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NCATSTranslator / minihackathons

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BTE no results on Workflow A.8 #202

Closed vgardner-renci closed 2 years ago

vgardner-renci commented 2 years ago

https://arax.ncats.io/?source=ARS&id=cd380ba8-7688-4b1c-9156-8fc73c1f2e7a

https://github.com/NCATSTranslator/minihackathons/blob/main/2021-12_demo/workflowA/A.8_EGFR_simple.json

image


{
  "logs": [
    {
      "code": null,
      "level": "DEBUG",
      "message": "BTE identified 2 QNodes from your query graph",
      "timestamp": "2021-08-12T01:47:27.538Z"
    },
    {
      "code": null,
      "level": "DEBUG",
      "message": "BTE identified 1 QEdges from your query graph",
      "timestamp": "2021-08-12T01:47:27.539Z"
    },
    {
      "code": null,
      "level": "DEBUG",
      "message": "BTE identified your query graph as a 1-depth query graph",
      "timestamp": "2021-08-12T01:47:27.539Z"
    },
    {
      "code": null,
      "level": "DEBUG",
      "message": "REDIS cache is not enabled.",
      "timestamp": "2021-08-12T01:47:27.591Z"
    },
    {
      "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": "2021-08-12T01:47:27.593Z"
    },
    {
      "code": null,
      "level": "DEBUG",
      "message": "BTE found 171 smartapi edges corresponding to e0. These smartaip edges comes from 11 unique APIs. They are MyVariant.info API,MyDisease.info API,MyChem.info API,SEMMED Biological Process API,SEMMED Disease API,SEMMED Gene API,SEMMED Chemical API,Text Mining Targeted Association API,Multiomics Wellness KP API,BioThings DGIdb API,Clinical Risk KP API",
      "timestamp": "2021-08-12T01:47:27.617Z"
    },
    {
      "code": null,
      "level": "DEBUG",
      "message": "BTE found 14 bte edges for this batch.",
      "timestamp": "2021-08-12T01:47:27.658Z"
    },
    {
      "code": null,
      "level": "DEBUG",
      "message": "call-apis: Resolving ID feature is turned on",
      "timestamp": "2021-08-12T01:47:27.659Z"
    },
    {
      "code": null,
      "level": "DEBUG",
      "message": "call-apis: Number of BTE Edges received is 14",
      "timestamp": "2021-08-12T01:47:27.659Z"
    },
    {
      "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": "2021-08-12T01:47:27.727Z"
    },
    {
      "code": null,
      "level": "DEBUG",
      "message": "call-apis: After transformation, BTE is able to retrieve 0 hits!",
      "timestamp": "2021-08-12T01:47:27.728Z"
    },
    {
      "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": "2021-08-12T01:47:27.728Z"
    },
    {
      "code": null,
      "level": "DEBUG",
      "message": "call-apis: After transformation, BTE is able to retrieve 0 hits!",
      "timestamp": "2021-08-12T01:47:27.728Z"
    },
    {
      "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": "2021-08-12T01:47:27.751Z"
    },
    {
      "code": null,
      "level": "DEBUG",
      "message": "call-apis: After transformation, BTE is able to retrieve 0 hits!",
      "timestamp": "2021-08-12T01:47:27.751Z"
    },
    {
      "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": "2021-08-12T01:47:27.764Z"
    },
    {
      "code": null,
      "level": "DEBUG",
      "message": "call-apis: After transformation, BTE is able to retrieve 0 hits!",
      "timestamp": "2021-08-12T01:47:27.764Z"
    },
    {
      "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": "2021-08-12T01:47:27.772Z"
    },
    {
      "code": null,
      "level": "DEBUG",
      "message": "call-apis: After transformation, BTE is able to retrieve 30 hits!",
      "timestamp": "2021-08-12T01:47:27.787Z"
    },
    {
      "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": "2021-08-12T01:47:27.790Z"
    },
    {
      "code": null,
      "level": "DEBUG",
      "message": "call-apis: After transformation, BTE is able to retrieve 90 hits!",
      "timestamp": "2021-08-12T01:47:27.828Z"
    },
    {
