{
  "$schema": "http://json-schema.org/draft-07/schema#",
   "description" : "Message schema for the ClinGen Data Exchange Kafka topic actionability. This topic tracks the actionability curation events specific for a topic context within gene-condition  and varaint-condition curation framework.",
  "title": "Actionability topic message schema - version 2.0.0",
  "definitions": {
    "affiliations": {
      "type": "object",
      "$id": "#affiliations",
      "properties": {
        "id": {
          "type": "string",
          "enum": [
            "Adult AWG",
            "Pediatric AWG"
          ]
        },
        "name": {
          "type": "string",
          "enum": [
            "Adult Actionability Working Group",
            "Pediatric Actionability Working Group"
          ]
        }
      },
      "required": [
        "name"
      ]
    },
    "genes": {
      "type": "array",
      "$id": "#genes",
      "items": {
        "type": "object",
        "properties": {
          "ontology": {
            "type": "string",
            "default": "HGNC"
          },
          "symbol": {
            "type": "string"
          },
          "curie": {
            "type": "string",
            "format": "regex",
            "pattern": "^HGNC:\\d+$"
          },
          "uri": {
            "type": "string"
          }
        },
        "required": [
          "ontology",
          "symbol",
          "curie",
          "uri"
        ]
      },
      "minItems": 1
    },
    "variants": {
      "type": "array",
      "$id": "#variants",
      "items": {
        "type": "object",
        "properties": {
          "variantId": {
            "type": "string",
            "description": "CAR IDs if present"
          },
          "type": {
            "type": "string",
            "enum": [
              "Aneuploidy",
              "Copy Number Variant",
              "Methylation",
              "Poly Nucleotide Repeat",
              "Structural Variant",
              "Triple Repeat",
              "Other"
            ],
            "description": "Type of variant"
          },
          "description": {
            "type": "string",
            "description": "text description about the variant"
          },
          "descriptor": {
            "type": "array",
            "items": {
              "type": "string",
              "format": "regex",
              "pattern": "/^(?:(?<hgvsDesc>(?<refSeq>(?<seqId>[^ \t\n:]+)(?:\.(?<seqIdVer>\d+))):(?<seqType>[cgmnopr])\.(?<mod>\S+))|(?<svDesc>(?<assem>(?:GRCh38|GRCh37|NCBI36)) (?<bandLoc>[^\s\(]*)\((?<genLoc>chr[^:\s]+((::?[^\s]+)*))\)(?<otherMod>(inv|ins|dup|del|::)*)(?<extra>\S*))))$/"
            },
            "minItems": 1
          }
        },
        "required": [
          "type",
          "descriptor"
        ]
      },
      "minItems": 1
    },
    "conditions": {
      "type": "array",
      "$id": "#conditions",
      "description": "All the gene-condition pairs",
      "items": {
        "type": "object",
        "properties": {
          "ontology": {
            "type": "string",
            "default": "MONDO"
          },
          "curie": {
            "type": "string",
            "format": "regex",
            "pattern": "^MONDO:\\d+$"
          },
          "uri": {
            "type": "string"
          },
          "iri": {
            "type": "string",
            "format": "uri",
            "description": "link to MONDO"
          },
          "gene": {
            "type": "string",
            "format": "regex",
            "pattern": "^HGNC:\\d+$"
          },
          "variantId": {
            "type": "string",
            "description": "CAR IDs if present"
          },
          "type": {
            "type": "string",
            "enum": [
              "Aneuploidy",
              "Copy Number Variant",
              "Methylation",
              "Poly Nucleotide Repeat",
              "Structural Variant",
              "Triple Repeat",
              "Other"
            ],
            "description": "Type of variant"
          },
          "description": {
            "type": "string",
            "description": "text description about the variant"
          },
          "descriptor": {
            "type": "array",
            "items": {
              "type": "string",
              "format": "regex",
              "pattern": "/^(?:(?<hgvsDesc>(?<refSeq>(?<seqId>[^ \t\n:]+)(?:\.(?<seqIdVer>\d+))):(?<seqType>[cgmnopr])\.(?<mod>\S+))|(?<svDesc>(?<assem>(?:GRCh38|GRCh37|NCBI36)) (?<bandLoc>[^\s\(]*)\((?<genLoc>chr[^:\s]+((::?[^\s]+)*))\)(?<otherMod>(inv|ins|dup|del|::)*)(?<extra>\S*))))$/"
