metakb_grouped_statement_example.json

{
  "id": "metakb.placeholder:1",
  "type": "Statement",
  "specifiedBy": { "id": "placeholder" },
  "proposition": {
    "type": "VariantTherapeuticResponseProposition",
    "subjectVariant": {
      "id": "catvar equivalent of GA4GH.VAxxxx from below, we can come up with something",
      "content": "the catvar etc"
    },
    "geneContextQualifier": {
      "id": "normalize.gene.hgnc:11110",
      "description": "the object that comes from the normalizer"
    },
    "predicate": "predictsSensitivityTo",
    "objectTherapeutic": {
      "id": "normalize.therapy.rxcui:1546019",
      "description": "stuff from normalizer"
    },
    "conditionQualifier": {
      "id": "normalize.disease.ncit:C4978",
      "description": "stuff from normalizer"
    }
  },
  "hasEvidenceLines": {
    "type": "EvidenceLine",
    "directionOfEvidenceProvided": "Supports",
    "hasEvidenceItems": [
      {
        "id": "civic.eid:4487",
        "type": "Statement",
        "specifiedBy": {
          "id": "civic.method:2019",
          "type": "Method",
          "name": "CIViC Curation SOP (2019)",
          "methodType": "variant curation standard operating procedure",
          "reportedIn": {
            "id": "pmid:31779674",
            "type": "Document",
            "name": "Danos et al., 2019, Genome Med.",
            "title": "Standard operating procedure for curation and clinical interpretation of variants in cancer",
            "doi": "10.1186/s13073-019-0687-x",
            "pmid": 31779674
          }
        },
        "reportedIn": [
          {
            "id": "civic.source:1706",
            "type": "Document",
            "name": "Miller et al., 2016",
            "title": "Synthetic Lethal Targeting of ARID1A-Mutant Ovarian Clear Cell Tumors with Dasatinib.",
            "pmid": 27364904
          }
        ],
        "proposition": {
          "type": "VariantTherapeuticResponseProposition",
          "subjectVariant": {
            "id": "civic.mpid:1418",
            "type": "CategoricalVariant",
            "name": "ARID1A Q456*",
            "aliases": ["Q73X"],
            "constraints": [
              {
                "type": "DefiningAlleleConstraint",
                "allele": {
                  "id": "ga4gh:VA.9JThLjSdIhDMPE04jxRG7NqJiG53yrJO",
                  "type": "Allele",
                  "name": "Q456*",
                  "location": {
                    "id": "ga4gh:SL.qe09RRJFZqlctMPPFDZEcfemcs8cIYxi",
                    "type": "SequenceLocation",
                    "sequenceReference": {
                      "type": "SequenceReference",
                      "refgetAccession": "SQ.Xtsz5dT90bJbR0_r5EawKzOdC11qEH0y"
                    },
                    "start": 455,
                    "end": 456,
                    "sequence": "Q"
                  },
                  "state": {
                    "type": "LiteralSequenceExpression",
                    "sequence": "*"
                  }
                }
              }
            ],
            "mappings": [
              {
                "coding": {
                  "id": "civic.vid:1510",
                  "system": "https://civicdb.org/variants/",
                  "code": "1510"
                },
                "relation": "exactMatch"
              },
              {
                "coding": {
                  "system": "https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_canonicalid?canonicalid=",
                  "code": "CA339267901"
                },
                "relation": "relatedMatch"
              },
              {
                "coding": {
                  "system": "https://www.ncbi.nlm.nih.gov/clinvar/variation/",
                  "code": "NONE FOUND"
                },
                "relation": "relatedMatch"
              }
            ]
          },
          "geneContextQualifier": {
            "id": "civic.gid:6559",
            "conceptType": "Gene",
            "name": "ARID1A",
            "mappings": [
              {
                "coding": {
                  "id": "ncbigene:8289",
                  "system": "https://www.ncbi.nlm.nih.gov/gene/",
                  "code": "8289"
                },
                "relation": "exactMatch"
              }
            ]
          },
          "alleleOriginQualifier": { "name": "somatic" },
          "predicate": "predictsSensitivityTo",
          "objectTherapeutic": {
            "id": "civic.tid:20",
            "conceptType": "Therapy",
            "name": "Dasatinib",
            "mappings": [
              {
                "coding": {
                  "id": "ncit:C38713",
                  "system": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=",
                  "code": "C38713"
                },
                "relation": "exactMatch"
              }
            ]
          },
          "conditionQualifier": {
            "id": "civic.did:11",
            "conceptType": "Disease",
            "name": "Colorectal Cancer",
            "mappings": [
              {
                "coding": {
                  "id": "DOID:9256",
                  "system": "https://disease-ontology.org/?id=",
                  "code": "DOID:9256"
                },
                "relation": "exactMatch"
              }
            ]
          }
        },
        "direction": "supports",
        "strength": {
          "name": "Preclinical evidence",
          "primaryCoding": {
            "system": "https://civic.readthedocs.io/en/latest/model/evidence/level.html",
            "code": "D"
          },
          "mappings": [
            {
              "coding": {
                "name": "preclinical evidence",
                "system": "https://go.osu.edu/evidence-codes",
                "code": "e000009"
              },
              "relation": "exactMatch"
            }
          ]
        }
      }
    ]
  }
}