Terminology Rename, and named-graphs for explainability (#682)

Terminology Rename, and named-graphs for explainability data

Changed terminology:
  - session -> question
  - retrieval -> exploration
  - selection -> focus
  - answer -> synthesis

- uris.py: Renamed query_session_uri → question_uri,
  retrieval_uri → exploration_uri, selection_uri → focus_uri,
  answer_uri → synthesis_uri
- triples.py: Renamed corresponding triple generation functions with
  updated labels ("GraphRAG question", "Exploration", "Focus",
  "Synthesis")
- namespaces.py: Added named graph constants GRAPH_DEFAULT,
  GRAPH_SOURCE, GRAPH_RETRIEVAL
- init.py: Updated exports
- graph_rag.py: Updated to use new terminology
- invoke_graph_rag.py: Updated CLI to display new stage names
  (Question, Exploration, Focus, Synthesis)

Query-Time Explainability → Named Graph
- triples.py: Added set_graph() helper function to set named graph
  on triples
- graph_rag.py: All explainability triples now use GRAPH_RETRIEVAL
  named graph
- rag.py: Explainability triples stored in user's collection (not
  separate collection) with named graph

Extraction Provenance → Named Graph
- relationships/extract.py: Provenance triples use GRAPH_SOURCE
  named graph
- definitions/extract.py: Provenance triples use GRAPH_SOURCE
  named graph
- chunker.py: Provenance triples use GRAPH_SOURCE named graph
- pdf_decoder.py: Provenance triples use GRAPH_SOURCE named graph

CLI Updates
- show_graph.py: Added -g/--graph option to filter by named graph and
  --show-graph to display graph column

Also:
- Fix knowledge core schemas

tests/integration/test_graph_rag_integration.py

@@ -168,7 +168,7 @@ class TestGraphRagIntegration:
         assert isinstance(response, str)
         assert "machine learning" in response.lower()
 
-        # Verify provenance was emitted in real-time (4 events: session, retrieval, selection, answer)
+        # Verify provenance was emitted in real-time (4 events: question, exploration, focus, synthesis)
         assert len(provenance_events) == 4
         for triples, prov_id in provenance_events:
             assert isinstance(triples, list)

tests/unit/test_retrieval/test_graph_rag.py

@@ -644,7 +644,7 @@ class TestQuery:
             # Verify response text
             assert response == expected_response
 
-            # Verify provenance was emitted incrementally (4 events: session, retrieval, selection, answer)
+            # Verify provenance was emitted incrementally (4 events: question, exploration, focus, synthesis)
             assert len(provenance_events) == 4
 
             # Verify each event has triples and a URN
@@ -653,11 +653,11 @@ class TestQuery:
                 assert len(triples) > 0
                 assert prov_id.startswith("urn:trustgraph:")
 
-            # Verify order: session, retrieval, selection, answer
-            assert "session" in provenance_events[0][1]
-            assert "retrieval" in provenance_events[1][1]
-            assert "selection" in provenance_events[2][1]
-            assert "answer" in provenance_events[3][1]
+            # Verify order: question, exploration, focus, synthesis
+            assert "question" in provenance_events[0][1]
+            assert "exploration" in provenance_events[1][1]
+            assert "focus" in provenance_events[2][1]
+            assert "synthesis" in provenance_events[3][1]
 
         finally:
             # Restore original methods

trustgraph-base/trustgraph/messaging/translators/retrieval.py

@@ -104,10 +104,10 @@ class GraphRagResponseTranslator(MessageTranslator):
         if explain_id:
             result["explain_id"] = explain_id
 
-        # Include explain_collection for explain messages
-        explain_collection = getattr(obj, "explain_collection", None)
-        if explain_collection:
-            result["explain_collection"] = explain_collection
+        # Include explain_graph for explain messages (named graph filter)
+        explain_graph = getattr(obj, "explain_graph", None)
+        if explain_graph is not None:
+            result["explain_graph"] = explain_graph
 
         # Include end_of_stream flag (LLM stream complete)
         result["end_of_stream"] = getattr(obj, "end_of_stream", False)

trustgraph-base/trustgraph/provenance/__init__.py

@@ -41,10 +41,10 @@ from . uris import (
     statement_uri,
     agent_uri,
     # Query-time provenance URIs
-    query_session_uri,
-    retrieval_uri,
-    selection_uri,
-    answer_uri,
+    question_uri,
+    exploration_uri,
+    focus_uri,
+    synthesis_uri,
 )
 
 # Namespace constants
@@ -65,6 +65,8 @@ from . namespaces import (
     TG_SOURCE_TEXT, TG_SOURCE_CHAR_OFFSET, TG_SOURCE_CHAR_LENGTH,
     # Query-time provenance predicates
     TG_QUERY, TG_EDGE_COUNT, TG_SELECTED_EDGE, TG_REASONING, TG_CONTENT,
+    # Named graphs
+    GRAPH_DEFAULT, GRAPH_SOURCE, GRAPH_RETRIEVAL,
 )
 
 # Triple builders
@@ -73,10 +75,12 @@ from . triples import (
     derived_entity_triples,
     triple_provenance_triples,
     # Query-time provenance triple builders
-    query_session_triples,
-    retrieval_triples,
-    selection_triples,
-    answer_triples,
+    question_triples,
+    exploration_triples,
+    focus_triples,
+    synthesis_triples,
+    # Utility
+    set_graph,
 )
 
