rjawesome
commented
1 month ago @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
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 https://github.com/biothings/biothings_explorer/issues/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.
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_typeoroutput_typeof 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
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: