diff --git a/trustgraph-flow/trustgraph/embeddings/graph_embeddings/embeddings.py b/trustgraph-flow/trustgraph/embeddings/graph_embeddings/embeddings.py
index 4726be4d..7b2c779b 100755
--- a/trustgraph-flow/trustgraph/embeddings/graph_embeddings/embeddings.py
+++ b/trustgraph-flow/trustgraph/embeddings/graph_embeddings/embeddings.py
@@ -73,12 +73,13 @@ class Processor(FlowProcessor):
                     )
                 )
 
-            r = GraphEmbeddings(
-                metadata=v.metadata,
-                entities=entities,
-            )
+            if entities:
+                r = GraphEmbeddings(
+                    metadata=v.metadata,
+                    entities=entities,
+                )
 
-            await flow("output").send(r)
+                await flow("output").send(r)
 
         except Exception as e:
             logger.error("Exception occurred", exc_info=True)
diff --git a/trustgraph-flow/trustgraph/extract/kg/definitions/extract.py b/trustgraph-flow/trustgraph/extract/kg/definitions/extract.py
index 8c278c25..9cf87e9a 100755
--- a/trustgraph-flow/trustgraph/extract/kg/definitions/extract.py
+++ b/trustgraph-flow/trustgraph/extract/kg/definitions/extract.py
@@ -168,27 +168,29 @@ class Processor(FlowProcessor):
 
                 entities.append(ec)
 
-            await self.emit_triples(
-                flow("triples"),
-                Metadata(
-                    id=v.metadata.id,
-                    metadata=[],
-                    user=v.metadata.user,
-                    collection=v.metadata.collection,
-                ),
-                triples
-            )
+            if triples:
+                await self.emit_triples(
+                    flow("triples"),
+                    Metadata(
+                        id=v.metadata.id,
+                        metadata=[],
+                        user=v.metadata.user,
+                        collection=v.metadata.collection,
+                    ),
+                    triples
+                )
 
-            await self.emit_ecs(
-                flow("entity-contexts"),
-                Metadata(
-                    id=v.metadata.id,
-                    metadata=[],
-                    user=v.metadata.user,
-                    collection=v.metadata.collection,
-                ),
-                entities
-            )
+            if entities:
+                await self.emit_ecs(
+                    flow("entity-contexts"),
+                    Metadata(
+                        id=v.metadata.id,
+                        metadata=[],
+                        user=v.metadata.user,
+                        collection=v.metadata.collection,
+                    ),
+                    entities
+                )
 
         except Exception as e:
             logger.error(f"Definitions extraction exception: {e}", exc_info=True)
diff --git a/trustgraph-flow/trustgraph/extract/kg/ontology/extract.py b/trustgraph-flow/trustgraph/extract/kg/ontology/extract.py
index adcbe0a8..1644f729 100644
--- a/trustgraph-flow/trustgraph/extract/kg/ontology/extract.py
+++ b/trustgraph-flow/trustgraph/extract/kg/ontology/extract.py
@@ -282,17 +282,6 @@ class Processor(FlowProcessor):
 
             if not ontology_subsets:
                 logger.warning("No relevant ontology elements found for chunk")
-                # Emit empty outputs
-                await self.emit_triples(
-                    flow("triples"),
-                    v.metadata,
-                    []
-                )
-                await self.emit_entity_contexts(
-                    flow("entity-contexts"),
-                    v.metadata,
-                    []
-                )
                 return
 
             # Merge subsets if multiple ontologies matched
@@ -327,35 +316,26 @@ class Processor(FlowProcessor):
             entity_contexts = self.build_entity_contexts(all_triples)
 
             # Emit all triples (extracted + ontology definitions)
-            await self.emit_triples(
-                flow("triples"),
-                v.metadata,
-                all_triples
-            )
+            if all_triples:
+                await self.emit_triples(
+                    flow("triples"),
+                    v.metadata,
+                    all_triples
+                )
 