 # Vocabulary bootstrap
@@ -99,10 +103,10 @@ __all__ = [
     "statement_uri",
     "agent_uri",
     # Query-time provenance URIs
-    "query_session_uri",
-    "retrieval_uri",
-    "selection_uri",
-    "answer_uri",
+    "question_uri",
+    "exploration_uri",
+    "focus_uri",
+    "synthesis_uri",
     # Namespaces
     "PROV", "PROV_ENTITY", "PROV_ACTIVITY", "PROV_AGENT",
     "PROV_WAS_DERIVED_FROM", "PROV_WAS_GENERATED_BY",
@@ -116,15 +120,19 @@ __all__ = [
     "TG_SOURCE_TEXT", "TG_SOURCE_CHAR_OFFSET", "TG_SOURCE_CHAR_LENGTH",
     # Query-time provenance predicates
     "TG_QUERY", "TG_EDGE_COUNT", "TG_SELECTED_EDGE", "TG_REASONING", "TG_CONTENT",
+    # Named graphs
+    "GRAPH_DEFAULT", "GRAPH_SOURCE", "GRAPH_RETRIEVAL",
     # Triple builders
     "document_triples",
     "derived_entity_triples",
     "triple_provenance_triples",
     # Query-time provenance triple builders
-    "query_session_triples",
-    "retrieval_triples",
-    "selection_triples",
-    "answer_triples",
+    "question_triples",
+    "exploration_triples",
+    "focus_triples",
+    "synthesis_triples",
+    # Utility
+    "set_graph",
     # Vocabulary
     "get_vocabulary_triples",
     "PROV_CLASS_LABELS",

trustgraph-base/trustgraph/provenance/namespaces.py

@@ -67,3 +67,9 @@ TG_EDGE = TG + "edge"
 TG_REASONING = TG + "reasoning"
 TG_CONTENT = TG + "content"
 TG_DOCUMENT = TG + "document"  # Reference to document in librarian
+
+# Named graph URIs for RDF datasets
+# These separate different types of data while keeping them in the same collection
+GRAPH_DEFAULT = ""                       # Core knowledge facts (triples extracted from documents)
+GRAPH_SOURCE = "urn:graph:source"        # Extraction provenance (which document/chunk a triple came from)
+GRAPH_RETRIEVAL = "urn:graph:retrieval"  # Query-time explainability (question, exploration, focus, synthesis)

trustgraph-base/trustgraph/provenance/triples.py

@@ -25,6 +25,26 @@ from . namespaces import (
 from . uris import activity_uri, agent_uri, edge_selection_uri
 
 
+def set_graph(triples: List[Triple], graph: str) -> List[Triple]:
+    """
+    Set the named graph on a list of triples.
+
+    This creates new Triple objects with the graph field set,
+    leaving the original triples unchanged.
+
+    Args:
+        triples: List of Triple objects
+        graph: Named graph URI (e.g., "urn:graph:retrieval")
+
+    Returns:
+        List of Triple objects with graph field set
+    """
+    return [
+        Triple(s=t.s, p=t.p, o=t.o, g=graph)
+        for t in triples
+    ]
+
+
 def _iri(uri: str) -> Term:
     """Create an IRI term."""
     return Term(type=IRI, iri=uri)
@@ -258,21 +278,27 @@ def triple_provenance_triples(
 
 
 # Query-time provenance triple builders
+#
+# Terminology:
+#   Question    - What was asked, the anchor for everything
+#   Exploration - Casting wide, what do we know about this space
+#   Focus       - Closing down, what's actually relevant here
+#   Synthesis   - Weaving the relevant pieces into an answer
 
-def query_session_triples(
-    session_uri: str,
+def question_triples(
+    question_uri: str,
     query: str,
     timestamp: Optional[str] = None,
 ) -> List[Triple]:
     """
-    Build triples for a query session activity.
+    Build triples for a question activity.
 
     Creates:
-    - Activity declaration for the query session
+    - Activity declaration for the question
     - Query text and timestamp
 
     Args:
-        session_uri: URI of the session (from query_session_uri)
+        question_uri: URI of the question (from question_uri)
         query: The user's query text
         timestamp: ISO timestamp (defaults to now)
 
@@ -283,39 +309,39 @@ def query_session_triples(
         timestamp = datetime.utcnow().isoformat() + "Z"
 
     return [
-        _triple(session_uri, RDF_TYPE, _iri(PROV_ACTIVITY)),
-        _triple(session_uri, RDFS_LABEL, _literal("GraphRAG query session")),
-        _triple(session_uri, PROV_STARTED_AT_TIME, _literal(timestamp)),
-        _triple(session_uri, TG_QUERY, _literal(query)),
+        _triple(question_uri, RDF_TYPE, _iri(PROV_ACTIVITY)),
+        _triple(question_uri, RDFS_LABEL, _literal("GraphRAG question")),
+        _triple(question_uri, PROV_STARTED_AT_TIME, _literal(timestamp)),
+        _triple(question_uri, TG_QUERY, _literal(query)),
     ]
 
 
-def retrieval_triples(
-    retrieval_uri: str,
-    session_uri: str,
+def exploration_triples(
+    exploration_uri: str,
+    question_uri: str,
     edge_count: int,
 ) -> List[Triple]:
     """
-    Build triples for a retrieval entity (all edges retrieved from subgraph).
+    Build triples for an exploration entity (all edges retrieved from subgraph).
 
