{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "$id": "https://w3id.org/clingen/schema/clinvar-gkm/1.1.0/clinvar-gkm-bundle.schema.json",
  "title": "ClinVar-GKM Bundle",
  "description": "A ClinVar-GKM bundle: a single JSON object whose root properties are named sections, each a non-empty map from a typed record id to a GKM object. Objects cross-reference each other by '#/<section>/<id>' JSON pointers. The same shape covers the monthly full bundle, the weekly delta, and sub-bundle extracts, so no individual section is required (a delta or sub-bundle carries only the sections it touches). Beyond this schema, a producer must also guarantee that every bundle-local '#/...' pointer resolves within the bundle.",
  "type": "object",
  "minProperties": 1,
  "additionalProperties": false,
  "allOf": [
    {
      "description": "Every proposition section (any section whose name contains 'proposition'): a proposition's geneContextQualifier must match ClinvarGeneContextQualifier, which restricts the 'geneContextSource' extension value to its four defined values. This also covers the GA4GH VA-Spec proposition types, whose own schemas leave qualifier extensions open. It sits in allOf so it does not widen the root's additionalProperties.",
      "patternProperties": {
        "proposition": {
          "additionalProperties": {
            "properties": {
              "geneContextQualifier": {
                "anyOf": [
                  {
                    "$ref": "https://w3id.org/clingen/schema/clinvar-gkm/1.1.0/json/ClinvarGeneContextQualifier"
                  },
                  {
                    "$ref": "https://w3id.org/ga4gh/schema/gkm-core/1.3.0/json/iriReference"
                  }
                ]
              }
            }
          }
        }
      }
    }
  ],
  "properties": {
    "schema_version": {
      "type": "string",
      "const": "1.1.0",
      "description": "The clinvar-gkm bundle schema version this bundle conforms to (semver; matches this schema's $id version). Lets a consumer identify the version from the bundle alone. See ADR 0004. Optional so sub-bundle extracts may omit it; full and delta releases always emit it."
    },
    "sequenceReference": {
      "type": "object",
      "title": "sequenceReference",
      "description": "VRS SequenceReference records (NCBI RefSeq sequences).",
      "minProperties": 1,
      "patternProperties": {
        "^SQ\\..+": {
          "$ref": "https://w3id.org/ga4gh/schema/vrs/2.1.1/json/SequenceReference"
        }
      },
      "additionalProperties": false
    },
    "location": {
      "type": "object",
      "title": "location",
      "description": "VRS SequenceLocation records.",
      "minProperties": 1,
      "patternProperties": {
        "^ga4gh:SL\\..+": {
          "$ref": "https://w3id.org/ga4gh/schema/vrs/2.1.1/json/SequenceLocation"
        }
      },
      "additionalProperties": false
    },
    "allele": {
      "type": "object",
      "title": "allele",
      "description": "VRS Allele records.",
      "minProperties": 1,
      "patternProperties": {
        "^ga4gh:VA\\..+": {
          "$ref": "https://w3id.org/ga4gh/schema/vrs/2.1.1/json/Allele"
        }
      },
      "additionalProperties": false
    },
    "copyNumberCount": {
      "type": "object",
      "title": "copyNumberCount",
      "description": "VRS CopyNumberCount records.",
      "minProperties": 1,
      "patternProperties": {
        "^ga4gh:CN\\..+": {
          "$ref": "https://w3id.org/ga4gh/schema/vrs/2.1.1/json/CopyNumberCount"
        }
      },
      "additionalProperties": false
    },
    "copyNumberChange": {
      "type": "object",
      "title": "copyNumberChange",
      "description": "VRS CopyNumberChange records.",
      "minProperties": 1,
      "patternProperties": {
        "^ga4gh:CX\\..+": {
          "$ref": "https://w3id.org/ga4gh/schema/vrs/2.1.1/json/CopyNumberChange"
        }
      },
      "additionalProperties": false
    },
    "gene": {
      "type": "object",
      "title": "gene",