            },
            "minItems": 1
          }
        },
        "required": [
          "ontology",
          "curie",
          "uri",
          "iri"
        ]
      },
      "minItems": 1
    },
    "preferred_conditions": {
      "type": "array",
      "$id": "#conditions",
      "description": "All the gene-preferred MONDO condition pairs",
      "items": {
        "type": "object",
        "properties": {
          "ontology": {
            "type": "string",
            "default": "MONDO"
          },
          "curie": {
            "type": "string",
            "format": "regex",
            "pattern": "^MONDO:\\d+$"
          },
          "uri": {
            "type": "string"
          },
          "iri": {
            "type": "string",
            "format": "uri",
            "description": "link to MONDO"
          },
          "gene": {
            "type": "string",
            "format": "regex",
            "pattern": "^HGNC:\\d+$"
          },
          "variantId": {
            "type": "string",
            "description": "CAR IDs if present"
          },
          "type": {
            "type": "string",
            "enum": [
              "Aneuploidy",
              "Copy Number Variant",
              "Methylation",
              "Poly Nucleotide Repeat",
              "Structural Variant",
              "Triple Repeat",
              "Other"
            ],
            "description": "Type of variant"
          },
          "description": {
            "type": "string",
            "description": "text description about the variant"
          },
          "descriptor": {
            "type": "array",
            "items": {
              "type": "string",
              "format": "regex",
              "pattern": "/^(?:(?<hgvsDesc>(?<refSeq>(?<seqId>[^ \t\n:]+)(?:\.(?<seqIdVer>\d+))):(?<seqType>[cgmnopr])\.(?<mod>\S+))|(?<svDesc>(?<assem>(?:GRCh38|GRCh37|NCBI36)) (?<bandLoc>[^\s\(]*)\((?<genLoc>chr[^:\s]+((::?[^\s]+)*))\)(?<otherMod>(inv|ins|dup|del|::)*)(?<extra>\S*))))$/"
            },
            "minItems": 1
          }
        },
        "required": [
          "ontology",
          "curie",
          "uri",
          "iri",
          "gene"
        ]
      },
      "minItems": 1
    },
    "scores": {
      "type": "array",
      "$id": "#scores",
      "description": "scores for outcome intervention pair for a specific scoring group",
      "items": {
        "type": "object",
        "properties": {
          "Outcome": {
            "type": "string",
            "description": "outcome name"
          },
          "ScoringGroups": {
            "type": "array",
            "items": {
              "type": "object",
              "properties": {
                "Severity": {
                  "type": "string",
                  "description": "outcome scoring category"
                },
                "Likelihood": {
                  "type": "string",
                  "description": "outcome scoring category"
                },
                "ScoringGroup": {
                  "type": "object",
                  "properties": {
                    "variantId": {
                      "type": "string",
                      "description": "CAR IDs if present"
                    },
                    "type": {
                      "type": "string",
                      "enum": [
                        "Aneuploidy",
                        "Copy Number Variant",
                        "Methylation",
                        "Poly Nucleotide Repeat",
                        "Structural Variant",
                        "Triple Repeat",
                        "Other"
                      ],
                      "description": "Type of variant"
                    },
                    "description": {
                      "type": "string",
                      "description": "text description about the variant"
                    },
                    "descriptor": {
                      "type": "array",
                      "items": {
                        "type": "string",
                        "format": "regex",
                        "pattern": "/^(?:(?<hgvsDesc>(?<refSeq>(?<seqId>[^ \t\n:]+)(?:.(?<seqIdVer>d+))):(?<seqType>[cgmnopr]).(?<mod>S+))|(?<svDesc>(?<assem>(?:GRCh38|GRCh37|NCBI36)) (?<bandLoc>[^s(]*)((?<genLoc>chr[^:s]+::?[^s)]+))(?<extra>S*)))$/"
                      },
                      "minItems": 1
