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Allele

Dereferenced schema · Source · Referenced version

A VRS Allele with its SequenceLocation embedded. The referenced hgvs.* keys become expressions and the state_* keys become state.

Fields

Field Type Required Description
id string matching ^ga4gh:VA.[A-Za-z0-9_-]{32}$ yes
type always Allele yes
name string yes
aliases array of string yes
description string yes
digest string yes
expressions array of objects yes
expressions[].syntax one of hgvs.g, hgvs.c, hgvs.p yes
expressions[].value string yes
expressions[].extensions array of extensions: hgvs.c_short (string), hgvs.p_short (string)
location SequenceLocation yes
state LiteralSequenceExpression or ReferenceLengthExpression yes The allele's state, one of the VRS state types defined in $defs, selected by type.

Definitions

LiteralSequenceExpression

A state given as a literal sequence.

Field Type Required Description
type always LiteralSequenceExpression yes
sequence string yes

ReferenceLengthExpression

A state given as a length relative to the reference, e.g. a repeat expansion or deletion.

Field Type Required Description
type always ReferenceLengthExpression yes
sequence string yes
length integer at least 0 yes
repeatSubunitLength integer at least 0 yes

JSON Schema

Full JSON Schema 
{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "$id": "https://moalmanac.org/schemas/dereferenced/alleles.schema.json",
  "title": "Allele",
  "description": "A VRS Allele with its SequenceLocation embedded. The referenced `hgvs.*` keys become `expressions` and the `state_*` keys become `state`.",
  "type": "object",
  "properties": {
    "id": {
      "type": "string",
      "pattern": "^ga4gh:VA\\.[A-Za-z0-9_-]{32}$"
    },
    "type": {
      "const": "Allele"
    },
    "name": {
      "type": "string"
    },
    "aliases": {
      "type": "array",
      "items": {
        "type": "string"
      }
    },
    "description": {
      "type": "string"
    },
    "digest": {
      "type": "string"
    },
    "expressions": {
      "type": "array",
      "items": {
        "type": "object",
        "properties": {
          "syntax": {
            "enum": [
              "hgvs.g",
              "hgvs.c",
              "hgvs.p"
            ]
          },
          "value": {
            "type": "string"
          },
          "extensions": {
            "type": "array",
            "items": {
              "anyOf": [
                {
                  "$ref": "extension.schema.json",
                  "properties": {
                    "name": {
                      "const": "hgvs.c_short"
                    },
                    "value": {
                      "type": "string"
                    }
                  }
                },
                {
                  "$ref": "extension.schema.json",
                  "properties": {
                    "name": {
                      "const": "hgvs.p_short"
                    },
                    "value": {
                      "type": "string"
                    }
                  }
                }
              ]
            }
          }
        },
        "required": [
          "syntax",
          "value"
        ],
        "additionalProperties": false
      }
    },
    "location": {
      "$ref": "sequence_locations.schema.json"
    },
    "state": {
      "description": "The allele's state, one of the VRS state types defined in `$defs`, selected by `type`.",
      "oneOf": [
        {
          "$ref": "#/$defs/LiteralSequenceExpression"
        },
        {
          "$ref": "#/$defs/ReferenceLengthExpression"
        }
      ]
    }
  },
  "required": [
    "id",
    "type",
    "name",
    "aliases",
    "description",
    "digest",
    "expressions",
    "location",
    "state"
  ],
  "additionalProperties": false,
  "$defs": {
    "LiteralSequenceExpression": {
      "description": "A state given as a literal sequence.",
      "type": "object",
      "properties": {
        "type": {
          "const": "LiteralSequenceExpression"
        },
        "sequence": {
          "type": "string"
        }
      },
      "required": [
        "type",
        "sequence"
      ],
      "additionalProperties": false
    },
    "ReferenceLengthExpression": {
      "description": "A state given as a length relative to the reference, e.g. a repeat expansion or deletion.",
      "type": "object",
      "properties": {
        "type": {
          "const": "ReferenceLengthExpression"
        },
        "sequence": {
          "type": "string"
        },
        "length": {
          "type": "integer",
          "minimum": 0
        },
        "repeatSubunitLength": {
          "type": "integer",
          "minimum": 0
        }
      },
      "required": [
        "type",
        "sequence",
        "length",
        "repeatSubunitLength"
      ],
      "additionalProperties": false
    }
  }
}