     Creates:
-    - Entity declaration for retrieval
-    - wasGeneratedBy link to session
+    - Entity declaration for exploration
+    - wasGeneratedBy link to question
     - Edge count metadata
 
     Args:
-        retrieval_uri: URI of the retrieval entity (from retrieval_uri)
-        session_uri: URI of the parent session
+        exploration_uri: URI of the exploration entity (from exploration_uri)
+        question_uri: URI of the parent question
         edge_count: Number of edges retrieved
 
     Returns:
         List of Triple objects
     """
     return [
-        _triple(retrieval_uri, RDF_TYPE, _iri(PROV_ENTITY)),
-        _triple(retrieval_uri, RDFS_LABEL, _literal("Retrieved edges")),
-        _triple(retrieval_uri, PROV_WAS_GENERATED_BY, _iri(session_uri)),
-        _triple(retrieval_uri, TG_EDGE_COUNT, _literal(edge_count)),
+        _triple(exploration_uri, RDF_TYPE, _iri(PROV_ENTITY)),
+        _triple(exploration_uri, RDFS_LABEL, _literal("Exploration")),
+        _triple(exploration_uri, PROV_WAS_GENERATED_BY, _iri(question_uri)),
+        _triple(exploration_uri, TG_EDGE_COUNT, _literal(edge_count)),
     ]
 
 
@@ -327,28 +353,28 @@ def _quoted_triple(s: str, p: str, o: str) -> Term:
     )
 
 
-def selection_triples(
-    selection_uri: str,
-    retrieval_uri: str,
+def focus_triples(
+    focus_uri: str,
+    exploration_uri: str,
     selected_edges_with_reasoning: List[dict],
     session_id: str = "",
 ) -> List[Triple]:
     """
-    Build triples for a selection entity (selected edges with reasoning).
+    Build triples for a focus entity (selected edges with reasoning).
 
     Creates:
-    - Entity declaration for selection
-    - wasDerivedFrom link to retrieval
+    - Entity declaration for focus
+    - wasDerivedFrom link to exploration
     - For each selected edge: an edge selection entity with quoted triple and reasoning
 
     Structure:
-        <selection> tg:selectedEdge <edge_sel_1> .
+        <focus> tg:selectedEdge <edge_sel_1> .
         <edge_sel_1> tg:edge << <s> <p> <o> >> .
         <edge_sel_1> tg:reasoning "reason" .
 
     Args:
-        selection_uri: URI of the selection entity (from selection_uri)
-        retrieval_uri: URI of the parent retrieval entity
+        focus_uri: URI of the focus entity (from focus_uri)
+        exploration_uri: URI of the parent exploration entity
         selected_edges_with_reasoning: List of dicts with 'edge' (s,p,o tuple) and 'reasoning'
         session_id: Session UUID for generating edge selection URIs
 
@@ -356,9 +382,9 @@ def selection_triples(
         List of Triple objects
     """
     triples = [
-        _triple(selection_uri, RDF_TYPE, _iri(PROV_ENTITY)),
-        _triple(selection_uri, RDFS_LABEL, _literal("Selected edges")),
-        _triple(selection_uri, PROV_WAS_DERIVED_FROM, _iri(retrieval_uri)),
+        _triple(focus_uri, RDF_TYPE, _iri(PROV_ENTITY)),
+        _triple(focus_uri, RDFS_LABEL, _literal("Focus")),
+        _triple(focus_uri, PROV_WAS_DERIVED_FROM, _iri(exploration_uri)),
     ]
 
     # Add each selected edge with its reasoning via intermediate entity
@@ -372,9 +398,9 @@ def selection_triples(
             # Create intermediate entity for this edge selection
             edge_sel_uri = edge_selection_uri(session_id, idx)
 
-            # Link selection to edge selection entity
+            # Link focus to edge selection entity
             triples.append(
-                _triple(selection_uri, TG_SELECTED_EDGE, _iri(edge_sel_uri))
+                _triple(focus_uri, TG_SELECTED_EDGE, _iri(edge_sel_uri))
             )
 
             # Attach quoted triple to edge selection entity
@@ -392,23 +418,23 @@ def selection_triples(
     return triples
 
 
-def answer_triples(
-    answer_uri: str,
-    selection_uri: str,
+def synthesis_triples(
+    synthesis_uri: str,
+    focus_uri: str,
     answer_text: str = "",
     document_id: Optional[str] = None,
 ) -> List[Triple]:
     """
-    Build triples for an answer entity (final synthesis text).
+    Build triples for a synthesis entity (final answer text).
 
     Creates:
-    - Entity declaration for answer
-    - wasDerivedFrom link to selection
+    - Entity declaration for synthesis
+    - wasDerivedFrom link to focus
     - Either document reference (if document_id provided) or inline content
 
     Args:
-        answer_uri: URI of the answer entity (from answer_uri)
-        selection_uri: URI of the parent selection entity
+        synthesis_uri: URI of the synthesis entity (from synthesis_uri)
+        focus_uri: URI of the parent focus entity
         answer_text: The synthesized answer text (used if no document_id)
         document_id: Optional librarian document ID (preferred over inline content)
 
