BTE no results Workflow A.9

[vgardner-renci]

https://github.com/NCATSTranslator/minihackathons/blob/main/2021-12_demo/workflowA/A.9_EGFR_advanced.json

{
  "logs": [
    {
      "code": null,
      "level": "DEBUG",
      "message": "BTE identified 2 QNodes from your query graph",
      "timestamp": "2021-08-12T15:57:38.952Z"
    },
    {
      "code": null,
      "level": "DEBUG",
      "message": "BTE identified 1 QEdges from your query graph",
      "timestamp": "2021-08-12T15:57:38.953Z"
    },
    {
      "code": null,
      "level": "DEBUG",
      "message": "BTE identified your query graph as a 1-depth query graph",
      "timestamp": "2021-08-12T15:57:38.953Z"
    },
    {
      "code": null,
      "level": "DEBUG",
      "message": "REDIS cache is not enabled.",
      "timestamp": "2021-08-12T15:57:39.057Z"
    },
    {
      "code": null,
      "level": "DEBUG",
      "message": "BTE is trying to find SmartAPI edges connecting from OrganismTaxon,Event,AdministrativeEntity,Agent,InformationContentEntity,Dataset,DatasetDistribution,DatasetVersion,DatasetSummary,ConfidenceLevel,EvidenceType,InformationResource,Publication,Book,BookChapter,Serial,Article,PhysicalEntity,MaterialSample,Activity,Procedure,Phenomenon,Device,PlanetaryEntity,EnvironmentalProcess,EnvironmentalFeature,GeographicLocation,GeographicLocationAtTime,BiologicalEntity,BiologicalProcessOrActivity,MolecularActivity,BiologicalProcess,Pathway,PhysiologicalProcess,Behavior,Death,PathologicalProcess,OrganismalEntity,LifeStage,IndividualOrganism,Case,PopulationOfIndividualOrganisms,StudyPopulation,Cohort,AnatomicalEntity,CellularComponent,Cell,GrossAnatomicalStructure,PathologicalAnatomicalStructure,CellLine,DiseaseOrPhenotypicFeature,Disease,PhenotypicFeature,BehavioralFeature,ClinicalFinding,Gene,Genome,Polypeptide,Protein,ProteinIsoform,GeneFamily,Genotype,Haplotype,SequenceVariant,Snv,ReagentTargetedGene,ChemicalEntity,MolecularEntity,SmallMolecule,NucleicAcidEntity,Exon,Transcript,RnaProduct,RnaProductIsoform,NoncodingRnaProduct,MicroRna,SiRna,CodingSequence,ChemicalMixture,MolecularMixture,Drug,ComplexMolecularMixture,ProcessedMaterial,Food,EnvironmentalFoodContaminant,FoodAdditive,Nutrient,Macronutrient,Micronutrient,Vitamin,ClinicalEntity,ClinicalTrial,ClinicalIntervention,Hospitalization,Treatment,NamedThing to SmallMolecule with predicate undefined",
      "timestamp": "2021-08-12T15:57:39.059Z"
    },
    {
      "code": null,
      "level": "DEBUG",
      "message": "BTE found 171 smartapi edges corresponding to e0. These smartaip edges comes from 11 unique APIs. They are MyDisease.info API,MyVariant.info API,SEMMED Disease API,SEMMED Gene API,SEMMED Chemical API,SEMMED Biological Process API,MyChem.info API,Text Mining Targeted Association API,BioThings DGIdb API,Multiomics Wellness KP API,Clinical Risk KP API",
      "timestamp": "2021-08-12T15:57:39.093Z"
    },
    {
      "code": null,
      "level": "DEBUG",
      "message": "BTE found 14 bte edges for this batch.",
      "timestamp": "2021-08-12T15:57:39.142Z"
    },
    {
      "code": null,
      "level": "DEBUG",
      "message": "call-apis: Resolving ID feature is turned on",
      "timestamp": "2021-08-12T15:57:39.142Z"
    },
    {
      "code": null,
      "level": "DEBUG",
      "message": "call-apis: Number of BTE Edges received is 14",
      "timestamp": "2021-08-12T15:57:39.142Z"
    },
    {
      "code": null,
      "level": "DEBUG",
