Allele¶

Referenced schema · Source · Dereferenced version

A VRS Allele. The hgvs.* and state_* keys are flat here and are folded into expressions and state upon dereference.

Fields¶

Field	Type	Required	Description
`id`	string matching `^ga4gh:VA.[A-Za-z0-9_-]{32}$`	yes
`type`	always `Allele`	yes
`name`	string	yes
`aliases`	array of string	yes
`description`	string	yes
`digest`	string	yes
`hgvs.g`	string or null	yes
`hgvs.c`	string or null	yes
`hgvs.c_short`	string or null	yes
`hgvs.p`	string or null	yes
`hgvs.p_short`	string or null	yes
`location`	string matching `^ga4gh:SL.[A-Za-z0-9_-]{32}$`	yes	Foreign key to `sequence_locations.id`.
`state_type`	one of `LiteralSequenceExpression`, `ReferenceLengthExpression`	yes
`state_sequence`	string	yes
`state_length`	integer or null	yes	Only populated for a ReferenceLengthExpression.
`state_repeat_subunit_length`	integer or null	yes	Only populated for a ReferenceLengthExpression.

Additional rules¶

These rules also apply to every record:

When state_type is ReferenceLengthExpression: state_length is integer and state_repeat_subunit_length is integer. Otherwise: state_length is null and state_repeat_subunit_length is null.

JSON Schema¶

Full JSON Schema

{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "$id": "https://moalmanac.org/schemas/referenced/alleles.schema.json",
  "title": "Allele",
  "description": "A VRS Allele. The `hgvs.*` and `state_*` keys are flat here and are folded into `expressions` and `state` upon dereference.",
  "type": "object",
  "properties": {
    "id": {
      "type": "string",
      "pattern": "^ga4gh:VA\\.[A-Za-z0-9_-]{32}$"
    },
    "type": {
      "const": "Allele"
    },
    "name": {
      "type": "string"
    },
    "aliases": {
      "type": "array",
      "items": {
        "type": "string"
      }
    },
    "description": {
      "type": "string"
    },
    "digest": {
      "type": "string"
    },
    "hgvs.g": {
      "type": [
        "string",
        "null"
      ]
    },
    "hgvs.c": {
      "type": [
        "string",
        "null"
      ]
    },
    "hgvs.c_short": {
      "type": [
        "string",
        "null"
      ]
    },
    "hgvs.p": {
      "type": [
        "string",
        "null"
      ]
    },
    "hgvs.p_short": {
      "type": [
        "string",
        "null"
      ]
    },
    "location": {
      "type": "string",
      "pattern": "^ga4gh:SL\\.[A-Za-z0-9_-]{32}$",
      "description": "Foreign key to `sequence_locations.id`."
    },
    "state_type": {
      "enum": [
        "LiteralSequenceExpression",
        "ReferenceLengthExpression"
      ]
    },
    "state_sequence": {
      "type": "string"
    },
    "state_length": {
      "type": [
        "integer",
        "null"
      ],
      "description": "Only populated for a ReferenceLengthExpression."
    },
    "state_repeat_subunit_length": {
      "type": [
        "integer",
        "null"
      ],
      "description": "Only populated for a ReferenceLengthExpression."
    }
  },
  "required": [
    "id",
    "type",
    "name",
    "aliases",
    "description",
    "digest",
    "hgvs.g",
    "hgvs.c",
    "hgvs.c_short",
    "hgvs.p",
    "hgvs.p_short",
    "location",
    "state_type",
    "state_sequence",
    "state_length",
    "state_repeat_subunit_length"
  ],
  "additionalProperties": false,
  "if": {
    "properties": {
      "state_type": {
        "const": "ReferenceLengthExpression"
      }
    },
    "required": [
      "state_type"
    ]
  },
  "then": {
    "properties": {
      "state_length": {
        "type": "integer"
      },
      "state_repeat_subunit_length": {
        "type": "integer"
      }
    }
  },
  "else": {
    "properties": {
      "state_length": {
        "type": "null"
      },
      "state_repeat_subunit_length": {
        "type": "null"
      }
    }
  }
}