@@ -416,16 +442,16 @@ def answer_triples(
         List of Triple objects
     """
     triples = [
-        _triple(answer_uri, RDF_TYPE, _iri(PROV_ENTITY)),
-        _triple(answer_uri, RDFS_LABEL, _literal("GraphRAG answer")),
-        _triple(answer_uri, PROV_WAS_DERIVED_FROM, _iri(selection_uri)),
+        _triple(synthesis_uri, RDF_TYPE, _iri(PROV_ENTITY)),
+        _triple(synthesis_uri, RDFS_LABEL, _literal("Synthesis")),
+        _triple(synthesis_uri, PROV_WAS_DERIVED_FROM, _iri(focus_uri)),
     ]
 
     if document_id:
         # Store reference to document in librarian (as IRI)
-        triples.append(_triple(answer_uri, TG_DOCUMENT, _iri(document_id)))
+        triples.append(_triple(synthesis_uri, TG_DOCUMENT, _iri(document_id)))
     elif answer_text:
         # Fallback: store inline content
-        triples.append(_triple(answer_uri, TG_CONTENT, _literal(answer_text)))
+        triples.append(_triple(synthesis_uri, TG_CONTENT, _literal(answer_text)))
 
     return triples

trustgraph-base/trustgraph/provenance/uris.py

@@ -65,59 +65,65 @@ def agent_uri(component_name: str) -> str:
 # Query-time provenance URIs
 # These URIs use the urn:trustgraph: namespace to distinguish query-time
 # provenance from extraction-time provenance (which uses https://trustgraph.ai/)
+#
+# Terminology:
+#   Question    - What was asked, the anchor for everything
+#   Exploration - Casting wide, what do we know about this space
+#   Focus       - Closing down, what's actually relevant here
+#   Synthesis   - Weaving the relevant pieces into an answer
 
-def query_session_uri(session_id: str = None) -> str:
+def question_uri(session_id: str = None) -> str:
     """
-    Generate URI for a query session activity.
+    Generate URI for a question activity.
 
     Args:
         session_id: Optional UUID string. Auto-generates if not provided.
 
     Returns:
-        URN in format: urn:trustgraph:session:{uuid}
+        URN in format: urn:trustgraph:question:{uuid}
     """
     if session_id is None:
         session_id = str(uuid.uuid4())
-    return f"urn:trustgraph:session:{session_id}"
+    return f"urn:trustgraph:question:{session_id}"
 
 
-def retrieval_uri(session_id: str) -> str:
+def exploration_uri(session_id: str) -> str:
     """
-    Generate URI for a retrieval entity (edges retrieved from subgraph).
+    Generate URI for an exploration entity (edges retrieved from subgraph).
 
     Args:
-        session_id: The session UUID (same as query_session_uri).
+        session_id: The session UUID (same as question_uri).
 
     Returns:
-        URN in format: urn:trustgraph:prov:retrieval:{uuid}
+        URN in format: urn:trustgraph:prov:exploration:{uuid}
     """
-    return f"urn:trustgraph:prov:retrieval:{session_id}"
+    return f"urn:trustgraph:prov:exploration:{session_id}"
 
 
-def selection_uri(session_id: str) -> str:
+def focus_uri(session_id: str) -> str:
     """
-    Generate URI for a selection entity (selected edges with reasoning).
+    Generate URI for a focus entity (selected edges with reasoning).
 
     Args:
-        session_id: The session UUID (same as query_session_uri).
+        session_id: The session UUID (same as question_uri).
 
     Returns:
-        URN in format: urn:trustgraph:prov:selection:{uuid}
+        URN in format: urn:trustgraph:prov:focus:{uuid}
     """
-    return f"urn:trustgraph:prov:selection:{session_id}"
+    return f"urn:trustgraph:prov:focus:{session_id}"
 
 
-def answer_uri(session_id: str) -> str:
+def synthesis_uri(session_id: str) -> str:
     """
-    Generate URI for an answer entity (final synthesis text).
+    Generate URI for a synthesis entity (final answer text).
 
     Args:
-        session_id: The session UUID (same as query_session_uri).
+        session_id: The session UUID (same as question_uri).
 
     Returns:
-        URN in format: urn:trustgraph:prov:answer:{uuid}
+        URN in format: urn:trustgraph:prov:synthesis:{uuid}
     """
-    return f"urn:trustgraph:prov:answer:{session_id}"
+    return f"urn:trustgraph:prov:synthesis:{session_id}"
 
 
 def edge_selection_uri(session_id: str, edge_index: int) -> str:

trustgraph-base/trustgraph/schema/services/retrieval.py

@@ -23,7 +23,7 @@ class GraphRagResponse:
     response: str = ""
     end_of_stream: bool = False       # LLM response stream complete
     explain_id: str | None = None     # Single explain URI (announced as created)
-    explain_collection: str | None = None  # Collection where explain was stored
+    explain_graph: str | None = None  # Named graph where explain was stored (e.g., urn:graph:retrieval)
     message_type: str = ""            # "chunk" or "explain"
     end_of_session: bool = False      # Entire session complete
 

trustgraph-cli/trustgraph/cli/invoke_graph_rag.py

@@ -36,14 +36,14 @@ RDFS_LABEL = "http://www.w3.org/2000/01/rdf-schema#label"
 
 def _get_event_type(prov_id):
     """Extract event type from provenance_id"""
-    if "session" in prov_id:
-        return "session"
-    elif "retrieval" in prov_id:
-        return "retrieval"
-    elif "selection" in prov_id:
-        return "selection"
-    elif "answer" in prov_id:
-        return "answer"
+    if "question" in prov_id:
+        return "question"
+    elif "exploration" in prov_id:
+        return "exploration"
+    elif "focus" in prov_id:
+        return "focus"
+    elif "synthesis" in prov_id:
+        return "synthesis"
     return "provenance"
 
 
@@ -51,7 +51,7 @@ def _format_provenance_details(event_type, triples):
     """Format provenance details based on event type and triples"""
     lines = []
 
-    if event_type == "session":
+    if event_type == "question":
         # Show query and timestamp
         for s, p, o in triples:
             if p == TG_QUERY:
@@ -59,32 +59,32 @@ def _format_provenance_details(event_type, triples):
             elif p == PROV_STARTED_AT_TIME:
                 lines.append(f"    Time: {o}")
 
