{
   "$schema": "http://json-schema.org/draft-07/schema",
   "title": "GA4GH-VRS-Definitions",
   "type": "object",
   "definitions": {
      "Variation": {
         "description": "A representation of the state of one or more biomolecules.",
         "oneOf": [
            {
               "$ref": "#/definitions/MolecularVariation"
            },
            {
               "$ref": "#/definitions/SystemicVariation"
            },
            {
               "$ref": "#/definitions/UtilityVariation"
            }
         ],
         "discriminator": {
            "propertyName": "type"
         }
      },
      "MolecularVariation": {
         "description": "A variation on a contiguous molecule.",
         "oneOf": [
            {
               "$ref": "#/definitions/Allele"
            },
            {
               "$ref": "#/definitions/Haplotype"
            }
         ],
         "discriminator": {
            "propertyName": "type"
         }
      },
      "UtilityVariation": {
         "description": "A collection of Variation subclasses that cannot be constrained to a specific class of biological variation, but are necessary for some applications of VRS.",
         "oneOf": [
            {
               "$ref": "#/definitions/Text"
            },
            {
               "$ref": "#/definitions/VariationSet"
            }
         ],
         "discriminator": {
            "propertyName": "type"
         }
      },
      "SystemicVariation": {
         "description": "A Variation of multiple molecules in the context of a system, e.g. a genome, sample, or homologous chromosomes.",
         "oneOf": [
            {
               "$ref": "#/definitions/CopyNumber"
            }
         ],
         "discriminator": {
            "propertyName": "type"
         }
      },
      "Allele": {
         "description": "The state of a molecule at a Location.",
         "additionalProperties": false,
         "type": "object",
         "properties": {
            "_id": {
               "$ref": "#/definitions/CURIE",
               "description": "Variation Id. MUST be unique within document."
            },
            "type": {
               "type": "string",
               "const": "Allele",
               "default": "Allele",
               "description": "MUST be \"Allele\""
            },
            "location": {
               "oneOf": [
                  {
                     "$ref": "#/definitions/CURIE"
                  },
                  {
                     "$ref": "#/definitions/Location"
                  }
               ],
               "description": "Where Allele is located"
            },
            "state": {
               "oneOf": [
                  {
                     "$ref": "#/definitions/SequenceExpression"
                  },
                  {
                     "$ref": "#/definitions/SequenceState"
                  }
               ],
               "description": "An expression of the sequence state",
               "deprecated": [
                  {
                     "$ref": "#/definitions/SequenceState"
                  }
               ]
            }
         },
         "required": [
            "location",
            "state",
            "type"
         ]
      },
      "Haplotype": {
         "description": "A set of non-overlapping Allele members that co-occur on the same molecule.",
         "additionalProperties": false,
         "type": "object",
         "properties": {
            "_id": {
               "$ref": "#/definitions/CURIE",
               "description": "Variation Id. MUST be unique within document."
            },
            "type": {
               "type": "string",
               "const": "Haplotype",
               "default": "Haplotype",
               "description": "MUST be \"Haplotype\""
            },
            "members": {
               "type": "array",
               "minItems": 1,
               "uniqueItems": true,
               "items": {
                  "oneOf": [
                     {
                        "$ref": "#/definitions/Allele"
                     },
                     {
                        "$ref": "#/definitions/CURIE"
                     }
                  ]
               },
               "description": "List of Alleles, or references to Alleles, that comprise this Haplotype."
            }
         },
         "required": [
            "members",
            "type"
         ]
      },
      "Text": {
         "description": "A free-text definition of variation.",
         "additionalProperties": false,
         "type": "object",
         "properties": {
            "_id": {
               "$ref": "#/definitions/CURIE",
               "description": "Variation Id. MUST be unique within document."
            },
            "type": {
               "type": "string",
               "const": "Text",
               "default": "Text",
               "description": "MUST be \"Text\""
            },
            "definition": {
               "type": "string",
               "description": "A textual representation of variation not representable by other subclasses of Variation."