      "message": "call-apis: Succesfully made the following query: {\"url\":\"https://biothings.ncats.io/semmedgene/query\",\"params\":{\"fields\":\"affected_by\"},\"data\":\"q=C1414313&scopes=umls\",\"method\":\"post\",\"timeout\":50000}",
      "timestamp": "2021-08-12T15:57:39.187Z"
    },
    {
      "code": null,
      "level": "DEBUG",
      "message": "call-apis: After transformation, BTE is able to retrieve 0 hits!",
      "timestamp": "2021-08-12T15:57:39.187Z"
    },
    {
      "code": null,
      "level": "DEBUG",
      "message": "call-apis: Succesfully made the following query: {\"url\":\"https://mychem.info/v1/query\",\"params\":{\"fields\":\"drugbank.id\",\"size\":\"1000\"},\"data\":\"q=EGFR&scopes=drugbank.enzymes.gene_name\",\"method\":\"post\",\"timeout\":50000}",
      "timestamp": "2021-08-12T15:57:39.197Z"
    },
    {
      "code": null,
      "level": "DEBUG",
      "message": "call-apis: After transformation, BTE is able to retrieve 0 hits!",
      "timestamp": "2021-08-12T15:57:39.197Z"
    },
    {
      "code": null,
      "level": "DEBUG",
      "message": "call-apis: Succesfully made the following query: {\"url\":\"https://biothings.ncats.io/semmedgene/query\",\"params\":{\"fields\":\"affects\"},\"data\":\"q=C1414313&scopes=umls\",\"method\":\"post\",\"timeout\":50000}",
      "timestamp": "2021-08-12T15:57:39.214Z"
    },
    {
      "code": null,
      "level": "DEBUG",
      "message": "call-apis: After transformation, BTE is able to retrieve 0 hits!",
      "timestamp": "2021-08-12T15:57:39.214Z"
    },
    {
      "code": null,
      "level": "DEBUG",
      "message": "call-apis: Succesfully made the following query: {\"url\":\"https://biothings.ncats.io/semmedgene/query\",\"params\":{\"fields\":\"disrupted_by\"},\"data\":\"q=C1414313&scopes=umls\",\"method\":\"post\",\"timeout\":50000}",
      "timestamp": "2021-08-12T15:57:39.247Z"
    },
    {
      "code": null,
      "level": "DEBUG",
      "message": "call-apis: After transformation, BTE is able to retrieve 0 hits!",
      "timestamp": "2021-08-12T15:57:39.247Z"
    },
    {
      "code": null,
      "level": "DEBUG",
      "message": "call-apis: Succesfully made the following query: {\"url\":\"https://biothings.ncats.io/dgidb/query\",\"params\":{\"fields\":\"object.CHEMBL_COMPOUND,association\",\"size\":1000},\"data\":\"q=1956&scopes=subject.NCBIGene\",\"method\":\"post\",\"timeout\":50000}",
      "timestamp": "2021-08-12T15:57:39.287Z"
    },
    {
      "code": null,
      "level": "DEBUG",
      "message": "call-apis: After transformation, BTE is able to retrieve 456 hits!",
      "timestamp": "2021-08-12T15:57:39.727Z"
    },
    {
      "code": null,
      "level": "DEBUG",
      "message": "call-apis: Succesfully made the following query: {\"url\":\"https://mychem.info/v1/query\",\"params\":{\"fields\":\"drugbank.id\",\"size\":\"1000\"},\"data\":\"q=EGFR&scopes=drugbank.targets.gene_name\",\"method\":\"post\",\"timeout\":50000}",
      "timestamp": "2021-08-12T15:57:39.730Z"
    },
    {
      "code": null,
      "level": "DEBUG",
      "message": "call-apis: After transformation, BTE is able to retrieve 30 hits!",
      "timestamp": "2021-08-12T15:57:39.743Z"
    },
    {
      "code": null,
      "level": "DEBUG",
      "message": "call-apis: Succesfully made the following query: {\"url\":\"https://mychem.info/v1/query\",\"params\":{\"fields\":\"drugcentral.xrefs.chembl_id\",\"size\":\"1000\"},\"data\":\"q=EGFR&scopes=drugcentral.bioactivity.uniprot.gene_symbol\",\"method\":\"post\",\"timeout\":50000}",
