Pathfinder: templates appear to not be filled out properly

[colleenXu]

What's happening

(1) The filled-out templates written in the TRAPI/console logs look strange. They're missing category/predicate assignments. Is that okay? (these logs come from #862)

From running example 5: affects all 3 filled-out templates

        {
            "timestamp": "2024-10-24T07:38:05.950Z",
            "level": "INFO",
            "message": "Got 3 pathfinder query templates.",
            "code": null
        },
        {
            "timestamp": "2024-10-24T07:38:05.950Z",
            "level": "INFO",
            "message": "Pathfinder Template A: (NCBIGene:3458) -()-> (Gene) -(regulates,regulated_by,affects,affected_by,interacts_with,occurs_together_in_literature_with,produces)-> (CHEBI:16828)",
            "code": null
        },
        {
            "timestamp": "2024-10-24T07:38:05.950Z",
            "level": "INFO",
            "message": "Pathfinder Template B: (NCBIGene:3458) -()-> (Gene) -()-> () -()-> (CHEBI:16828)",
            "code": null
        },
        {
            "timestamp": "2024-10-24T07:38:05.950Z",
            "level": "INFO",
            "message": "Pathfinder Template C: (NCBIGene:3458) -()-> () -()-> (Gene) -()-> (CHEBI:16828)",
            "code": null
        },

From running example 3: affects only 3rd filled-out template ("C")

        {
            "timestamp": "2024-10-24T07:51:24.909Z",
            "level": "INFO",
            "message": "Got 3 pathfinder query templates.",
            "code": null
        },
        {
            "timestamp": "2024-10-24T07:51:24.909Z",
            "level": "INFO",
            "message": "Pathfinder Template A: (MONDO:0005011) -(condition_associated_with_gene,has_biomarker,affected_by,contribution_from)-> (SequenceVariant,Gene) -(gene_associated_with_condition,biomarker_for,affects,contributes_to)-> (MONDO:0005180)",
            "code": null
        },
        {
            "timestamp": "2024-10-24T07:51:24.909Z",
            "level": "INFO",
            "message": "Pathfinder Template B: (MONDO:0005011) -(condition_associated_with_gene,has_biomarker,affected_by,contribution_from)-> (SequenceVariant,Gene) -(affects,produced_by,located_in,part_of,interacts_with)-> (Cell) -(location_of,affected_by,interacts_with)-> (MONDO:0005180)",
            "code": null
        },
        {
            "timestamp": "2024-10-24T07:51:24.909Z",
            "level": "INFO",
            "message": "Pathfinder Template C: (MONDO:0005011) -()-> () -()-> (SequenceVariant,Gene) -()-> (MONDO:0005180)",
            "code": null
        },

(2) Some of those filled-out templates terminate early because no matching MetaKG edges were found.

• Example 5: Happened to 2nd + 3rd templates. I don't imagine this was intended, but I don't have 9/6 notes on those templates because they weren't run then.
• Example 3: Happened to 3rd template. This may have happened during original development based on the 9/6 notes

Logs

Example 5:

• 2024-10-24T07:38:11.514Z WARNING: [Template-2]: Query Edges [(reversed b_obj), (reversed un_b)] have no MetaKG edges. Your query terminates.
• 2024-10-24T07:38:10.841Z WARNING: [Template-3]: Query Edges [(sub_c), (c_un)] have no MetaKG edges. Your query terminates.

Example 3:

• 2024-10-24T07:51:30.533Z WARNING: [Template-3]: Query Edges [(sub_c), (c_un)] have no MetaKG edges. Your query terminates.

(3) The templates that terminate early have odd console logs, where the input_type or output_type of a QEdge to execute (qXEdge? APIEdge?) is an empty array.