            }
         },
         "required": [
            "definition",
            "type"
         ]
      },
      "VariationSet": {
         "description": "An unconstrained set of Variation members.",
         "type": "object",
         "additionalProperties": false,
         "properties": {
            "_id": {
               "$ref": "#/definitions/CURIE",
               "description": "Variation Id. MUST be unique within document."
            },
            "type": {
               "type": "string",
               "const": "VariationSet",
               "default": "VariationSet",
               "description": "MUST be \"VariationSet\""
            },
            "members": {
               "type": "array",
               "uniqueItems": true,
               "items": {
                  "oneOf": [
                     {
                        "$ref": "#/definitions/CURIE"
                     },
                     {
                        "$ref": "#/definitions/Variation"
                     }
                  ]
               },
               "description": "List of Variation objects or identifiers. Attribute is required, but MAY be empty."
            }
         },
         "required": [
            "members",
            "type"
         ]
      },
      "CopyNumber": {
         "additionalProperties": false,
         "type": "object",
         "description": "The absolute count of discrete copies of a MolecularVariation, Feature, SequenceExpression, or a CURIE reference within a system (e.g. genome, cell, etc.).",
         "properties": {
            "_id": {
               "$ref": "#/definitions/CURIE",
               "description": "Variation Id. MUST be unique within document."
            },
            "type": {
               "type": "string",
               "const": "CopyNumber",
               "default": "CopyNumber",
               "description": "MUST be \"CopyNumber\""
            },
            "subject": {
               "oneOf": [
                  {
                     "$ref": "#/definitions/MolecularVariation"
                  },
                  {
                     "$ref": "#/definitions/Feature"
                  },
                  {
                     "$ref": "#/definitions/SequenceExpression"
                  },
                  {
                     "$ref": "#/definitions/CURIE"
                  }
               ],
               "description": "Subject of the Copy Number object"
            },
            "copies": {
               "oneOf": [
                  {
                     "$ref": "#/definitions/Number"
                  },
                  {
                     "$ref": "#/definitions/IndefiniteRange"
                  },
                  {
                     "$ref": "#/definitions/DefiniteRange"
                  }
               ],
               "description": "The integral number of copies of the subject in a system"
            }
         },
         "allOf": [
            {
               "if": {
                  "properties": {
                     "copies": {
                        "$ref": "#/definitions/Number"
                     }
                  }
               },
               "then": {
                  "properties": {
                     "copies": {
                        "properties": {
                           "value": {
                              "minimum": 0
                           }
                        }
                     }
                  }
               }
            },
            {
               "if": {
                  "properties": {
                     "copies": {
                        "$ref": "#/definitions/IndefiniteRange"
                     }
                  }
               },
               "then": {
                  "properties": {
                     "copies": {
                        "properties": {
                           "value": {
                              "minimum": 0
                           }
                        }
                     }
                  }
               }
            },
            {
               "if": {
                  "properties": {
                     "copies": {
                        "$ref": "#/definitions/DefiniteRange"
                     }
                  }
               },
               "then": {
                  "properties": {
                     "copies": {
                        "properties": {
                           "min": {
                              "minimum": 0
                           },
                           "max": {
                              "minimum": 0
                           }
                        }
                     }
                  }
               }
            }
         ],
         "required": [
            "copies",
            "subject",
            "type"
         ]
      },
      "Location": {
         "description": "A contiguous segment of a biological sequence.",
         "oneOf": [
            {
               "$ref": "#/definitions/ChromosomeLocation"
            },
            {
               "$ref": "#/definitions/SequenceLocation"
            }
         ],
         "discriminator": {
            "propertyName": "type"
         }
      },
      "ChromosomeLocation": {
         "additionalProperties": false,
         "description": "A Location on a chromosome defined by a species and chromosome name.",
         "type": "object",
         "properties": {
            "_id": {
               "$ref": "#/definitions/CURIE",
               "description": "Location Id. MUST be unique within document."