      "timestamp": "2021-08-12T15:57:39.744Z"
    },
    {
      "code": null,
      "level": "DEBUG",
      "message": "call-apis: After transformation, BTE is able to retrieve 90 hits!",
      "timestamp": "2021-08-12T15:57:39.782Z"
    },
    {
      "code": null,
      "level": "DEBUG",
      "message": "call-apis: Succesfully made the following query: {\"url\":\"https://biothings.ncats.io/semmedgene/query\",\"params\":{\"fields\":\"disrupts\"},\"data\":\"q=C1414313&scopes=umls\",\"method\":\"post\",\"timeout\":50000}",
      "timestamp": "2021-08-12T15:57:39.812Z"
    },
    {
      "code": null,
      "level": "DEBUG",
      "message": "call-apis: After transformation, BTE is able to retrieve 0 hits!",
      "timestamp": "2021-08-12T15:57:39.813Z"
    },
    {
      "code": null,
      "level": "DEBUG",
      "message": "call-apis: Succesfully made the following query: {\"url\":\"https://biothings.ncats.io/semmedgene/query\",\"params\":{\"fields\":\"negatively_regulated_by\"},\"data\":\"q=C1414313&scopes=umls\",\"method\":\"post\",\"timeout\":50000}",
      "timestamp": "2021-08-12T15:57:39.844Z"
    },
    {
      "code": null,
      "level": "DEBUG",
      "message": "call-apis: After transformation, BTE is able to retrieve 0 hits!",
      "timestamp": "2021-08-12T15:57:39.844Z"
    },
    {
      "code": null,
      "level": "DEBUG",
      "message": "call-apis: Succesfully made the following query: {\"url\":\"https://biothings.ncats.io/semmedgene/query\",\"params\":{\"fields\":\"negatively_regulates\"},\"data\":\"q=C1414313&scopes=umls\",\"method\":\"post\",\"timeout\":50000}",
      "timestamp": "2021-08-12T15:57:39.865Z"
    },
    {
      "code": null,
      "level": "DEBUG",
      "message": "call-apis: After transformation, BTE is able to retrieve 0 hits!",
      "timestamp": "2021-08-12T15:57:39.865Z"
    },
    {
      "code": null,
      "level": "DEBUG",
      "message": "call-apis: Succesfully made the following query: {\"url\":\"https://biothings.ncats.io/semmedgene/query\",\"params\":{\"fields\":\"physically_interacts_with\"},\"data\":\"q=C1414313&scopes=umls\",\"method\":\"post\",\"timeout\":50000}",
      "timestamp": "2021-08-12T15:57:39.923Z"
    },
    {
      "code": null,
      "level": "DEBUG",
      "message": "call-apis: After transformation, BTE is able to retrieve 0 hits!",
      "timestamp": "2021-08-12T15:57:39.923Z"
    },
    {
      "code": null,
      "level": "DEBUG",
      "message": "call-apis: Succesfully made the following query: {\"url\":\"https://biothings.ncats.io/semmedgene/query\",\"params\":{\"fields\":\"positively_regulated_by\"},\"data\":\"q=C1414313&scopes=umls\",\"method\":\"post\",\"timeout\":50000}",
      "timestamp": "2021-08-12T15:57:39.953Z"
    },
    {
      "code": null,
      "level": "DEBUG",
      "message": "call-apis: After transformation, BTE is able to retrieve 0 hits!",
      "timestamp": "2021-08-12T15:57:39.953Z"
    },
    {
      "code": null,
      "level": "DEBUG",
      "message": "call-apis: Succesfully made the following query: {\"url\":\"https://biothings.ncats.io/semmedgene/query\",\"params\":{\"fields\":\"positively_regulates\"},\"data\":\"q=C1414313&scopes=umls\",\"method\":\"post\",\"timeout\":50000}",
      "timestamp": "2021-08-12T15:57:39.977Z"
    },
    {