From Example 5, 2nd template

  bte:biothings-explorer-trapi:edge-manager (3) Edge manager is managing 3 qEdges. +6ms
  bte:biothings-explorer-trapi:edge-manager (4) Edges not yet executed = 3 +0ms
  bte:biothings-explorer-trapi:edge-manager (5) Sending next edge 'b_obj' WITH entity count...(1) +0ms
  bte:biothings-explorer-trapi:edge-manager Checking entity max : (1)--(0) +0ms
  bte:biothings-explorer-trapi:edge-manager (5) Checking direction of edge with one set of entities... +0ms
  bte:biothings-explorer-trapi:edge-manager 'sub_un' : (1) --> (0) +0ms
  bte:biothings-explorer-trapi:edge-manager 'un_b' : (0) --> (0) +0ms
  bte:biothings-explorer-trapi:edge-manager 'b_obj' : (0) <-- (1) +0ms
  bte:biothings-explorer-trapi:qedge2btedge Input node is creativeQueryObject +139ms
  bte:biothings-explorer-trapi:qedge2btedge Output node is nb +0ms
  bte:biothings-explorer-trapi:qedge2btedge KG Filters: {
  bte:biothings-explorer-trapi:qedge2btedge   "input_type": [
  bte:biothings-explorer-trapi:qedge2btedge     "SmallMolecule",
  bte:biothings-explorer-trapi:qedge2btedge     "MolecularEntity",
  bte:biothings-explorer-trapi:qedge2btedge     "NucleicAcidEntity",
  bte:biothings-explorer-trapi:qedge2btedge     "ChemicalMixture",
  bte:biothings-explorer-trapi:qedge2btedge     "MolecularMixture",
  bte:biothings-explorer-trapi:qedge2btedge     "Drug",
  bte:biothings-explorer-trapi:qedge2btedge     "ComplexMolecularMixture",
  bte:biothings-explorer-trapi:qedge2btedge     "ProcessedMaterial",
  bte:biothings-explorer-trapi:qedge2btedge     "Food",
  bte:biothings-explorer-trapi:qedge2btedge     "EnvironmentalFoodContaminant",
  bte:biothings-explorer-trapi:qedge2btedge     "FoodAdditive",
  bte:biothings-explorer-trapi:qedge2btedge     "ChemicalEntity"
  bte:biothings-explorer-trapi:qedge2btedge   ],
  bte:biothings-explorer-trapi:qedge2btedge   "output_type": []
  bte:biothings-explorer-trapi:qedge2btedge } +0ms
  bte:biothings-explorer-trapi:qedge2btedge No smartapi edge found for b_obj +136ms
  bte:biothings-explorer-trapi:edge-manager (4) Edges not yet executed = 2 +136ms
  bte:biothings-explorer-trapi:edge-manager (5) Sending next edge 'un_b' WITH entity count...(1) +0ms
  bte:biothings-explorer-trapi:edge-manager Checking entity max : (0)--(0) +0ms
  bte:biothings-explorer-trapi:edge-manager (5) Checking direction of edge with one set of entities... +0ms
  bte:biothings-explorer-trapi:edge-manager 'sub_un' : (1) --> (0) +0ms
  bte:biothings-explorer-trapi:edge-manager 'un_b' : (0) <-- (1) +0ms
  bte:biothings-explorer-trapi:edge-manager 'b_obj' : (1) <-- (1) +0ms
  bte:biothings-explorer-trapi:qedge2btedge Input node is nb +0ms
  bte:biothings-explorer-trapi:qedge2btedge Output node is un +0ms
  bte:biothings-explorer-trapi:qedge2btedge KG Filters: {
  bte:biothings-explorer-trapi:qedge2btedge   "input_type": [],
  bte:biothings-explorer-trapi:qedge2btedge   "output_type": [
  bte:biothings-explorer-trapi:qedge2btedge     "Gene",
  bte:biothings-explorer-trapi:qedge2btedge     "ProteinIsoform",
  bte:biothings-explorer-trapi:qedge2btedge     "Protein"
  bte:biothings-explorer-trapi:qedge2btedge   ]
  bte:biothings-explorer-trapi:qedge2btedge } +0ms
  bte:biothings-explorer-trapi:qedge2btedge No smartapi edge found for un_b +130ms
  bte:biothings-explorer-trapi:edge-manager (4) Edges not yet executed = 1 +130ms
  bte:biothings-explorer-trapi:edge-manager (5) Sending next edge 'sub_un' WITH entity count...(1) +0ms
  bte:biothings-explorer-trapi:edge-manager Checking entity max : (0)--(1) +0ms
  bte:biothings-explorer-trapi:QEdge (8) Choosing lower entity count in edge... +266ms
  bte:biothings-explorer-trapi:QNode (8) Node "un" holding undefined aside. +266ms
  bte:biothings-explorer-trapi:QEdge (8) Sub - Obj were same but chose subject (1) +0ms
  bte:biothings-explorer-trapi:edge-manager 'sub_un' : (1) --> (1) +0ms
  bte:biothings-explorer-trapi:edge-manager 'un_b' : (1) <-- (1) +0ms
  bte:biothings-explorer-trapi:edge-manager 'b_obj' : (1) <-- (1) +0ms
  bte:biothings-explorer-trapi:qedge2btedge Input node is creativeQuerySubject +0ms
  bte:biothings-explorer-trapi:qedge2btedge Output node is un +0ms
  bte:biothings-explorer-trapi:qedge2btedge KG Filters: {
  bte:biothings-explorer-trapi:qedge2btedge   "input_type": [
  bte:biothings-explorer-trapi:qedge2btedge     "Gene",
  bte:biothings-explorer-trapi:qedge2btedge     "ProteinIsoform",
  bte:biothings-explorer-trapi:qedge2btedge     "Protein"
  bte:biothings-explorer-trapi:qedge2btedge   ],
  bte:biothings-explorer-trapi:qedge2btedge   "output_type": [
  bte:biothings-explorer-trapi:qedge2btedge     "Gene",
  bte:biothings-explorer-trapi:qedge2btedge     "ProteinIsoform",
  bte:biothings-explorer-trapi:qedge2btedge     "Protein"
  bte:biothings-explorer-trapi:qedge2btedge   ]
  bte:biothings-explorer-trapi:qedge2btedge } +0ms
  bte:biothings-explorer-trapi:main Query Edges [(reversed b_obj), (reversed un_b)] have no MetaKG edges. Your query terminates. +399ms