            },
            "type": {
               "type": "string",
               "const": "ChromosomeLocation",
               "default": "ChromosomeLocation",
               "description": "MUST be \"ChromosomeLocation\""
            },
            "species_id": {
               "$ref": "#/definitions/CURIE",
               "default": "taxonomy:9606",
               "description": "CURIE representing a species from the [NCBI species taxonomy](https://registry.identifiers.org/registry/taxonomy). Default: \"taxonomy:9606\" (human)"
            },
            "chr": {
               "type": "string",
               "description": "The symbolic chromosome name. For humans, For humans, chromosome names MUST be one of 1..22, X, Y (case-sensitive)"
            },
            "interval": {
               "$ref": "#/definitions/CytobandInterval",
               "description": "The chromosome region defined by a CytobandInterval"
            }
         },
         "required": [
            "chr",
            "interval",
            "species_id",
            "type"
         ]
      },
      "SequenceLocation": {
         "additionalProperties": false,
         "description": "A Location defined by an interval on a referenced Sequence.",
         "type": "object",
         "properties": {
            "_id": {
               "$ref": "#/definitions/CURIE",
               "description": "Location Id. MUST be unique within document."
            },
            "type": {
               "type": "string",
               "const": "SequenceLocation",
               "default": "SequenceLocation",
               "description": "MUST be \"SequenceLocation\""
            },
            "sequence_id": {
               "$ref": "#/definitions/CURIE",
               "description": "A VRS Computed Identifier for the reference Sequence."
            },
            "interval": {
               "oneOf": [
                  {
                     "$ref": "#/definitions/SequenceInterval"
                  },
                  {
                     "$ref": "#/definitions/SimpleInterval"
                  }
               ],
               "description": "Reference sequence region defined by a SequenceInterval."
            }
         },
         "required": [
            "interval",
            "sequence_id",
            "type"
         ]
      },
      "SequenceInterval": {
         "description": "A SequenceInterval represents a span on a Sequence. Positions are always represented by contiguous spans using interbase coordinates or coordinate ranges.",
         "type": "object",
         "additionalProperties": false,
         "properties": {
            "type": {
               "type": "string",
               "const": "SequenceInterval",
               "default": "SequenceInterval",
               "description": "MUST be \"SequenceInterval\""
            },
            "start": {
               "oneOf": [
                  {
                     "$ref": "#/definitions/Number"
                  },
                  {
                     "$ref": "#/definitions/IndefiniteRange"
                  },
                  {
                     "$ref": "#/definitions/DefiniteRange"
                  }
               ],
               "description": "The start coordinate or range of the interval. The minimum value of this coordinate or range is 0. MUST represent a coordinate or range less than the value of `end`."
            },
            "end": {
               "oneOf": [
                  {
                     "$ref": "#/definitions/Number"
                  },
                  {
                     "$ref": "#/definitions/IndefiniteRange"
                  },
                  {
                     "$ref": "#/definitions/DefiniteRange"
                  }
               ],
               "description": "The end coordinate or range of the interval. The minimum value of this coordinate or range is 0. MUST represent a coordinate or range greater than the value of `start`."