      "code": null,
      "level": "DEBUG",
      "message": "call-apis: After transformation, BTE is able to retrieve 0 hits!",
      "timestamp": "2021-08-12T15:57:39.977Z"
    },
    {
      "code": null,
      "level": "DEBUG",
      "message": "call-apis: Succesfully made the following query: {\"url\":\"https://biothings.ncats.io/semmedgene/query\",\"params\":{\"fields\":\"related_to\"},\"data\":\"q=C1414313&scopes=umls\",\"method\":\"post\",\"timeout\":50000}",
      "timestamp": "2021-08-12T15:57:40.021Z"
    },
    {
      "code": null,
      "level": "DEBUG",
      "message": "call-apis: After transformation, BTE is able to retrieve 0 hits!",
      "timestamp": "2021-08-12T15:57:40.021Z"
    },
    {
      "code": null,
      "level": "DEBUG",
      "message": "call-apis: Total number of results returned for this query is 576",
      "timestamp": "2021-08-12T15:57:40.022Z"
    },
    {
      "code": null,
      "level": "DEBUG",
      "message": "call-apis: Query completes",
      "timestamp": "2021-08-12T15:57:40.906Z"
    },
    {
      "code": null,
      "level": "DEBUG",
      "message": "query_graph_handler: Post-query predicate restrictions: [\"abundance_decreased_by\",\"activity_decreased_by\",\"expression_decreased_by\",\"synthesis_decreased_by\",\"degradation_increased_by\",\"disrupted_by\",\"entity_negatively_regulated_by_entity\"].",
      "timestamp": "2021-08-12T15:57:40.909Z"
    },
    {
      "code": null,
      "level": "DEBUG",
      "message": "query_graph_handler: Successfully applied post-query predicate restriction: 576 down to 0 results.",
      "timestamp": "2021-08-12T15:57:40.909Z"
    }
  ],
  "message": {
    "knowledge_graph": {
      "edges": {},
      "nodes": {}
    },
    "query_graph": {
      "edges": {
        "e0": {
          "object": "n1",
          "predicates": [
            "biolink:decreases_abundance_of",
            "biolink:decreases_activity_of",
            "biolink:decreases_expression_of",
            "biolink:decreases_synthesis_of",
            "biolink:increases_degradation_of",
            "biolink:disrupts",
            "biolink:entity_negatively_regulates_entity"
          ],
          "subject": "n0"
        }
      },
      "nodes": {
        "n0": {
          "categories": [
            "biolink:SmallMolecule"
          ],
          "constraints": [
            {
              "id": "biolink:highest_FDA_approval_status",
              "name": "highest FDA approval status",
              "operator": "==",
              "value": "regular approval"
            }
          ],
          "name": "Small Molecule"
        },
        "n1": {
          "ids": [
            "NCBIGene:1956"
          ],
          "name": "EGFR"
        }
      }
    },
    "results": []
  },
  "validation_result": {
    "message": "",
    "n_edges": 0,
    "n_nodes": 0,
    "provenance_summary": {
      "n_sources": 0,
      "predicate_counts": {},
      "provenance_counts": {}
    },
    "size": "15 kB",
    "status": "PASS",
    "version": "1.1.1"
  },
  "workflow": [
    {
      "id": "lookup"
    }
  ],
  "araxui_provider": "ARS",
  "araxui_response": "e4286769-39e7-48ea-bf5d-d1a76b39894b"
}

[tursynay]

@andrewsu to update the issue

[andrewsu]

our implementation of node constraints is being tracked in biothings/biothings_explorer#174

[vgardner-renci]

Results https://arax.ncats.io/?source=ARS&id=c9c02a08-5574-45e2-836c-cf16f95fa964