                    },
                    "vuuid": {
                      "type": "string",
                      "description": "uuuid for the variant object"
                    },
                    "disOmim": {
                      "type": "string",
                      "description": "Condition OMIM ID"
                    },
                    "geneOmim": {
                      "type": "string",
                      "description": "Gene OMIM ID"
                    },
                    "preferredMondo": {
                      "type": "string",
                      "description": "Preferred Mondo ID"
                    },
                    "gene": {
                      "type": "string",
                      "description": "Gene HGNC name"
                    }
                  }
                },
                "Interventions": {
                  "type": "array",
                  "items": {
                    "type": "object",
                    "properties": {
                      "Intervention": {
                        "type": "string",
                        "description": "intervention name"
                      },
                      "ScoringGroups": {
                        "type": "array",
                        "items": {
                          "type": "object",
                          "properties": {
                            "Effectiveness": {
                              "type": "string",
                              "description": "intervention scoring category"
                            },
                            "Total": {
                              "type": "string",
                              "description": "total score"
                            },
                            "Nature of Intervention": {
                              "type": "string",
                              "description": "intervention scoring category"
                            },
                            "ScoringGroup": {
                              "type": "array",
                              "items": {
                                "type": "string",
                                "format": "regex",
                                "pattern": "^HGNC:\\d+$"
                              },
                              "minItems": 1
                            }
                          },
                          "required": [
                            "Effectiveness",
                            "Total",
                            "Nature of Intervention"
                          ]
                        },
                        "minItems": 1
                      }
                    },
                    "required": [
                      "Intervention"
                    ]
                  },
                  "minItems": 1
                }
              },
              "required": [
                "Severity",
                "Likelihood"
              ]
            },
            "minItems": 1
          }
        },
        "required": [
          "Outcome"
        ]
      },
      "minItems": 0
    },
    "assertions": {
      "type": "array",
      "$id": "#assertions",
      "description": "Assertion for each gene-condition",
      "items": {
        "type": "object",
        "properties": {
          "ontology": {
            "type": "string",
            "default": "MONDO"
          },
          "curie": {
            "type": "string",
            "format": "regex",
            "pattern": "^MONDO:\\d+$"
          },
          "uri": {
            "type": "string"
          },
          "iri": {
            "type": "string",
            "format": "uri",
            "description": "link to MONDO"
          },
          "gene": {
            "type": "string",
            "format": "regex",
            "pattern": "^HGNC:\\d+$"
          },
          "assertions": {
            "type": "string",
            "enum": [
              "Definitive Actionability",
              "Strong Actionability",
              "Moderate Actionability",
              "Limited Actionability",
              "Insufficient Actionability",
              "No Actionability",
              "N/A - Insufficient evidence: early rule-out",
              "N/A - Insufficient evidence: expert review",
              "Assertion Pending",
              "No Assertion: scoring group absence"
            ]
          },
          "variantId": {
            "type": "string",
            "description": "CAR IDs if present"
          },
