VRS - ChromosomeLocation

A ChromosomeLocation is a schema used to represent a single or a range of cytogenetic bands.

Please note that several parameters - e.g. species_id - are required as part of the VRS specification but may be deemed unnecessary when used in other contexts.

{S}[B] Contributors

Schema Overview1

title: ChromosomeLocation
description: >-
  A Location on a chromosome defined by the chromosome name and cytobands.
  **Implementation Note**: The `type` and `species_id` properties are required
  when used as part of the VRS specification.
type: object
properties:
  _id:
    $ref: './CURIE.yaml'
    description: >-
      Location Id. MUST be unique within document.
  type:
    type: string
    const: 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
examples:
  - chr: 8
    interval:
      start: q22
      end: q24.1
required:
  - chr
  - interval
additionalProperties: false

definitions:
  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.
      **Implementation Note**: The `type` property is required when used as part
      of the VRS specification
    type: object
    properties:
      type:
        type: string
        const: 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:
        $ref: '#/definitions/HumanCytoband'
        description: >-
          The end cytoband region. MUST specify a region nearer the terminal
          end (telomere) of the chromosome q-arm than `start`.
    examples:
      - type: CytobandInterval
        start: q22.2
        end: q22.3
    required:
      - start
      - end
    additionalProperties: false
  HumanCytoband:
    description: >-
      A character string representing cytobands derived from the *International
      System for Human Cytogenomic Nomenclature* (ISCN)
      [guidelines](http://doi.org/10.1159/isbn.978-3-318-06861-0).
    type: string
    pattern: ^cen|[pq](ter|([1-9][0-9]*(\.[1-9][0-9]*)?))$
    example: q22.3
    additionalProperties: false

  1. Please note that the schema here is provided for illustration purposes, may represent an approximation and possibly excludes technical components of a proper JSON Schema format. ↩