 for reference in references.split(",") if references else []:
@@ -131,17 +131,20 @@ def test_gilda(self):
         reference = NamedReference.from_curie("test:1", "test")
         label = Reference.from_curie("rdfs:label")
         synonym_1 = Synonym(
-            text="tests", scope=v.has_exact_synonym, type=v.plural_form, reference=reference
+            text="tests", predicate=v.has_exact_synonym, type=v.plural_form, reference=reference
         )
         gilda_term_1 = synonym_1.to_gilda()
         self.assertEqual("synonym", gilda_term_1.status)
 
-        synonym_2 = Synonym(text="test", scope=label, reference=reference)
+        synonym_2 = Synonym(text="test", predicate=label, reference=reference)
         gilda_term_2 = synonym_2.to_gilda()
         self.assertEqual("name", gilda_term_2.status)
 
         synonym_3 = Synonym(
-            text="old test", scope=v.has_exact_synonym, reference=reference, type=v.previous_name
+            text="old test",
+            predicate=v.has_exact_synonym,
+            reference=reference,
+            type=v.previous_name,
         )
         gilda_term_3 = synonym_3.to_gilda()
         self.assertEqual("former_name", gilda_term_3.status)