Adding option for non-redundant entialed relationships.

Fixes #739

src/oaklib/cli.py

@@ -3409,6 +3409,12 @@ def definitions(
     show_default=True,
     help="Include entailed indirect relationships",
 )
+@click.option(
+    "--non-redundant-entailed/--no-non-redundant-entailed",
+    default=False,
+    show_default=True,
+    help="Include entailed but exclude entailed redundant relationships",
+)
 @click.option(
     "--include-tbox/--no-include-tbox",
     default=True,
@@ -3439,6 +3445,7 @@ def relationships(
     include_entailed: bool,
     include_tbox: bool,
     include_abox: bool,
+    non_redundant_entailed: bool,
     include_metadata: bool,
 ):
     """
@@ -3509,6 +3516,15 @@ def relationships(
         include_tbox=include_tbox,
         include_entailed=include_entailed,
     )
+    if non_redundant_entailed:
+        if not isinstance(impl, OboGraphInterface):
+            raise NotImplementedError(f"Cannot execute this using {impl} of type {type(impl)}")
+        up_it = impl.non_redundant_entailed_relationships(
+            subjects=curies,
+            predicates=actual_predicates,
+            include_abox=include_abox,
+            include_tbox=include_tbox,
+        )
     if direction is None or direction == Direction.up.value:
         it = up_it
     elif direction == Direction.down.value:

src/oaklib/interfaces/obograph_interface.py

@@ -259,6 +259,36 @@ def descendant_graph(
             self.transitive_query_cache[key] = g
         return g
 
+    def non_redundant_entailed_relationships(
+        self,
+        predicates: List[PRED_CURIE] = None,
+        **kwargs,
+    ) -> Iterator[RELATIONSHIP]:
+        """
+        Yields all relationships that are directly entailed.
+
+        See https://github.com/INCATools/ontology-access-kit/issues/739
+
+        :param kwargs: same as relationships
+        :return:
+        """
+        if "include_entailed" in kwargs:
+            kwargs.pop("include_entailed")
+        relationships = list(
+            self.relationships(predicates=predicates, include_entailed=True, **kwargs)
+        )
+        rel_by_sp = defaultdict(list)
+        for s, p, o in relationships:
+            rel_by_sp[(s, p)].append(o)
+        for (s, p), objs in rel_by_sp.items():
+            redundant_set = set()
+            for o in objs:
+                ancs = list(self.ancestors(o, predicates=predicates, reflexive=False))
+                redundant_set.update(ancs)
+            for o in objs:
+                if o not in redundant_set:
+                    yield s, p, o
+
     def ancestors(
         self,
         start_curies: Union[CURIE, List[CURIE]],