vrs-source.yaml

# VRS uses yaml as the source document for json schema
#
# To convert vrs.yaml to vrs.json:
#   make vrs.json
# You'll probably have to `pip install pyyaml` first.
#
# To watch for changes and update automatically:
#   make watch &

# https://json-schema.org/understanding-json-schema/reference/schema.html
$schema: "http://json-schema.org/draft-07/schema"
title: "GA4GH-VRS-Definitions"
type: object

definitions:
  # VRS definitions are presented top-down.  Everything rolls up to
  # Variation, which is a polymorphic abstraction of many kinds of
  # variation.

  # =============================================================================
  # Kinds of Variation
  # =============================================================================

  Variation.v2:
    maturity: draft
    description: >-
      A representation of the state of one or more biomolecules.
    oneOf:
      - $ref: "#/definitions/MolecularVariation.v2"
      - $ref: "#/definitions/SystemicVariation.v2"
      - $ref: "#/definitions/UtilityVariation"
    heritable_properties:
      id:
        $ref: "#/definitions/CURIE"
        description: >-
          Variation Id. MUST be unique within document.
      type:
        type: string
        description: >-
          The Variation class type. MUST match child class type.
    heritable_required: ["type"]

    discriminator:
      propertyName: type

  MolecularVariation.v2:
    maturity: draft
    description: >-
      A :ref:`variation` on a contiguous molecule.
    oneOf:
      - $ref: "#/definitions/Allele.v2"
      - $ref: "#/definitions/Haplotype"
    discriminator:
      propertyName: type

  UtilityVariation:
    maturity: stable
    description: >-
      A collection of :ref:`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.v2:
    maturity: draft
    description: >-
      A Variation of multiple molecules in the context of a system, e.g.
      a genome, sample, or homologous chromosomes.
    oneOf:
      - $ref: "#/definitions/AbsoluteCopyNumber"
      - $ref: "#/definitions/RelativeCopyNumber"
    discriminator:
      propertyName: type

  # =============================================================================
  # IDENTIFIABLE TYPES
  # Have a `type` and `id` attribute
  # =============================================================================

  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Molecular Variation

  Allele.v2:
    description: >-
      The state of a molecule at a :ref:`Location`.
    additionalProperties: false
    type: object
    maturity: draft
    prefix: VA.v2
    properties:
      type:
        type: string
        const: "Allele"
        description: >-
          MUST be "Allele"
      location:
        oneOf:
          - $ref: "#/definitions/CURIE"
          - $ref: "#/definitions/SequenceLocation.v2"
        description: >-
          Where Allele is located
      state:
        $ref: "#/definitions/SequenceExpression"
        description: >-
          An expression of the sequence state
    required: [ "location", "state" ]

  Haplotype:
    description: >-
      A set of non-overlapping :ref:`Allele` members that co-occur on the same molecule.
    additionalProperties: false
    type: "object"
    properties:
      type:
        type: string
        const: "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" ]


  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # UtilityVariation

  Text:
    description: >-
      A free-text definition of variation.
    additionalProperties: false
    type: object
    properties:
      type:
        type: string
        const: "Text"
        description: MUST be "Text"
      definition:
        type: string
        description: >-
          A textual representation of variation not representable by
          other subclasses of Variation.
    required: [ "definition" ]

  VariationSet:
    description: >-
      An unconstrained set of Variation members.
    type: object
    additionalProperties: false
    properties:
      type:
        type: string
        const: "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" ]


  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # SystemicVariation

  AbsoluteCopyNumber:
    additionalProperties: false
    type: object
    maturity: draft
    prefix: VACN.v1
    description: >-
      The absolute count of discrete copies of a :ref:`MolecularVariation`,
      :ref:`Feature`, :ref:`SequenceExpression`, or a :ref:`CURIE` reference
      within a system (e.g. genome, cell, etc.).
    properties:
      type:
        type: string
        const: "AbsoluteCopyNumber"
        description: >-
          MUST be "AbsoluteCopyNumber"
      subject:
        oneOf:
          - $ref: "#/definitions/SequenceLocation"
          - $ref: "#/definitions/Feature"
        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: [ "subject", "copies" ]

  RelativeCopyNumber:
    additionalProperties: false
    type: object
    maturity: draft
    prefix: VRCN.v1
    description: >-
      The relative copies of a :ref:`MolecularVariation`,
      :ref:`Feature`, :ref:`SequenceExpression`, or a :ref:`CURIE` reference
      against an unspecified baseline in a system (e.g. genome, cell, etc.).
    properties:
      type:
        type: string
        const: "RelativeCopyNumber"
        description: >-
          MUST be "RelativeCopyNumber"
      subject:
        oneOf:
          - $ref: "#/definitions/SequenceLocation"
          - $ref: "#/definitions/Feature"
        description: >-
          Subject of the Copy Number object
      relative_copy_class:
        type: string
        enum: [ "complete loss", "partial loss", "copy neutral", "low-level gain", "high-level gain" ]
        description: >-
          MUST be one of "complete loss", "partial loss", "copy neutral", "low-level gain" or "high-level gain".
    required: [ "subject", "relative_copy_class" ]