      "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": "2021-08-12T01:47:27.831Z"
    },
    {
      "code": null,
      "level": "DEBUG",
      "message": "call-apis: After transformation, BTE is able to retrieve 456 hits!",
      "timestamp": "2021-08-12T01:47:28.278Z"
    },
    {
      "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": "2021-08-12T01:47:28.309Z"
    },
    {
      "code": null,
      "level": "DEBUG",
      "message": "call-apis: After transformation, BTE is able to retrieve 0 hits!",
      "timestamp": "2021-08-12T01:47:28.310Z"
    },
    {
      "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": "2021-08-12T01:47:28.340Z"
    },
    {
      "code": null,
      "level": "DEBUG",
      "message": "call-apis: After transformation, BTE is able to retrieve 0 hits!",
      "timestamp": "2021-08-12T01:47:28.340Z"
    },
    {
      "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": "2021-08-12T01:47:28.361Z"
    },
    {
      "code": null,
      "level": "DEBUG",
      "message": "call-apis: After transformation, BTE is able to retrieve 0 hits!",
      "timestamp": "2021-08-12T01:47:28.361Z"
    },
    {
      "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": "2021-08-12T01:47:28.420Z"
    },
    {
      "code": null,
      "level": "DEBUG",
      "message": "call-apis: After transformation, BTE is able to retrieve 0 hits!",
      "timestamp": "2021-08-12T01:47:28.420Z"
    },
    {
      "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": "2021-08-12T01:47:28.451Z"
    },
    {
      "code": null,
      "level": "DEBUG",
      "message": "call-apis: After transformation, BTE is able to retrieve 0 hits!",
      "timestamp": "2021-08-12T01:47:28.451Z"
    },
    {
      "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": "2021-08-12T01:47:28.473Z"
    },
    {
      "code": null,
      "level": "DEBUG",
      "message": "call-apis: After transformation, BTE is able to retrieve 0 hits!",
      "timestamp": "2021-08-12T01:47:28.473Z"
    },
    {
      "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": "2021-08-12T01:47:28.518Z"
    },
    {
      "code": null,
      "level": "DEBUG",
      "message": "call-apis: After transformation, BTE is able to retrieve 0 hits!",
      "timestamp": "2021-08-12T01:47:28.518Z"
    },
    {
      "code": null,
      "level": "DEBUG",
      "message": "call-apis: Total number of results returned for this query is 576",
      "timestamp": "2021-08-12T01:47:28.519Z"
    },
    {
      "code": null,
      "level": "DEBUG",
      "message": "call-apis: Query completes",
      "timestamp": "2021-08-12T01:47:32.291Z"
    },
    {
      "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": "2021-08-12T01:47:32.293Z"
    },
    {
      "code": null,
      "level": "DEBUG",
      "message": "query_graph_handler: Successfully applied post-query predicate restriction: 576 down to 0 results.",
      "timestamp": "2021-08-12T01:47:32.293Z"
    }
  ],
  "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"
          ],
          "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": "14 kB",
    "status": "PASS",
    "version": "1.1.1"
  },
  "workflow": [
    {
      "id": "lookup"
    }
  ],
  "araxui_provider": "ARS",
  "araxui_response": "e3ee40d6-23b6-42fc-8b3d-f75c4a05c93d"
}
tursynay commented 2 years ago

@andrewsu to update the issue

andrewsu commented 2 years ago

BTE is successfully executing this query but is returning no results because we do not have data sources using those predicates. (When adding biolink:related_to to the list of predicates, results are returned.) So I don't think this is a bug per se, but I'm keeping this issue open so we can examine what knowledge sources other teams are using to retrieve their results to see if there are other APIs we need to integrate into BTE.

vgardner-renci commented 2 years ago

Results https://arax.ncats.io/?source=ARS&id=3d70d422-974d-4c47-b61c-7ca0d928cd22