From Example 5, 3rd template

  bte:biothings-explorer-trapi:edge-manager (3) Edge manager is managing 3 qEdges. +0ms
  bte:biothings-explorer-trapi:edge-manager (4) Edges not yet executed = 3 +0ms
  bte:biothings-explorer-trapi:edge-manager (5) Sending next edge 'un_obj' WITH entity count...(1) +0ms
  bte:biothings-explorer-trapi:edge-manager Checking entity max : (1)--(0) +0ms
  bte:biothings-explorer-trapi:edge-manager (5) Checking direction of edge with one set of entities... +0ms
  bte:biothings-explorer-trapi:edge-manager 'sub_c' : (1) --> (0) +1ms
  bte:biothings-explorer-trapi:edge-manager 'c_un' : (0) --> (0) +0ms
  bte:biothings-explorer-trapi:edge-manager 'un_obj' : (0) <-- (1) +0ms
  bte:biothings-explorer-trapi:qedge2btedge Input node is creativeQueryObject +0ms
  bte:biothings-explorer-trapi:qedge2btedge Output node is un +0ms
  bte:biothings-explorer-trapi:qedge2btedge KG Filters: {
  bte:biothings-explorer-trapi:qedge2btedge   "input_type": [
  bte:biothings-explorer-trapi:qedge2btedge     "SmallMolecule",
  bte:biothings-explorer-trapi:qedge2btedge     "MolecularEntity",
  bte:biothings-explorer-trapi:qedge2btedge     "NucleicAcidEntity",
  bte:biothings-explorer-trapi:qedge2btedge     "ChemicalMixture",
  bte:biothings-explorer-trapi:qedge2btedge     "MolecularMixture",
  bte:biothings-explorer-trapi:qedge2btedge     "Drug",
  bte:biothings-explorer-trapi:qedge2btedge     "ComplexMolecularMixture",
  bte:biothings-explorer-trapi:qedge2btedge     "ProcessedMaterial",
  bte:biothings-explorer-trapi:qedge2btedge     "Food",
  bte:biothings-explorer-trapi:qedge2btedge     "EnvironmentalFoodContaminant",
  bte:biothings-explorer-trapi:qedge2btedge     "FoodAdditive",
  bte:biothings-explorer-trapi:qedge2btedge     "ChemicalEntity"
  bte:biothings-explorer-trapi:qedge2btedge   ],
  bte:biothings-explorer-trapi:qedge2btedge   "output_type": [
  bte:biothings-explorer-trapi:qedge2btedge     "Gene",
  bte:biothings-explorer-trapi:qedge2btedge     "ProteinIsoform",
  bte:biothings-explorer-trapi:qedge2btedge     "Protein"
  bte:biothings-explorer-trapi:qedge2btedge   ]
  bte:biothings-explorer-trapi:qedge2btedge } +0ms
  bte:biothings-explorer-trapi:edge-manager (4) Edges not yet executed = 2 +159ms
  bte:biothings-explorer-trapi:edge-manager (5) Sending next edge 'sub_c' WITH entity count...(1) +0ms
  bte:biothings-explorer-trapi:edge-manager Checking entity max : (0)--(1) +0ms
  bte:biothings-explorer-trapi:edge-manager 'sub_c' : (1) --> (0) +0ms
  bte:biothings-explorer-trapi:edge-manager 'c_un' : (0) --> (322) +0ms
  bte:biothings-explorer-trapi:edge-manager 'un_obj' : (322) <-- (1) +0ms
  bte:biothings-explorer-trapi:qedge2btedge Input node is creativeQuerySubject +159ms
  bte:biothings-explorer-trapi:qedge2btedge Output node is nc +0ms
  bte:biothings-explorer-trapi:qedge2btedge KG Filters: {
  bte:biothings-explorer-trapi:qedge2btedge   "input_type": [
  bte:biothings-explorer-trapi:qedge2btedge     "Gene",
  bte:biothings-explorer-trapi:qedge2btedge     "ProteinIsoform",
  bte:biothings-explorer-trapi:qedge2btedge     "Protein"
  bte:biothings-explorer-trapi:qedge2btedge   ],
  bte:biothings-explorer-trapi:qedge2btedge   "output_type": []
  bte:biothings-explorer-trapi:qedge2btedge } +1ms
  bte:biothings-explorer-trapi:qedge2btedge No smartapi edge found for sub_c +142ms
  bte:biothings-explorer-trapi:edge-manager (4) Edges not yet executed = 1 +143ms
  bte:biothings-explorer-trapi:edge-manager (5) Sending next edge 'c_un' WITH entity count...(1) +0ms
  bte:biothings-explorer-trapi:edge-manager Checking entity max : (0)--(0) +0ms
  bte:biothings-explorer-trapi:QEdge (8) Choosing lower entity count in edge... +304ms
  bte:biothings-explorer-trapi:QNode (8) Node "un" holding undefined aside. +304ms
  bte:biothings-explorer-trapi:QEdge (8) Chose lower entity value in subject (1) +0ms
  bte:biothings-explorer-trapi:edge-manager 'sub_c' : (1) --> (1) +0ms
  bte:biothings-explorer-trapi:edge-manager 'c_un' : (1) --> (322) +0ms
  bte:biothings-explorer-trapi:edge-manager 'un_obj' : (322) <-- (1) +0ms
  bte:biothings-explorer-trapi:qedge2btedge Input node is nc +0ms
  bte:biothings-explorer-trapi:qedge2btedge Output node is un +0ms
  bte:biothings-explorer-trapi:qedge2btedge KG Filters: {
  bte:biothings-explorer-trapi:qedge2btedge   "input_type": [],
  bte:biothings-explorer-trapi:qedge2btedge   "output_type": [
  bte:biothings-explorer-trapi:qedge2btedge     "Gene",
  bte:biothings-explorer-trapi:qedge2btedge     "ProteinIsoform",
  bte:biothings-explorer-trapi:qedge2btedge     "Protein"
  bte:biothings-explorer-trapi:qedge2btedge   ]
  bte:biothings-explorer-trapi:qedge2btedge } +0ms
  bte:biothings-explorer-trapi:qedge2btedge No smartapi edge found for c_un +130ms
  bte:biothings-explorer-trapi:main Query Edges [(sub_c), (c_un)] have no MetaKG edges. Your query terminates. +434ms