-    elif event_type == "retrieval":
+    elif event_type == "exploration":
         # Show edge count
         for s, p, o in triples:
             if p == TG_EDGE_COUNT:
-                lines.append(f"    Edges retrieved: {o}")
+                lines.append(f"    Edges explored: {o}")
 
-    elif event_type == "selection":
-        # For selection, just count edge selection URIs
+    elif event_type == "focus":
+        # For focus, just count edge selection URIs
         # The actual edge details are fetched separately via edge_selections parameter
         edge_sel_uris = []
         for s, p, o in triples:
             if p == TG_SELECTED_EDGE:
                 edge_sel_uris.append(o)
         if edge_sel_uris:
-            lines.append(f"    Selected {len(edge_sel_uris)} edge(s)")
+            lines.append(f"    Focused on {len(edge_sel_uris)} edge(s)")
 
-    elif event_type == "answer":
+    elif event_type == "synthesis":
         # Show content length (not full content - it's already streamed)
         for s, p, o in triples:
             if p == TG_CONTENT:
-                lines.append(f"    Answer length: {len(o)} chars")
+                lines.append(f"    Synthesis length: {len(o)} chars")
 
     return lines
 
 
-async def _query_triples_once(ws_url, flow_id, prov_id, user, collection, debug=False):
+async def _query_triples_once(ws_url, flow_id, prov_id, user, collection, graph=None, debug=False):
     """Query triples for a provenance node (single attempt)"""
     request = {
         "id": "triples-request",
@@ -97,6 +97,9 @@ async def _query_triples_once(ws_url, flow_id, prov_id, user, collection, debug=
             "limit": 100
         }
     }
+    # Add graph filter if specified (for named graph queries)
+    if graph is not None:
+        request["request"]["g"] = graph
 
     if debug:
         print(f"    [debug] querying triples for s={prov_id}", file=sys.stderr)
@@ -155,10 +158,10 @@ async def _query_triples_once(ws_url, flow_id, prov_id, user, collection, debug=
     return triples
 
 
-async def _query_triples(ws_url, flow_id, prov_id, user, collection, max_retries=5, retry_delay=0.2, debug=False):
+async def _query_triples(ws_url, flow_id, prov_id, user, collection, graph=None, max_retries=5, retry_delay=0.2, debug=False):
     """Query triples for a provenance node with retries for race condition"""
     for attempt in range(max_retries):
-        triples = await _query_triples_once(ws_url, flow_id, prov_id, user, collection, debug)
+        triples = await _query_triples_once(ws_url, flow_id, prov_id, user, collection, graph=graph, debug=debug)
         if triples:
             return triples
         # Wait before retry if empty (triples may not be stored yet)
@@ -515,14 +518,14 @@ async def _question_explainable(
                 if message_type == "explain":
                     # Display explain event with details
                     explain_id = resp.get("explain_id", "")
-                    explain_collection = resp.get("explain_collection", "explainability")
+                    explain_graph = resp.get("explain_graph")  # Named graph (e.g., urn:graph:retrieval)
                     if explain_id:
                         event_type = _get_event_type(explain_id)
                         print(f"\n  [{event_type}] {explain_id}", file=sys.stderr)
 
-                        # Query triples for this explain node (using explain collection from event)
+                        # Query triples for this explain node (using named graph filter)
                         triples = await _query_triples(
-                            ws_url, flow_id, explain_id, user, explain_collection, debug=debug
+                            ws_url, flow_id, explain_id, user, collection, graph=explain_graph, debug=debug
                         )
 
                         # Format and display details
@@ -530,17 +533,17 @@ async def _question_explainable(
                         for line in details:
                             print(line, file=sys.stderr)
 
-                        # For selection events, query each edge selection for details
-                        if event_type == "selection":
+                        # For focus events, query each edge selection for details
+                        if event_type == "focus":
                             for s, p, o in triples:
                                 if debug:
                                     print(f"    [debug] triple: p={p}, o={o}, o_type={type(o).__name__}", file=sys.stderr)
                                 if p == TG_SELECTED_EDGE and isinstance(o, str):
                                     if debug:
                                         print(f"    [debug] querying edge selection: {o}", file=sys.stderr)
-                                    # Query the edge selection entity (using explain collection from event)
+                                    # Query the edge selection entity (using named graph filter)
                                     edge_triples = await _query_triples(
-                                        ws_url, flow_id, o, user, explain_collection, debug=debug
+                                        ws_url, flow_id, o, user, collection, graph=explain_graph, debug=debug
                                     )
                                     if debug:
                                         print(f"    [debug] got {len(edge_triples)} edge triples", file=sys.stderr)
@@ -743,7 +746,7 @@ def main():
     parser.add_argument(
         '-x', '--explainable',
         action='store_true',
-        help='Show provenance events for explainability (implies streaming)'
+        help='Show provenance events: Question, Exploration, Focus, Synthesis (implies streaming)'
     )
 
     parser.add_argument(

trustgraph-cli/trustgraph/cli/show_graph.py

@@ -1,6 +1,11 @@
 """
 Connects to the graph query service and dumps all graph edges.
 Uses streaming mode for lower time-to-first-result and reduced memory overhead.
+
+Named graphs:
+  - Default graph (empty): Core knowledge facts
+  - urn:graph:source: Extraction provenance (document/chunk sources)
+  - urn:graph:retrieval: Query-time explainability (question, exploration, focus, synthesis)
 """
 
 import argparse
@@ -12,7 +17,13 @@ default_user = 'trustgraph'
 default_collection = 'default'
 default_token = os.getenv("TRUSTGRAPH_TOKEN", None)
 