      "description": "Gene records (MappableConcept with NCBI Gene / HGNC codings).",
      "minProperties": 1,
      "patternProperties": {
        "^ncbigene:[0-9]+$": {
          "$ref": "https://w3id.org/ga4gh/schema/gkm-core/1.3.0/json/MappableConcept"
        }
      },
      "additionalProperties": false
    },
    "variation": {
      "type": "object",
      "title": "variation",
      "description": "Cat-VRS CategoricalVariant records \u2014 one of the ClinVar variant shapes.",
      "minProperties": 1,
      "patternProperties": {
        "^clinvar:[0-9]+$": {
          "$ref": "https://w3id.org/clingen/schema/clinvar-gkm/1.1.0/json/ClinvarCategoricalVariant"
        }
      },
      "additionalProperties": false
    },
    "condition": {
      "type": "object",
      "title": "condition",
      "description": "Condition / trait records (MappableConcept).",
      "minProperties": 1,
      "patternProperties": {
        "^clinvar\\.trait:[0-9]+$": {
          "$ref": "https://w3id.org/ga4gh/schema/gkm-core/1.3.0/json/MappableConcept"
        }
      },
      "additionalProperties": false
    },
    "conditionSet": {
      "type": "object",
      "title": "conditionSet",
      "description": "ConditionSet records (multi-condition) \u2014 submitted (clinvar.traitset:) or aggregate (clinvar.conditionset:).",
      "minProperties": 1,
      "patternProperties": {
        "^clinvar\\.(trait[sS]et|conditionset):.+": {
          "$ref": "https://w3id.org/ga4gh/schema/va-spec/1.1.0/json/ConditionSet"
        }
      },
      "additionalProperties": false
    },
    "therapy": {
      "type": "object",
      "title": "therapy",
      "description": "Therapy records (MappableConcept, content-addressed).",
      "minProperties": 1,
      "patternProperties": {
        "^clinvar\\.therapy:.+": {
          "$ref": "https://w3id.org/ga4gh/schema/gkm-core/1.3.0/json/MappableConcept"
        }
      },
      "additionalProperties": false
    },
    "therapyGroup": {
      "type": "object",
      "title": "therapyGroup",
      "description": "TherapyGroup records (combination therapies, content-addressed).",
      "minProperties": 1,
      "patternProperties": {
        "^clinvar\\.therapygroup:.+": {
          "$ref": "https://w3id.org/ga4gh/schema/va-spec/1.1.0/json/TherapyGroup"
        }
      },
      "additionalProperties": false
    },
    "submitter": {
      "type": "object",
      "title": "submitter",
      "description": "Submitter organization records (Agent).",
      "minProperties": 1,
      "patternProperties": {
        "^clinvar\\.submitter:[0-9]+$": {
          "$ref": "https://w3id.org/ga4gh/schema/va-spec/1.1.0/json/Agent"
        }
      },
      "additionalProperties": false
    },
    "propositionPathogenicity": {
      "type": "object",
      "title": "propositionPathogenicity",
      "description": "Variant pathogenicity propositions (germline classifications, SCV/RCV/VCV).",
      "minProperties": 1,
      "patternProperties": {
        "^(SCV|VCV|RCV).+": {
          "$ref": "https://w3id.org/ga4gh/schema/va-spec/1.1.0/json/VariantPathogenicityProposition"
        }
      },
      "additionalProperties": false
    },
    "propositionOncogenicity": {
      "type": "object",
      "title": "propositionOncogenicity",
      "description": "Variant oncogenicity propositions (SCV/RCV/VCV).",
      "minProperties": 1,
      "patternProperties": {
        "^(SCV|VCV|RCV).+": {
          "$ref": "https://w3id.org/ga4gh/schema/va-spec/1.1.0/json/VariantOncogenicityProposition"
        }
      },
      "additionalProperties": false
    },
    "propositionSomaticClinicalImpact": {
      "type": "object",
      "title": "propositionSomaticClinicalImpact",
      "description": "Somatic clinical impact propositions: clinical significance (SCV/RCV/VCV) and the diagnostic, prognostic and therapeutic-response propositions that SCV evidence lines target.",
      "minProperties": 1,
      "patternProperties": {
        "^(SCV|VCV|RCV).+": {
          "anyOf": [
            {
              "$ref": "https://w3id.org/ga4gh/schema/va-spec/1.1.0/json/VariantClinicalSignificanceProposition"