From Example 3, 3rd template

  bte:biothings-explorer-trapi:edge-manager (3) Edge manager is managing 3 qEdges. +6ms
  bte:biothings-explorer-trapi:edge-manager (4) Edges not yet executed = 3 +0ms
  bte:biothings-explorer-trapi:edge-manager (5) Sending next edge 'sub_c' WITH entity count...(11) +0ms
  bte:biothings-explorer-trapi:edge-manager Checking entity max : (0)--(11) +0ms
  bte:biothings-explorer-trapi:edge-manager 'sub_c' : (11) --> (0) +0ms
  bte:biothings-explorer-trapi:edge-manager 'c_un' : (0) --> (0) +0ms
  bte:biothings-explorer-trapi:edge-manager 'un_obj' : (0) <-- (28) +0ms
  bte:biothings-explorer-trapi:qedge2btedge Input node is creativeQuerySubject +131ms
  bte:biothings-explorer-trapi:qedge2btedge Output node is nc +0ms
  bte:biothings-explorer-trapi:qedge2btedge KG Filters: {
  bte:biothings-explorer-trapi:qedge2btedge   "input_type": [
  bte:biothings-explorer-trapi:qedge2btedge     "Disease",
  bte:biothings-explorer-trapi:qedge2btedge     "PhenotypicFeature",
  bte:biothings-explorer-trapi:qedge2btedge     "BehavioralFeature",
  bte:biothings-explorer-trapi:qedge2btedge     "ClinicalFinding",
  bte:biothings-explorer-trapi:qedge2btedge     "DiseaseOrPhenotypicFeature"
  bte:biothings-explorer-trapi:qedge2btedge   ],
  bte:biothings-explorer-trapi:qedge2btedge   "output_type": []
  bte:biothings-explorer-trapi:qedge2btedge } +0ms
  bte:biothings-explorer-trapi:qedge2btedge No smartapi edge found for sub_c +131ms
  bte:biothings-explorer-trapi:edge-manager (4) Edges not yet executed = 2 +131ms
  bte:biothings-explorer-trapi:edge-manager (5) Sending next edge 'c_un' WITH entity count...(1) +0ms
  bte:biothings-explorer-trapi:edge-manager Checking entity max : (0)--(0) +0ms
  bte:biothings-explorer-trapi:edge-manager 'sub_c' : (1) --> (1) +0ms
  bte:biothings-explorer-trapi:edge-manager 'c_un' : (1) --> (0) +0ms
  bte:biothings-explorer-trapi:edge-manager 'un_obj' : (0) <-- (28) +0ms
  bte:biothings-explorer-trapi:qedge2btedge Input node is nc +0ms
  bte:biothings-explorer-trapi:qedge2btedge Output node is un +0ms
  bte:biothings-explorer-trapi:qedge2btedge KG Filters: {
  bte:biothings-explorer-trapi:qedge2btedge   "input_type": [],
  bte:biothings-explorer-trapi:qedge2btedge   "output_type": [
  bte:biothings-explorer-trapi:qedge2btedge     "Snv",
  bte:biothings-explorer-trapi:qedge2btedge     "SequenceVariant",
  bte:biothings-explorer-trapi:qedge2btedge     "Gene",
  bte:biothings-explorer-trapi:qedge2btedge     "ProteinIsoform",
  bte:biothings-explorer-trapi:qedge2btedge     "Protein"
  bte:biothings-explorer-trapi:qedge2btedge   ]