  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Locations

  Location.v2:
    description: >-
      A contiguous segment of a biological sequence.
    oneOf:
      - $ref: "#/definitions/CytogenomicLocation.v2"
      - $ref: "#/definitions/SequenceLocation.v2"
    heritable_properties:
      id:
        $ref: "#/definitions/CURIE"
        description: >-
          Location Id. MUST be unique within document.
      type:
        type: string
        description: >-
          The Location class type. MUST match child class type.
    heritable_required: ["type"]
    discriminator:
      propertyName: type

  SequenceLocation.v2:
    additionalProperties: false
    description: >-
      A :ref:`Location` defined by an interval on a referenced :ref:`Sequence`.
    type: object
    maturity: draft
    prefix: VSL.v2
    properties:
      type:
        type: string
        const: "SequenceLocation"
        description: MUST be "SequenceLocation"
      sequence_id:
        $ref: "#/definitions/CURIE"
        description: >-
          A VRS :ref:`Computed Identifier <computed-identifiers>`
          for the reference :ref:`Sequence`.
      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`.
    required: [ "sequence_id", "start", "end" ]

  CytogenomicLocation.v2:
    additionalProperties: false
    description: >-
      A Location on a human chromosome defined by cytogenetic markers.
    type: object
    maturity: draft
    prefix: VCL.v2
    properties:
      type:
        type: string
        const: "CytogenomicLocation"
        description: MUST be "CytogenomicLocation"
      species_id:
        $ref: "#/definitions/CURIE"
        default: "taxonomy:9606"
        description: >-
          :ref:`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 :ref:`CytobandInterval`
    required: [ "species_id", "chr", "interval" ]

  # =============================================================================
  # NON-IDENTIFIABLE TYPES
  # These types have a `type` attribute
  # =============================================================================

  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Intervals

  SequenceInterval:
    description: >-
      A SequenceInterval represents a span on a :ref:`Sequence`. Positions are
      always represented by contiguous spans using interbase coordinates or
      coordinate ranges.
    type: object
    additionalProperties: false
    properties:
      type:
        type: string
        const: "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: [ "type", "start", "end" ]

  # SimpleInterval has been moved to DEPRECATED section at bottom.

  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"
        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: [ "type", "start", "end" ]


  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # SequenceExpression

  SequenceExpression:
    description: >-
      An expression describing a :ref:`Sequence`.
    oneOf:
      - $ref: "#/definitions/LiteralSequenceExpression"
      - $ref: "#/definitions/DerivedSequenceExpression"
      - $ref: "#/definitions/RepeatedSequenceExpression"
      - $ref: "#/definitions/ComposedSequenceExpression"
    discriminator:
      propertyName: type
    heritable_properties:
      type:
        type: string
        description: >-
          The SequenceExpression class type. MUST match child class type.
    heritable_required: ["type"]

  LiteralSequenceExpression:
    description: >-
      An explicit expression of a Sequence.
    type: object
    additionalProperties: false
    properties:
      type:
        type: string
        const: "LiteralSequenceExpression"
        description: MUST be "LiteralSequenceExpression"
      sequence:
        $ref: "#/definitions/Sequence"
        description: the literal :ref:`Sequence` expressed
    required: [ "sequence" ]

  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"
        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" ]

  RepeatedSequenceExpression:
    description: >-
      An expression of a sequence comprised of a tandem repeating subsequence.
    additionalProperties: false
    type: object
    properties:
      type:
        type: string
        const: "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: [ "seq_expr", "count" ]

  ComposedSequenceExpression:
    description: >-
      An expression of a sequence composed from multiple other
      :ref:`Sequence Expressions<SequenceExpression>`
      objects. MUST have at least one component that is not a
      ref:`LiteralSequenceExpression`. CANNOT be composed from
      nested composed sequence expressions.
    additionalProperties: false
    type: object
    properties:
      type:
        type: string
        const: "ComposedSequenceExpression"
        description: MUST be "ComposedSequenceExpression"
      components:
        type: array
        uniqueItems: true
        minItems: 2
        items:
          oneOf:
            - $ref: "#/definitions/LiteralSequenceExpression"
            - $ref: "#/definitions/RepeatedSequenceExpression"
            - $ref: "#/definitions/DerivedSequenceExpression"
        contains:
          oneOf:
            - $ref: "#/definitions/RepeatedSequenceExpression"
            - $ref: "#/definitions/DerivedSequenceExpression"
        description: >-
          An ordered list of :ref:`SequenceExpression` components
          comprising the expression.
    required: [ "components" ]

  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Feature

  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
    heritable_properties:
      type:
        type: string
        description: >-
          The Feature class type. MUST match child class type.
    heritable_required: [ "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"
        description: MUST be "Gene"
      gene_id:
        $ref: "#/definitions/CURIE"
        description: >-
          A CURIE reference to a Gene concept
    required: [ "gene_id" ]

  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Numerics, Comparators, and Ranges