            },
            {
              "$ref": "https://w3id.org/ga4gh/schema/va-spec/1.1.0/json/VariantDiagnosticProposition"
            },
            {
              "$ref": "https://w3id.org/ga4gh/schema/va-spec/1.1.0/json/VariantPrognosticProposition"
            },
            {
              "$ref": "https://w3id.org/ga4gh/schema/va-spec/1.1.0/json/VariantTherapeuticResponseProposition"
            }
          ]
        }
      },
      "additionalProperties": false
    },
    "propositionClinvarCustom": {
      "type": "object",
      "title": "propositionClinvarCustom",
      "description": "ClinVar custom germline propositions (the Clinvar*Proposition types, incl. ClinvarUndefinedProposition), SCV/RCV/VCV.",
      "minProperties": 1,
      "patternProperties": {
        "^(SCV|VCV|RCV).+": {
          "anyOf": [
            {
              "$ref": "https://w3id.org/clingen/schema/clinvar-gkm/1.1.0/json/ClinvarRiskFactorProposition"
            },
            {
              "$ref": "https://w3id.org/clingen/schema/clinvar-gkm/1.1.0/json/ClinvarProtectiveProposition"
            },
            {
              "$ref": "https://w3id.org/clingen/schema/clinvar-gkm/1.1.0/json/ClinvarDrugResponseProposition"
            },
            {
              "$ref": "https://w3id.org/clingen/schema/clinvar-gkm/1.1.0/json/ClinvarAffectsProposition"
            },
            {
              "$ref": "https://w3id.org/clingen/schema/clinvar-gkm/1.1.0/json/ClinvarAssociationProposition"
            },
            {
              "$ref": "https://w3id.org/clingen/schema/clinvar-gkm/1.1.0/json/ClinvarConfersSensitivityProposition"
            },
            {
              "$ref": "https://w3id.org/clingen/schema/clinvar-gkm/1.1.0/json/ClinvarOtherProposition"
            },
            {
              "$ref": "https://w3id.org/clingen/schema/clinvar-gkm/1.1.0/json/ClinvarNotProvidedProposition"
            },
            {
              "$ref": "https://w3id.org/clingen/schema/clinvar-gkm/1.1.0/json/ClinvarConflictingDataFromSubmitterProposition"
            },
            {
              "$ref": "https://w3id.org/clingen/schema/clinvar-gkm/1.1.0/json/ClinvarUndefinedProposition"
            }
          ]
        }
      },
      "additionalProperties": false
    },
    "evidenceLine": {
      "type": "object",
      "title": "evidenceLine",
      "description": "Evidence line records tying aggregate statements to their contributors.",
      "minProperties": 1,
      "patternProperties": {
        "^(clinvar\\.submission:SCV|VCV|RCV).+": {
          "anyOf": [
            {
              "$ref": "https://w3id.org/ga4gh/schema/va-spec/1.1.0/json/EvidenceLine"
            },
            {
              "$ref": "https://w3id.org/clingen/schema/clinvar-gkm/1.1.0/json/ClinvarSomaticEvidenceLine"
            }
          ]
        }
      },
      "additionalProperties": false
    },
    "scv": {
      "type": "object",
      "title": "scv",
      "description": "SCV (submitted) statement records.",
      "minProperties": 1,
      "patternProperties": {
        "^clinvar\\.submission:SCV[0-9]+\\.[0-9]+$": {
          "$ref": "https://w3id.org/clingen/schema/clinvar-gkm/1.1.0/json/ClinvarScvStatement"
        }
      },
      "additionalProperties": false
    },
    "vcv": {
      "type": "object",
      "title": "vcv",
      "description": "VCV (variation-level aggregate) statement records.",
      "minProperties": 1,
      "patternProperties": {
        "^VCV[0-9]+\\..+": {
          "$ref": "https://w3id.org/clingen/schema/clinvar-gkm/1.1.0/json/ClinvarVcvStatement"
        }
      },
      "additionalProperties": false
    },
    "rcv": {
      "type": "object",
      "title": "rcv",
      "description": "RCV (variation+condition aggregate) statement records.",
      "minProperties": 1,
      "patternProperties": {
        "^RCV[0-9]+\\..+": {
          "$ref": "https://w3id.org/clingen/schema/clinvar-gkm/1.1.0/json/ClinvarRcvStatement"
        }
      },
      "additionalProperties": false
    }
  }
}