            }
         },
         "allOf": [
            {
               "if": {
                  "properties": {
                     "start": {
                        "$ref": "#/definitions/Number"
                     }
                  }
               },
               "then": {
                  "properties": {
                     "start": {
                        "properties": {
                           "value": {
                              "minimum": 0
                           }
                        }
                     }
                  }
               }
            },
            {
               "if": {
                  "properties": {
                     "start": {
                        "$ref": "#/definitions/IndefiniteRange"
                     }
                  }
               },
               "then": {
                  "properties": {
                     "start": {
                        "properties": {
                           "value": {
                              "minimum": 0
                           }
                        }
                     }
                  }
               }
            },
            {
               "if": {
                  "properties": {
                     "start": {
                        "$ref": "#/definitions/DefiniteRange"
                     }
                  }
               },
               "then": {
                  "properties": {
                     "start": {
                        "properties": {
                           "min": {
                              "minimum": 0
                           },
                           "max": {
                              "minimum": 0
                           }
                        }
                     }
                  }
               }
            },
            {
               "if": {
                  "properties": {
                     "end": {
                        "$ref": "#/definitions/Number"
                     }
                  }
               },
               "then": {
                  "properties": {
                     "end": {
                        "properties": {
                           "value": {
                              "minimum": 0
                           }
                        }
                     }
                  }
               }
            },
            {
               "if": {
                  "properties": {
                     "end": {
                        "$ref": "#/definitions/IndefiniteRange"
                     }
                  }
               },
               "then": {
                  "properties": {
                     "end": {
                        "properties": {
                           "value": {
                              "minimum": 0
                           }
                        }
                     }
                  }
               }
            },
            {
               "if": {
                  "properties": {
                     "end": {
                        "$ref": "#/definitions/DefiniteRange"
                     }
                  }
               },
               "then": {
                  "properties": {
                     "end": {
                        "properties": {
                           "min": {
                              "minimum": 0
                           },
                           "max": {
                              "minimum": 0
                           }
                        }
                     }
                  }
               }
            }
         ],
         "required": [
            "end",
            "start",
            "type"
         ]
      },
      "CytobandInterval": {
         "description": "A contiguous span on a chromosome defined by cytoband features. The span includes the constituent regions described by the start and end cytobands, as well as any intervening regions.",
         "type": "object",
         "additionalProperties": false,
         "properties": {
            "type": {
               "type": "string",
               "const": "CytobandInterval",
               "default": "CytobandInterval",
               "description": "MUST be \"CytobandInterval\""
            },
            "start": {
               "$ref": "#/definitions/HumanCytoband",
               "description": "The start cytoband region. MUST specify a region nearer the terminal end (telomere) of the chromosome p-arm than `end`."
            },
            "end": {
               "$ref": "#/definitions/HumanCytoband",
               "description": "The start cytoband region. MUST specify a region nearer the terminal end (telomere) of the chromosome q-arm than `start`."
            }
         },
         "example": {
            "type": "CytobandInterval",
            "start": "q22.2",
            "end": "q22.3"
         },
         "required": [
            "end",
            "start",
            "type"
         ]
      },
      "SequenceExpression": {
         "description": "An expression describing a Sequence.",
         "oneOf": [
            {
               "$ref": "#/definitions/LiteralSequenceExpression"
            },
            {
               "$ref": "#/definitions/DerivedSequenceExpression"
            },
            {
               "$ref": "#/definitions/RepeatedSequenceExpression"
            }
         ],
         "discriminator": {
            "propertyName": "type"
         }
      },
      "LiteralSequenceExpression": {
         "description": "An explicit expression of a Sequence.",
         "type": "object",
         "additionalProperties": false,
         "properties": {
            "type": {
               "type": "string",
               "const": "LiteralSequenceExpression",
               "default": "LiteralSequenceExpression",
               "description": "MUST be \"LiteralSequenceExpression\""
            },
            "sequence": {
               "$ref": "#/definitions/Sequence",
