Supporting skos mappings for simpleobo and pronto. (#766)

* Supporting skos mappings for simpleobo and pronto.

* format

* add missing

* add missing

src/oaklib/implementations/pronto/pronto_implementation.py

@@ -40,7 +40,6 @@
  OWL_VERSION_INFO,
  SCOPE_TO_SYNONYM_PRED_MAP,
  SEMAPV,
- SKOS_CLOSE_MATCH,
  SKOS_MATCH_PREDICATES,
  TERM_REPLACED_BY,
  TERMS_MERGED,
@@ -549,6 +548,12 @@ def simple_mappings_by_curie(self, curie: CURIE) -> Iterable[Tuple[PRED_CURIE, C
  yield pred, v
  elif isinstance(s, ResourcePropertyValue):
  yield pred, s.resource
+ if isinstance(t, Term):
+ for rel_type, parents in t.relationships.items():
+ pred = self._get_pronto_relationship_type_curie(rel_type)
+ if pred in SKOS_MATCH_PREDICATES:
+ for parent in parents:
+ yield pred, parent.id
 
  def entity_metadata_map(self, curie: CURIE) -> METADATA_MAP:
  t = self._entity(curie)
@@ -662,7 +667,7 @@ def sssom_mappings(
  if x.id in curies:
  m = sssom.Mapping(
  subject_id=e,
- predicate_id=SKOS_CLOSE_MATCH,
+ predicate_id=HAS_DBXREF,
  object_id=x.id,
  mapping_justification=sssom.EntityReference(
  SEMAPV.UnspecifiedMatching.value

src/oaklib/implementations/simpleobo/simple_obo_implementation.py

@@ -59,7 +59,7 @@
  RDFS_RANGE,
  SCOPE_TO_SYNONYM_PRED_MAP,
  SEMAPV,
- SKOS_CLOSE_MATCH,
+ SKOS_MATCH_PREDICATES,
  SUBPROPERTY_OF,
  TERM_REPLACED_BY,
  TERMS_MERGED,
@@ -697,20 +697,46 @@ def get_sssom_mappings_by_curie(self, curie: Union[str, CURIE]) -> Iterator[ssso
  for x in s.simple_values(TAG_XREF):
  m = sssom.Mapping(
  subject_id=curie,
- predicate_id=SKOS_CLOSE_MATCH,
+ predicate_id=HAS_DBXREF,
  object_id=x,
  mapping_justification=sssom.EntityReference(SEMAPV.UnspecifiedMatching.value),
  )
  inject_mapping_sources(m)
  yield m
+ for x in s.property_values():
+ p = self.map_shorthand_to_curie(x[0])
+ if p in SKOS_MATCH_PREDICATES:
+ m = sssom.Mapping(
+ subject_id=curie,
+ predicate_id=p,
+ object_id=x[1],
+ mapping_justification=sssom.EntityReference(
+ SEMAPV.UnspecifiedMatching.value
+ ),
+ )
+ inject_mapping_sources(m)
+ yield m
+ for p, v in s.pair_values(TAG_RELATIONSHIP):
+ p = self.map_shorthand_to_curie(p)
+ if p in SKOS_MATCH_PREDICATES:
+ m = sssom.Mapping(
+ subject_id=curie,
+ predicate_id=p,
+ object_id=v,
+ mapping_justification=sssom.EntityReference(
+ SEMAPV.UnspecifiedMatching.value
+ ),
+ )
+ inject_mapping_sources(m)
+ yield m
  # TODO: use a cache to avoid re-calculating
  for _, stanza in self.obo_document.stanzas.items():
  if len(stanza.simple_values(TAG_XREF)) > 0:
  for x in stanza.simple_values(TAG_XREF):
  if x == curie:
  m = sssom.Mapping(
  subject_id=stanza.id,
- predicate_id=SKOS_CLOSE_MATCH,
+ predicate_id=HAS_DBXREF,
  object_id=curie,
  mapping_justification=SEMAPV.UnspecifiedMatching.value,
  )