             # Emit entity contexts
-            await self.emit_entity_contexts(
-                flow("entity-contexts"),
-                v.metadata,
-                entity_contexts
-            )
+            if entity_contexts:
+                await self.emit_entity_contexts(
+                    flow("entity-contexts"),
+                    v.metadata,
+                    entity_contexts
+                )
 
             logger.info(f"Extracted {len(triples)} content triples + {len(ontology_triples)} ontology triples "
                        f"= {len(all_triples)} total triples and {len(entity_contexts)} entity contexts")
 
         except Exception as e:
             logger.error(f"OntoRAG extraction exception: {e}", exc_info=True)
-            # Emit empty outputs on error
-            await self.emit_triples(
-                flow("triples"),
-                v.metadata,
-                []
-            )
-            await self.emit_entity_contexts(
-                flow("entity-contexts"),
-                v.metadata,
-                []
-            )
 
     async def extract_with_simplified_format(
         self,
diff --git a/trustgraph-flow/trustgraph/extract/kg/relationships/extract.py b/trustgraph-flow/trustgraph/extract/kg/relationships/extract.py
index be0bd705..c92a33e9 100755
--- a/trustgraph-flow/trustgraph/extract/kg/relationships/extract.py
+++ b/trustgraph-flow/trustgraph/extract/kg/relationships/extract.py
@@ -181,16 +181,17 @@ class Processor(FlowProcessor):
                         o=Term(type=IRI, iri=v.metadata.id)
                     ))
 
-            await self.emit_triples(
-                flow("triples"),
-                Metadata(
-                    id=v.metadata.id,
-                    metadata=[],
-                    user=v.metadata.user,
-                    collection=v.metadata.collection,
-                ),
-                triples
-            )
+            if triples:
+                await self.emit_triples(
+                    flow("triples"),
+                    Metadata(
+                        id=v.metadata.id,
+                        metadata=[],
+                        user=v.metadata.user,
+                        collection=v.metadata.collection,
+                    ),
+                    triples
+                )
 
         except Exception as e:
             logger.error(f"Relationship extraction exception: {e}", exc_info=True)
diff --git a/trustgraph-flow/trustgraph/storage/knowledge/store.py b/trustgraph-flow/trustgraph/storage/knowledge/store.py
index a79b7b83..475604b6 100644
--- a/trustgraph-flow/trustgraph/storage/knowledge/store.py
+++ b/trustgraph-flow/trustgraph/storage/knowledge/store.py
@@ -64,12 +64,14 @@ class Processor(FlowProcessor):
     async def on_triples(self, msg, consumer, flow):
 
         v = msg.value()
-        await self.table_store.add_triples(v)
+        if v.triples:
+            await self.table_store.add_triples(v)
 
     async def on_graph_embeddings(self, msg, consumer, flow):
 
         v = msg.value()
-        await self.table_store.add_graph_embeddings(v)
+        if v.entities:
+            await self.table_store.add_graph_embeddings(v)
 
     @staticmethod
     def add_args(parser):
diff --git a/trustgraph-flow/trustgraph/tables/knowledge.py b/trustgraph-flow/trustgraph/tables/knowledge.py
index 0e5d4e1d..6ea16499 100644
--- a/trustgraph-flow/trustgraph/tables/knowledge.py
+++ b/trustgraph-flow/trustgraph/tables/knowledge.py
@@ -435,14 +435,17 @@ class KnowledgeTableStore:
             else:
                 metadata = []
 
-            triples = [
-                Triple(
-                    s = tuple_to_term(elt[0], elt[1]),
-                    p = tuple_to_term(elt[2], elt[3]),
-                    o = tuple_to_term(elt[4], elt[5]),
-                )
-                for elt in row[3]
-            ]
+            if row[3]:
+                triples = [
+                    Triple(
+                        s = tuple_to_term(elt[0], elt[1]),
+                        p = tuple_to_term(elt[2], elt[3]),
+                        o = tuple_to_term(elt[4], elt[5]),
+                    )
+                    for elt in row[3]
+                ]
+            else:
+                triples = []
 
             await receiver(
                 Triples(
@@ -491,13 +494,16 @@ class KnowledgeTableStore:
             else:
                 metadata = []
 
-            entities = [
-                EntityEmbeddings(
-                    entity = tuple_to_term(ent[0][0], ent[0][1]),
-                    vectors = ent[1]
-                )
-                for ent in row[3]
-            ]
+            if row[3]:
+                entities = [
+                    EntityEmbeddings(
+                        entity = tuple_to_term(ent[0][0], ent[0][1]),
+                        vectors = ent[1]
+                    )
+                    for ent in row[3]
+                ]
+            else:
+                entities = []
 
             await receiver(
                 GraphEmbeddings(