  bte:biothings-explorer-trapi:qedge2btedge } +0ms
  bte:biothings-explorer-trapi:qedge2btedge No smartapi edge found for c_un +125ms
  bte:biothings-explorer-trapi:edge-manager (4) Edges not yet executed = 1 +125ms
  bte:biothings-explorer-trapi:edge-manager (5) Sending next edge 'un_obj' WITH entity count...(1) +0ms
  bte:biothings-explorer-trapi:edge-manager Checking entity max : (28)--(0) +1ms
  bte:biothings-explorer-trapi:QEdge (8) Choosing lower entity count in edge... +258ms
  bte:biothings-explorer-trapi:QNode (8) Node "creativeQueryObject" holding ["MONDO:0005180","MONDO:0008199","MONDO:0009830","MONDO:0010796","MONDO:0013167","MONDO:0017279","MONDO:0957576","MONDO:0008200","MONDO:0011562","MONDO:0011764","MONDO:0013060","MONDO:0013625","MONDO:0014604","MONDO:0014742","MONDO:0008193","MONDO:0000828","MONDO:0010360","MONDO:0010820","MONDO:0011220","MONDO:0011613","MONDO:0011658","MONDO:0011737","MONDO:0014233","MONDO:0014796","MONDO:0011706","MONDO:0014231","MONDO:0800369","MONDO:0017809"] aside. +258ms
  bte:biothings-explorer-trapi:QEdge (8) Chose lower entity value in subject (1) +0ms
  bte:biothings-explorer-trapi:edge-manager 'sub_c' : (1) --> (1) +0ms
  bte:biothings-explorer-trapi:edge-manager 'c_un' : (1) --> (1) +0ms
  bte:biothings-explorer-trapi:edge-manager 'un_obj' : (1) --> (28) +0ms
  bte:biothings-explorer-trapi:qedge2btedge Input node is un +1ms
  bte:biothings-explorer-trapi:qedge2btedge Output node is creativeQueryObject +0ms
  bte:biothings-explorer-trapi:qedge2btedge KG Filters: {
  bte:biothings-explorer-trapi:qedge2btedge   "input_type": [
  bte:biothings-explorer-trapi:qedge2btedge     "Snv",
  bte:biothings-explorer-trapi:qedge2btedge     "SequenceVariant",
  bte:biothings-explorer-trapi:qedge2btedge     "Gene",
  bte:biothings-explorer-trapi:qedge2btedge     "ProteinIsoform",
  bte:biothings-explorer-trapi:qedge2btedge     "Protein"
  bte:biothings-explorer-trapi:qedge2btedge   ],
  bte:biothings-explorer-trapi:qedge2btedge   "output_type": [
  bte:biothings-explorer-trapi:qedge2btedge     "Disease",
  bte:biothings-explorer-trapi:qedge2btedge     "PhenotypicFeature",
  bte:biothings-explorer-trapi:qedge2btedge     "BehavioralFeature",
  bte:biothings-explorer-trapi:qedge2btedge     "ClinicalFinding",
  bte:biothings-explorer-trapi:qedge2btedge     "DiseaseOrPhenotypicFeature"
  bte:biothings-explorer-trapi:qedge2btedge   ]
  bte:biothings-explorer-trapi:qedge2btedge } +0ms
  bte:biothings-explorer-trapi:main Query Edges [(sub_c), (c_un)] have no MetaKG edges. Your query terminates. +383ms