tests/input/mapping-predicates-test.obo

@@ -0,0 +1,30 @@
+format-version: 1.2
+ontology: test.obo
+idspace: dc http://purl.org/dc/elements/1.1/ 
+idspace: oboInOwl http://www.geneontology.org/formats/oboInOwl# 
+idspace: owl http://www.w3.org/2002/07/owl# 
+idspace: rdf http://www.w3.org/1999/02/22-rdf-syntax-ns# 
+idspace: rdfs http://www.w3.org/2000/01/rdf-schema# 
+idspace: terms http://purl.org/dc/terms/ 
+idspace: xml http://www.w3.org/XML/1998/namespace 
+idspace: xsd http://www.w3.org/2001/XMLSchema# 
+idspace: X http://purl.obolibrary.org/obo/X_
+
+[Term]
+id: X:0000001
+name: Person
+property_value: skos:exactMatch schema:Person
+relationship: skos:closeMatch prov:Agent
+xref: Y:1
+
+[Typedef]
+id: skos:exactMatch
+is_metadata_tag: true
+is_class_level: true
+
+
+[Typedef]
+id: skos:closeMatch
+is_metadata_tag: true
+is_class_level: true
+

tests/test_implementations/__init__.py

@@ -458,6 +458,19 @@ def test_multilingual(self, oi: BasicOntologyInterface):
  f"Definition for {lang} did not match",
  )
 
+ def test_skos_mappings(self, oi: MappingProviderInterface):
+ for curies in [None, ["X:0000001"]]:
+ mappings = [
+ (m.subject_id, m.predicate_id, m.object_id) for m in oi.sssom_mappings(curies)
+ ]
+ print(mappings)
+ expected = [
+ ("X:0000001", "oio:hasDbXref", "Y:1"),
+ ("X:0000001", "skos:exactMatch", "schema:Person"),
+ ("X:0000001", "skos:closeMatch", "prov:Agent"),
+ ]
+ self.test.assertCountEqual(expected, mappings)
+
  def test_sssom_mappings(self, oi: MappingProviderInterface):
  """
  Tests conformance of MappingProviderInterface.

tests/test_implementations/test_pronto.py

@@ -44,6 +44,7 @@
 TEST_SIMPLE_ONT = INPUT_DIR / "go-nucleus-simple.obo"
 TEST_ONT_COPY = OUTPUT_DIR / "go-nucleus.copy.obo"
 TEST_SUBGRAPH_OUT = OUTPUT_DIR / "vacuole.obo"
+TEST_SKOS_MAPPINGS_ONT = INPUT_DIR / "mapping-predicates-test.obo"
 
 
 class TestProntoImplementation(unittest.TestCase):
@@ -193,6 +194,16 @@ def test_obsolete_entities(self):
  oi = ProntoImplementation(resource)
  self.compliance_tester.test_obsolete_entities(oi)
 
+ @unittest.skip("Pronto does not handling dangling references")
+ def test_skos_mappings(self):
+ """
+ Tests mappings as SKOS properties.
+
+ :return:
+ """
+ adapter = get_adapter(f"pronto:{TEST_SKOS_MAPPINGS_ONT}")
+ self.compliance_tester.test_skos_mappings(adapter)
+
  def test_sssom_mappings(self):
  self.compliance_tester.test_sssom_mappings(self.oi)
 

tests/test_implementations/test_simple_obo.py

@@ -3,6 +3,7 @@
 from copy import deepcopy
 
 from kgcl_schema.datamodel import kgcl
+from oaklib import get_adapter
 from oaklib.datamodels import obograph
 from oaklib.datamodels.search import SearchConfiguration
 from oaklib.datamodels.search_datamodel import SearchProperty, SearchTermSyntax
@@ -59,6 +60,7 @@
 TEST_SIMPLE_ONT = INPUT_DIR / "go-nucleus-simple.obo"
 TEST_ONT_COPY = OUTPUT_DIR / "go-nucleus.copy.obo"
 TEST_SUBGRAPH_OUT = OUTPUT_DIR / "vacuole.obo"
+TEST_SKOS_MAPPINGS_ONT = INPUT_DIR / "mapping-predicates-test.obo"
 
 
 class TestSimpleOboImplementation(unittest.TestCase):
@@ -236,6 +238,15 @@ def test_synonyms_extra(self):
  def test_sssom_mappings(self):
  self.compliance_tester.test_sssom_mappings(self.oi)
 
+ def test_skos_mappings(self):
+ """
+ Tests mappings as SKOS properties.
+
+ :return:
+ """
+ adapter = get_adapter(f"simpleobo:{TEST_SKOS_MAPPINGS_ONT}")
+ self.compliance_tester.test_skos_mappings(adapter)
+
  def test_definitions(self):
  self.compliance_tester.test_definitions(self.oi, include_metadata=True)