-def show_graph(url, flow_id, user, collection, limit, batch_size, token=None):
+# Named graph constants for convenience
+GRAPH_DEFAULT = ""
+GRAPH_SOURCE = "urn:graph:source"
+GRAPH_RETRIEVAL = "urn:graph:retrieval"
+
+
+def show_graph(url, flow_id, user, collection, limit, batch_size, graph=None, show_graph_column=False, token=None):
 
     socket = Api(url, token=token).socket()
     flow = socket.flow(flow_id)
@@ -22,6 +33,7 @@ def show_graph(url, flow_id, user, collection, limit, batch_size, token=None):
             user=user,
             collection=collection,
             s=None, p=None, o=None,
+            g=graph,  # Filter by named graph (None = all graphs)
             limit=limit,
             batch_size=batch_size,
         ):
@@ -29,10 +41,15 @@ def show_graph(url, flow_id, user, collection, limit, batch_size, token=None):
                 s = triple.get("s", {})
                 p = triple.get("p", {})
                 o = triple.get("o", {})
+                g = triple.get("g")  # Named graph (None = default graph)
                 # Format terms for display
                 s_str = s.get("v", s.get("i", str(s)))
                 p_str = p.get("v", p.get("i", str(p)))
                 o_str = o.get("v", o.get("i", str(o)))
+                if show_graph_column:
+                    g_str = g if g else "(default)"
+                    print(f"[{g_str}]", s_str, p_str, o_str)
+                else:
                     print(s_str, p_str, o_str)
     finally:
         socket.close()
@@ -88,8 +105,25 @@ def main():
         help='Triples per streaming batch (default: 20)',
     )
 
+    parser.add_argument(
+        '-g', '--graph',
+        default=None,
+        help='Filter by named graph (e.g., urn:graph:source, urn:graph:retrieval). Use "" for default graph only.',
+    )
+
+    parser.add_argument(
+        '--show-graph',
+        action='store_true',
+        help='Show graph column in output',
+    )
+
     args = parser.parse_args()
 
+    # Handle empty string for default graph filter
+    graph = args.graph
+    if graph == '""' or graph == "''":
+        graph = ""  # Filter to default graph only
+
     try:
 
         show_graph(
@@ -99,6 +133,8 @@ def main():
             collection = args.collection,
             limit = args.limit,
             batch_size = args.batch_size,
+            graph = graph,
+            show_graph_column = args.show_graph,
             token = args.token,
         )
 

trustgraph-flow/trustgraph/chunking/recursive/chunker.py

@@ -14,6 +14,7 @@ from ... base import ChunkingService, ConsumerSpec, ProducerSpec
 from ... provenance import (
     page_uri, chunk_uri_from_page, chunk_uri_from_doc,
     derived_entity_triples, document_uri,
+    set_graph, GRAPH_SOURCE,
 )
 
 # Component identification for provenance
@@ -160,7 +161,7 @@ class Processor(ChunkingService):
                 title=f"Chunk {chunk_index}",
             )
 
-            # Emit provenance triples
+            # Emit provenance triples (stored in source graph for separation from core knowledge)
             prov_triples = derived_entity_triples(
                 entity_uri=chunk_uri,
                 parent_uri=parent_uri,
@@ -181,7 +182,7 @@ class Processor(ChunkingService):
                     user=v.metadata.user,
                     collection=v.metadata.collection,
                 ),
-                triples=prov_triples,
+                triples=set_graph(prov_triples, GRAPH_SOURCE),
             ))
 
             # Forward chunk ID + content (post-chunker optimization)

trustgraph-flow/trustgraph/decoding/pdf/pdf_decoder.py

@@ -24,6 +24,7 @@ from ... base import Consumer, Producer, ConsumerMetrics, ProducerMetrics
 
 from ... provenance import (
     document_uri, page_uri, derived_entity_triples,
+    set_graph, GRAPH_SOURCE,
 )
 
 # Component identification for provenance
@@ -285,7 +286,7 @@ class Processor(FlowProcessor):
                     title=f"Page {page_num}",
                 )
 
-                # Emit provenance triples
+                # Emit provenance triples (stored in source graph for separation from core knowledge)
                 doc_uri = document_uri(source_doc_id)
                 pg_uri = page_uri(source_doc_id, page_num)
 
@@ -305,7 +306,7 @@ class Processor(FlowProcessor):
                         user=v.metadata.user,
                         collection=v.metadata.collection,
                     ),
-                    triples=prov_triples,
+                    triples=set_graph(prov_triples, GRAPH_SOURCE),
                 ))
 
                 # Forward page document ID to chunker

trustgraph-flow/trustgraph/extract/kg/definitions/extract.py

@@ -20,7 +20,7 @@ from .... rdf import TRUSTGRAPH_ENTITIES, DEFINITION, RDF_LABEL, SUBJECT_OF
 from .... base import FlowProcessor, ConsumerSpec,  ProducerSpec
 from .... base import PromptClientSpec, ParameterSpec
 
-from .... provenance import statement_uri, triple_provenance_triples
+from .... provenance import statement_uri, triple_provenance_triples, set_graph, GRAPH_SOURCE
 from .... flow_version import __version__ as COMPONENT_VERSION
 
 DEFINITION_VALUE = Term(type=IRI, iri=DEFINITION)
@@ -175,6 +175,7 @@ class Processor(FlowProcessor):
                 triples.append(definition_triple)
 