Data

• Example 5 TRAPI response, run today. Took 1 min 49 s to run.
• Example 3 TRAPI response, run today. Took 1 min to run.

Commentary

This is likely happening in CI + Test, since I found examples of it happening Friday 10/18 and it's happening in my local (all main branches) right now.

I'm not sure if this is "expected" behavior or not. I lean towards unexpected, because I think the category/predicate mappings do exist but aren't being used in some templates. Some I noticed:

• Gene-Gene predicates
• Chem-Gene predicates
• Disease - SequenceVar/Gene predicates

[rjawesome]

@colleenXu
In Example 5 (Template A):

• NCBIGene:3458 has two categories: Protein & Gene
• Gene -> ChemicalEntity has no hits in the category table
• Protein -> ChemicalEntity has "Gene" in the category table, so it looks for a predicate from Protein -> Gene which is not present in the predicates table

In Example 5 (Template B)

• There are no categories in the category table from Gene -> ChemicalEntity, hence the entry between that has no categories (and thus cannot find predicates)

In Example 5 (Template C)

• There are no cateogries in the category table from Gene -> Gene, hence the entry between that has no categories

In Example 3 (Template C):

• Disease -> SequenceVariant and Disease -> Gene both have no categories in the category table, hence the entry between them has no categories

Maybe some sort of gene/protein conflation needs to be implemented in Pathfinder? Or should there be different behavior when no categories are found in the category table?

[tokebe]

Odd, I was under the impression that Gene/Protein conflation would happen prior to pathfinder handling, so Pathfinder template generation would have both to work with from the get go...

If that's not the case, we'll want an extra Gene/Protein conflation pass prior to template building in Pathfinder (Or, alternatively, Gene/Protein expansion when generating the in-memory table from the hard table)

If no categories are found, we'll want NamedThing, though again I was expecting that the internal query execution of a template would handle injecting that...

[colleenXu]

From my POV, there's several things to investigate/untangle:

• Is Gene/Protein conflation working as-intended? It seemed to work before but I didn't always take notes on what the filled-out-templated queries looked like. And I didn't save responses from those queries.
• "no intermediates for a category-pair":
  • the error-handling seems odd. Based on slide 8 from the original planning slidedeck, we wanted the error to pop up sooner and be specific to the pathfinder-template-generation. The error now is more like "no MetaKG edges found"...
  • Do we want to change it to NamedThing? It looks like previously we were fine "not executing" when we were missing category-pair info.
• "no predicates for an edge's category pair":
  • This is supposed to execute fine (no predicate restraints) - see slide 7. But I'm not sure that it is...
• It would be helpful if the logs looked different, so it was easier to tell apart the "intermediate" category slots vs the "predicates" for a filled-out template...

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Helpful to look back at slide deck and info in #832

[colleenXu]

Andrew told me that we don't have to rush to fix this. It's fine to not get this done by the end of this phase.