  Number:
    description: >-
      A simple integer value as a VRS class.
    type: object
    additionalProperties: false
    properties:
      type:
        type: string
        const: "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"
        description: MUST be "DefiniteRange"
      min:
        type: number
        description: The minimum value; inclusive
      max:
        type: number
        description: The maximum value; inclusive
    required: ["type", "min", "max"]

  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"
        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: [ "type", "value", "comparator" ]

  # =============================================================================
  # BASIC TYPES (STRUCTURES)
  # These types do NOT have a VRS `type` attribute
  # These types are used solely within other definitions.
  # =============================================================================

  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 :ref:`Residues <Residue>` that represents a biological
      sequence using the conventional sequence order (5’-to-3’ for
      nucleic acid sequences, and amino-to-carboxyl for amino acid
      sequences). IUPAC ambiguity codes are permitted in Sequences.
    type: string
    pattern: '^[A-Z*\-]*$'


  # =============================================================================
  # DEPRECATED
  # =============================================================================

  Variation:
    maturity: deprecated
    description: >-
      A representation of the state of one or more biomolecules.
    oneOf:
      - $ref: "#/definitions/MolecularVariation"
      - $ref: "#/definitions/SystemicVariation"
      - $ref: "#/definitions/UtilityVariation"
    heritable_properties:
      _id:
        $ref: "#/definitions/CURIE"
        description: >-
          Variation Id. MUST be unique within document.
      type:
        type: string
        description: >-
          The Variation class type. MUST match child class type.
    heritable_required: [ "type" ]

  MolecularVariation:
    maturity: deprecated
    description: >-
      A :ref:`variation` on a contiguous molecule.
    oneOf:
      - $ref: "#/definitions/Allele"
      - $ref: "#/definitions/Haplotype"
    discriminator:
      propertyName: type

  SystemicVariation:
    maturity: deprecated
    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 :ref:`Location`.
    additionalProperties: false
    type: object
    maturity: deprecated
    prefix: VA.v1
    properties:
      type:
        type: string
        const: "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" # DEPRECATED; remove in 2.0
        description: >-
          An expression of the sequence state
        deprecated:
          - $ref: "#/definitions/SequenceState"
    required: [ "location", "state" ]

  CopyNumber:
    additionalProperties: false
    type: object
    maturity: deprecated
    prefix: VCN.v1
    description: >-
      The absolute count of discrete copies of a :ref:`MolecularVariation`,
      :ref:`Feature`, :ref:`SequenceExpression`, or a :ref:`CURIE` reference
      within a system (e.g. genome, cell, etc.).
    properties:
      type:
        type: string
        const: "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: [ "subject", "copies" ]

  SequenceState:
    maturity: deprecated
    description: >-
      DEPRECATED. A :ref:`Sequence` as a :ref:`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 :ref:`LiteralSequenceExpression` instead.
    additionalProperties: false
    type: object
    properties:
      type:
        type: string
        const: "SequenceState"
        description: MUST be "SequenceState"
      sequence:
        $ref: "#/definitions/Sequence"
        description: A string of :ref:`Residues <Residue>`
    example:
      type: SequenceState
      sequence: C
    required: [ "type", "sequence" ]

  SimpleInterval:
    maturity: deprecated
    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"
        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: [ "type", "start", "end" ]

  Location:
    maturity: deprecated
    description: >-
      A contiguous segment of a biological sequence.
    oneOf:
      - $ref: "#/definitions/ChromosomeLocation"
      - $ref: "#/definitions/SequenceLocation"
    heritable_properties:
      _id:
        $ref: "#/definitions/CURIE"
        description: >-
          Location Id. MUST be unique within document.
      type:
        type: string
        description: >-
          The Location class type. MUST match child class type.
    heritable_required: [ "type" ]
    discriminator:
      propertyName: type

  ChromosomeLocation:
    additionalProperties: false
    description: >-
      A Location on a chromosome defined by a species and chromosome name.
    type: object
    maturity: deprecated
    prefix: VCL.v1
    properties:
      type:
        type: string
        const: "ChromosomeLocation"
        description: MUST be "ChromosomeLocation"
      species_id:
        $ref: "#/definitions/CURIE"
        default: "taxonomy:9606"
        description: >-
          :ref:`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 :ref:`CytobandInterval`
    required: [ "species_id", "chr", "interval" ]

  SequenceLocation:
    additionalProperties: false
    description: >-
      A :ref:`Location` defined by an interval on a referenced :ref:`Sequence`.
    type: object
    maturity: deprecated
    prefix: VSL.v1
    properties:
      type:
        type: string
        const: "SequenceLocation"
        description: MUST be "SequenceLocation"
      sequence_id:
        $ref: "#/definitions/CURIE"
        description: >-
          A VRS :ref:`Computed Identifier <computed-identifiers>`
          for the reference :ref:`Sequence`.
      interval:
        oneOf:
          - $ref: "#/definitions/SequenceInterval"
          - $ref: "#/definitions/SimpleInterval"
        description: >-
          Reference sequence region defined by a :ref:`SequenceInterval`.
    required: [ "sequence_id", "interval" ]