                 # Generate provenance for the definition triple (reification)
+                # Provenance triples go in the source graph for separation from core knowledge
                 stmt_uri = statement_uri()
                 prov_triples = triple_provenance_triples(
                     stmt_uri=stmt_uri,
@@ -185,7 +186,7 @@ class Processor(FlowProcessor):
                     llm_model=llm_model,
                     ontology_uri=ontology_uri,
                 )
-                triples.extend(prov_triples)
+                triples.extend(set_graph(prov_triples, GRAPH_SOURCE))
 
                 # Link entity to chunk (not top-level document)
                 triples.append(Triple(

trustgraph-flow/trustgraph/extract/kg/relationships/extract.py

@@ -20,7 +20,7 @@ from .... rdf import RDF_LABEL, TRUSTGRAPH_ENTITIES, SUBJECT_OF
 from .... base import FlowProcessor, ConsumerSpec,  ProducerSpec
 from .... base import PromptClientSpec, ParameterSpec
 
-from .... provenance import statement_uri, triple_provenance_triples
+from .... provenance import statement_uri, triple_provenance_triples, set_graph, GRAPH_SOURCE
 from .... flow_version import __version__ as COMPONENT_VERSION
 
 RDF_LABEL_VALUE = Term(type=IRI, iri=RDF_LABEL)
@@ -162,6 +162,7 @@ class Processor(FlowProcessor):
                 triples.append(relationship_triple)
 
                 # Generate provenance for the relationship triple (reification)
+                # Provenance triples go in the source graph for separation from core knowledge
                 stmt_uri = statement_uri()
                 prov_triples = triple_provenance_triples(
                     stmt_uri=stmt_uri,
@@ -172,7 +173,7 @@ class Processor(FlowProcessor):
                     llm_model=llm_model,
                     ontology_uri=ontology_uri,
                 )
-                triples.extend(prov_triples)
+                triples.extend(set_graph(prov_triples, GRAPH_SOURCE))
 
                 # Label for s
                 triples.append(Triple(

trustgraph-flow/trustgraph/retrieval/graph_rag/graph_rag.py

@@ -12,14 +12,16 @@ from ... schema import IRI, LITERAL
 
 # Provenance imports
 from trustgraph.provenance import (
-    query_session_uri,
-    retrieval_uri as make_retrieval_uri,
-    selection_uri as make_selection_uri,
-    answer_uri as make_answer_uri,
-    query_session_triples,
-    retrieval_triples,
-    selection_triples,
-    answer_triples,
+    question_uri,
+    exploration_uri as make_exploration_uri,
+    focus_uri as make_focus_uri,
+    synthesis_uri as make_synthesis_uri,
+    question_triples,
+    exploration_triples,
+    focus_triples,
+    synthesis_triples,
+    set_graph,
+    GRAPH_RETRIEVAL,
 )
 
 # Module logger
@@ -396,17 +398,20 @@ class GraphRag:
 
         # Generate explainability URIs upfront
         session_id = str(uuid.uuid4())
-        session_uri = query_session_uri(session_id)
-        ret_uri = make_retrieval_uri(session_id)
-        sel_uri = make_selection_uri(session_id)
-        ans_uri = make_answer_uri(session_id)
+        q_uri = question_uri(session_id)
+        exp_uri = make_exploration_uri(session_id)
+        foc_uri = make_focus_uri(session_id)
+        syn_uri = make_synthesis_uri(session_id)
 
         timestamp = datetime.utcnow().isoformat() + "Z"
 
-        # Emit session explainability immediately
+        # Emit question explainability immediately
         if explain_callback:
-            session_triples = query_session_triples(session_uri, query, timestamp)
-            await explain_callback(session_triples, session_uri)
+            q_triples = set_graph(
+                question_triples(q_uri, query, timestamp),
+                GRAPH_RETRIEVAL
+            )
+            await explain_callback(q_triples, q_uri)
 
         q = Query(
             rag = self, user = user, collection = collection,
@@ -418,10 +423,13 @@ class GraphRag:
 
         kg, uri_map = await q.get_labelgraph(query)
 
-        # Emit retrieval explain after graph retrieval completes
+        # Emit exploration explain after graph retrieval completes
         if explain_callback:
-            ret_triples = retrieval_triples(ret_uri, session_uri, len(kg))
-            await explain_callback(ret_triples, ret_uri)
+            exp_triples = set_graph(
+                exploration_triples(exp_uri, q_uri, len(kg)),
+                GRAPH_RETRIEVAL
+            )
+            await explain_callback(exp_triples, exp_uri)
 
         if self.verbose:
             logger.debug("Invoking LLM...")
@@ -511,12 +519,15 @@ class GraphRag:
         if self.verbose:
             logger.debug(f"Filtered to {len(selected_edges)} edges")
 
-        # Emit selection explain after edge selection completes
+        # Emit focus explain after edge selection completes
         if explain_callback:
-            sel_triples = selection_triples(
-                sel_uri, ret_uri, selected_edges_with_reasoning, session_id
+            foc_triples = set_graph(
+                focus_triples(
+                    foc_uri, exp_uri, selected_edges_with_reasoning, session_id
+                ),
+                GRAPH_RETRIEVAL
             )
-            await explain_callback(sel_triples, sel_uri)
+            await explain_callback(foc_triples, foc_uri)
 
         # Step 2: Synthesis - LLM generates answer from selected edges only
         selected_edge_dicts = [
@@ -554,30 +565,33 @@ class GraphRag:
         if self.verbose:
             logger.debug("Query processing complete")
 