               "description": "the literal Sequence expressed"
            }
         },
         "required": [
            "sequence",
            "type"
         ]
      },
      "DerivedSequenceExpression": {
         "description": "An approximate expression of a sequence that is derived from a referenced sequence location. Use of this class indicates that the derived sequence is *approximately equivalent* to the reference indicated, and is typically used for describing large regions in contexts where the use of an approximate sequence is inconsequential.",
         "type": "object",
         "additionalProperties": false,
         "properties": {
            "type": {
               "type": "string",
               "const": "DerivedSequenceExpression",
               "default": "DerivedSequenceExpression",
               "description": "MUST be \"DerivedSequenceExpression\""
            },
            "location": {
               "$ref": "#/definitions/SequenceLocation",
               "description": "The location from which the approximate sequence is derived"
            },
            "reverse_complement": {
               "type": "boolean",
               "description": "A flag indicating if the expressed sequence is the reverse complement of the sequence referred to by `location`"
            }
         },
         "required": [
            "location",
            "reverse_complement",
            "type"
         ]
      },
      "RepeatedSequenceExpression": {
         "description": "An expression of a sequence comprised of a tandem repeating subsequence.",
         "additionalProperties": false,
         "type": "object",
         "properties": {
            "type": {
               "type": "string",
               "const": "RepeatedSequenceExpression",
               "default": "RepeatedSequenceExpression",
               "description": "MUST be \"RepeatedSequenceExpression\""
            },
            "seq_expr": {
               "oneOf": [
                  {
                     "$ref": "#/definitions/LiteralSequenceExpression"
                  },
                  {
                     "$ref": "#/definitions/DerivedSequenceExpression"
                  }
               ],
               "description": "An expression of the repeating subsequence"
            },
            "count": {
               "oneOf": [
                  {
                     "$ref": "#/definitions/Number"
                  },
                  {
                     "$ref": "#/definitions/IndefiniteRange"
                  },
                  {
                     "$ref": "#/definitions/DefiniteRange"
                  }
               ],
               "description": "The count of repeated units, as an integer or inclusive range"
            }
         },
         "allOf": [
            {
               "if": {
                  "properties": {
                     "count": {
                        "$ref": "#/definitions/Number"
                     }
                  }
               },
               "then": {
                  "properties": {
                     "count": {
                        "properties": {
                           "value": {
                              "minimum": 0
                           }
                        }
                     }
                  }
               }
            },
            {
               "if": {
                  "properties": {
                     "count": {
                        "$ref": "#/definitions/IndefiniteRange"
                     }
                  }
               },
               "then": {
                  "properties": {
                     "count": {
                        "properties": {
                           "value": {
                              "minimum": 0
                           }
                        }
                     }
                  }
               }
            },
            {
               "if": {
                  "properties": {
                     "count": {
                        "$ref": "#/definitions/DefiniteRange"
                     }
                  }
               },
               "then": {
                  "properties": {
                     "count": {
                        "properties": {
                           "min": {
                              "minimum": 0
                           },
                           "max": {
                              "minimum": 0
                           }
                        }
                     }
                  }
               }
            }
         ],
         "required": [
            "count",
            "seq_expr",
            "type"
         ]
      },
      "Feature": {
         "description": "A named entity that can be mapped to a Location. Genes, protein domains, exons, and chromosomes are some examples of common biological entities that may be Features.",
         "oneOf": [
            {
               "$ref": "#/definitions/Gene"
            }
         ],
         "discriminator": {
            "propertyName": "type"
         }
      },
      "Gene": {
         "description": "A reference to a Gene as defined by an authority. For human genes, the use of [hgnc](https://registry.identifiers.org/registry/hgnc) as the gene authority is RECOMMENDED.",
         "type": "object",
         "additionalProperties": false,
         "properties": {
            "type": {
               "type": "string",
               "const": "Gene",
               "default": "Gene",
               "description": "MUST be \"Gene\""
            },
            "gene_id": {
               "$ref": "#/definitions/CURIE",
               "description": "A CURIE reference to a Gene concept"
            }
         },
         "required": [
            "gene_id",
            "type"
         ]
      },
      "Number": {
         "description": "A simple integer value as a VRS class.",
         "type": "object",
         "additionalProperties": false,