          "type": {
            "type": "string",
            "enum": [
              "Aneuploidy",
              "Copy Number Variant",
              "Methylation",
              "Poly Nucleotide Repeat",
              "Structural Variant",
              "Triple Repeat",
              "Other"
            ],
            "description": "Type of variant"
          },
          "description": {
            "type": "string",
            "description": "text description about the variant"
          },
          "descriptor": {
            "type": "array",
            "items": {
              "type": "string",
              "format": "regex",
              "pattern": "/^(?:(?<hgvsDesc>(?<refSeq>(?<seqId>[^ \t\n:]+)(?:\.(?<seqIdVer>\d+))):(?<seqType>[cgmnopr])\.(?<mod>\S+))|(?<svDesc>(?<assem>(?:GRCh38|GRCh37|NCBI36)) (?<bandLoc>[^\s\(]*)\((?<genLoc>chr[^:\s]+((::?[^\s]+)*))\)(?<otherMod>(inv|ins|dup|del|::)*)(?<extra>\S*))))$/"
            },
            "minItems": 1
          }
        },
        "required": [
          "ontology",
          "curie",
          "uri",
          "iri",
          "gene",
          "assertions"
        ]
      },
      "minItems": 0
    }
  },
  "type": "object",
  "properties": {
    "jsonMessageVersion": {
      "type": "string",
      "pattern": "^\\d+.\\d+.\\d+$",
      "format": "regex",
      "description": "Semantic versioning with major minor and patch versions"
    },
    "statusPublishFlag": {
      "type": "string",
      "default": "Publish"
    },
    "curationType": {
      "type": "string",
      "default": "Gene-Condition",
      "enum": [
        "Gene-Condition",
        "Variant-Condition"
      ]
    },
    "type": {
      "type": "string",
      "description": "Note that this will be deprecated from 2.0.0+ versions",
      "default": "actionability"
    },
    "iri": {
      "type": "string",
      "format": "uri",
      "description": "Iri to context specific sepio link. Example: https://actionability.clinicalgenome.org/ac/Adult/api/sepio/doc/AC002"
    },
    "title": {
      "type": "string",
      "description": "Condition - comma separated genes"
    },
    "curationVersion": {
      "type": "string",
      "pattern": "^\\d+.\\d+.\\d+$",
      "format": "regex",
      "description": "Semantic versioning with major minor and patch versions"
    },
    "statusFlag": {
      "type": "string",
      "enum": [
        "Entered",
        "Collecting",
        "Reviewing",
        "Released",
        "In Preparation",
        "Released - Under Revision",
        "Retracted",
        "NA"
      ],
      "description": "Curation status of the topic"
    },
    "dateISO8601": {
      "type": "string",
      "format": "date-time",
      "description": "time when the topic received this status"
    },
    "releaseNotes": {
      "type": "string",
      "minLength": 0,
      "description": "Release notes entered when the status is Released"
    },
    "earlyRuleOutStatus": {
      "type": "string",
      "enum": [
        "Complete",
        "Incomplete"
      ],
      "description": "Early rule out survey status."
    },
    "surveyDetails": {
      "type": "string",
      "format": "uri",
      "description": "Topic specific early rule out report link. Example: https://actionability.clinicalgenome.org/ac/ui/stg1RuleOutRpt?doc=AC1056"
    },
    "scoreDetails": {
      "type": "string",
      "format": "uri",
      "description": "Context specific summary report. Example: https://actionability.clinicalgenome.org/ac/Adult/ui/stg2SummaryRpt?doc=AC1056"
    },
    "affiliations": {
      "$ref": "#affiliations"
    },
    "genes": {
      "$ref": "#genes"
    },
    "variants": {
      "$ref": "#variants"
    },
    "conditions": {
      "$ref": "#conditions"
    },
    "preferred_conditions": {
      "$ref": "#preferred_conditions"
    },
    "scores": {
      "$ref": "#scores"
    },
    "assertions": {
      "$ref": "#assertions"
    },
    "searchDates": {
      "type": "array",
      "items": {
        "type": "string",
        "format": "date-time",
        "description": "time when the topic literature search was done."
      },
      "minItems": 0
    }
  },
  "required": [
    "jsonMessageVersion",
    "statusPublishFlag",
    "curationType",
    "type",
    "iri",
    "title",
    "curationVersion",
    "statusFlag",
    "dateISO8601",
    "releaseNotes",
    "earlyRuleOutStatus",
    "surveyDetails",
    "scoreDetails",
    "affiliations",
    "conditions",
    "preferred_conditions",
    "scores",
    "assertions",
    "searchDates"
  ]
}