-        # Emit answer explain after synthesis completes
+        # Emit synthesis explain after synthesis completes
         if explain_callback:
-            answer_doc_id = None
+            synthesis_doc_id = None
             answer_text = resp if resp else ""
 
             # Save answer to librarian if callback provided
             if save_answer_callback and answer_text:
                 # Generate document ID as URN matching query-time provenance format
-                answer_doc_id = f"urn:trustgraph:answer:{session_id}"
+                synthesis_doc_id = f"urn:trustgraph:synthesis:{session_id}"
                 try:
-                    await save_answer_callback(answer_doc_id, answer_text)
+                    await save_answer_callback(synthesis_doc_id, answer_text)
                     if self.verbose:
-                        logger.debug(f"Saved answer to librarian: {answer_doc_id}")
+                        logger.debug(f"Saved answer to librarian: {synthesis_doc_id}")
                 except Exception as e:
                     logger.warning(f"Failed to save answer to librarian: {e}")
-                    answer_doc_id = None  # Fall back to inline content
+                    synthesis_doc_id = None  # Fall back to inline content
 
             # Generate triples with document reference or inline content
-            ans_triples = answer_triples(
-                ans_uri, sel_uri,
-                answer_text="" if answer_doc_id else answer_text,
-                document_id=answer_doc_id,
+            syn_triples = set_graph(
+                synthesis_triples(
+                    syn_uri, foc_uri,
+                    answer_text="" if synthesis_doc_id else answer_text,
+                    document_id=synthesis_doc_id,
+                ),
+                GRAPH_RETRIEVAL
             )
-            await explain_callback(ans_triples, ans_uri)
+            await explain_callback(syn_triples, syn_uri)
 
         if self.verbose:
             logger.debug(f"Emitted explain for session {session_id}")

trustgraph-flow/trustgraph/retrieval/graph_rag/rag.py

@@ -13,6 +13,7 @@ from ... schema import GraphRagQuery, GraphRagResponse, Error
 from ... schema import Triples, Metadata
 from ... schema import LibrarianRequest, LibrarianResponse, DocumentMetadata
 from ... schema import librarian_request_queue, librarian_response_queue
+from ... provenance import GRAPH_RETRIEVAL
 from . graph_rag import GraphRag
 from ... base import FlowProcessor, ConsumerSpec, ProducerSpec
 from ... base import PromptClientSpec, EmbeddingsClientSpec
@@ -38,7 +39,6 @@ class Processor(FlowProcessor):
         triple_limit = params.get("triple_limit", 30)
         max_subgraph_size = params.get("max_subgraph_size", 150)
         max_path_length = params.get("max_path_length", 2)
-        explainability_collection = params.get("explainability_collection", "explainability")
 
         super(Processor, self).__init__(
             **params | {
@@ -48,7 +48,6 @@ class Processor(FlowProcessor):
                 "triple_limit": triple_limit,
                 "max_subgraph_size": max_subgraph_size,
                 "max_path_length": max_path_length,
-                "explainability_collection": explainability_collection,
             }
         )
 
@@ -56,7 +55,6 @@ class Processor(FlowProcessor):
         self.default_triple_limit = triple_limit
         self.default_max_subgraph_size = max_subgraph_size
         self.default_max_path_length = max_path_length
-        self.explainability_collection = explainability_collection
 
         # CRITICAL SECURITY: NEVER share data between users or collections
         # Each user/collection combination MUST have isolated data access
@@ -239,24 +237,25 @@ class Processor(FlowProcessor):
             explainability_refs_emitted = []
 
             # Real-time explainability callback - emits triples and IDs as they're generated
+            # Triples are stored in the user's collection with a named graph (urn:graph:retrieval)
             async def send_explainability(triples, explain_id):
-                # Send triples to explainability queue
+                # Send triples to explainability queue - stores in same collection with named graph
                 await flow("explainability").send(Triples(
                     metadata=Metadata(
                         id=explain_id,
                         metadata=[],
                         user=v.user,
-                        collection=self.explainability_collection,
+                        collection=v.collection,  # Store in user's collection, not separate explainability collection
                     ),
                     triples=triples,
                 ))
 
-                # Send explain ID and collection to response queue
+                # Send explain ID and graph to response queue
                 await flow("response").send(
                     GraphRagResponse(
                         message_type="explain",
                         explain_id=explain_id,
-                        explain_collection=self.explainability_collection,
+                        explain_graph=GRAPH_RETRIEVAL,
                     ),
                     properties={"id": id}
                 )
@@ -424,11 +423,8 @@ class Processor(FlowProcessor):
             help=f'Default max path length (default: 2)'
         )
 
-        parser.add_argument(
-            '--explainability-collection',
-            default='explainability',
-            help=f'Collection for storing explainability triples (default: explainability)'
-        )
+        # Note: Explainability triples are now stored in the user's collection
+        # with the named graph urn:graph:retrieval (no separate collection needed)
 
 def run():
 

trustgraph-flow/trustgraph/tables/knowledge.py

@@ -114,7 +114,7 @@ class KnowledgeTableStore:
                 entity_embeddings list<
                     tuple<
                         tuple<text, boolean>,
-                        list<list<double>>
+                        list<double>
                     >
                 >,
                 PRIMARY KEY ((user, document_id), id)
@@ -140,7 +140,7 @@ class KnowledgeTableStore:
                 chunks list<
                     tuple<
                         blob,
-                        list<list<double>>
+                        list<double>
                     >
                 >,
                 PRIMARY KEY ((user, document_id), id)