         "properties": {
            "type": {
               "type": "string",
               "const": "Number",
               "default": "Number",
               "description": "MUST be \"Number\""
            },
            "value": {
               "type": "integer",
               "description": "The value represented by Number"
            }
         },
         "required": [
            "type",
            "value"
         ]
      },
      "DefiniteRange": {
         "description": "A bounded, inclusive range of numbers.",
         "type": "object",
         "additionalProperties": false,
         "properties": {
            "type": {
               "type": "string",
               "const": "DefiniteRange",
               "default": "DefiniteRange",
               "description": "MUST be \"DefiniteRange\""
            },
            "min": {
               "type": "number",
               "description": "The minimum value; inclusive"
            },
            "max": {
               "type": "number",
               "description": "The maximum value; inclusive"
            }
         },
         "required": [
            "max",
            "min",
            "type"
         ]
      },
      "IndefiniteRange": {
         "description": "A half-bounded range of numbers represented as a number bound and associated comparator. The bound operator is interpreted as follows: '>=' are all numbers greater than and including `value`, '<=' are all numbers less than and including `value`.",
         "type": "object",
         "additionalProperties": false,
         "properties": {
            "type": {
               "type": "string",
               "const": "IndefiniteRange",
               "default": "IndefiniteRange",
               "description": "MUST be \"IndefiniteRange\""
            },
            "value": {
               "type": "number",
               "description": "The bounded value; inclusive"
            },
            "comparator": {
               "type": "string",
               "enum": [
                  "<=",
                  ">="
               ],
               "description": "MUST be one of \"<=\" or \">=\", indicating which direction the range is indefinite"
            }
         },
         "required": [
            "comparator",
            "type",
            "value"
         ]
      },
      "CURIE": {
         "additionalProperties": false,
         "description": "A [W3C Compact URI](https://www.w3.org/TR/curie/) formatted string. A CURIE string has the structure ``prefix``:``reference``, as defined by the W3C syntax.",
         "type": "string",
         "pattern": "^\\w[^:]*:.+$",
         "example": "ensembl:ENSG00000139618"
      },
      "HumanCytoband": {
         "additionalProperties": false,
         "description": "A character string representing cytobands derived from the *International System for Human Cytogenomic Nomenclature* (ISCN) [guidelines](http://doi.org/10.1159/isbn.978-3-318-06861-0).",
         "type": "string",
         "pattern": "^cen|[pq](ter|([1-9][0-9]*(\\.[1-9][0-9]*)?))$",
         "example": "q22.3"
      },
      "Residue": {
         "additionalProperties": false,
         "description": "A character representing a specific residue (i.e., molecular species) or groupings of these (\"ambiguity codes\"), using [one-letter IUPAC abbreviations](https://en.wikipedia.org/wiki/International_Union_of_Pure_and_Applied_Chemistry#Amino_acid_and_nucleotide_base_codes) for nucleic acids and amino acids.",
         "type": "string",
         "pattern": "[A-Z*\\-]"
      },
      "Sequence": {
         "additionalProperties": false,
         "description": "A character string of Residues that represents a biological sequence using the conventional sequence order (5\u2019-to-3\u2019 for nucleic acid sequences, and amino-to-carboxyl for amino acid sequences). IUPAC ambiguity codes are permitted in Sequences.",
         "type": "string",
         "pattern": "^[A-Z*\\-]*$"
      },
      "SequenceState": {
         "deprecated": true,
         "description": "DEPRECATED. A Sequence as a State. This is the State class to use for representing \"ref-alt\" style variation, including SNVs, MNVs, del, ins, and delins. This class is deprecated. Use LiteralSequenceExpression instead.",
         "additionalProperties": false,
         "type": "object",
         "properties": {
            "type": {
               "type": "string",
               "const": "SequenceState",
               "default": "SequenceState",
               "description": "MUST be \"SequenceState\""
            },
            "sequence": {
               "$ref": "#/definitions/Sequence",
               "description": "A string of Residues"
            }
         },
         "example": {
            "type": "SequenceState",
            "sequence": "C"
         },
         "required": [
            "sequence",
            "type"
         ]
      },
      "SimpleInterval": {
         "deprecated": true,
         "description": "DEPRECATED: A SimpleInterval represents a span of sequence. Positions are always represented by contiguous spans using interbase coordinates. This class is deprecated. Use SequenceInterval instead.",
         "additionalProperties": false,
         "type": "object",
         "properties": {
            "type": {
               "type": "string",
               "const": "SimpleInterval",
               "default": "SimpleInterval",
               "description": "MUST be \"SimpleInterval\""
            },
            "start": {
               "type": "integer",
               "description": "The start coordinate"
            },
            "end": {
               "type": "integer",
               "description": "The end coordinate"
            }
         },
         "example": {
            "type": "SimpleInterval",
            "start": 11,
            "end": 22
         },
         "required": [
            "end",
            "start",
            "type"
         ]
      }
   }
}