schema.yaml

# yaml-language-server: $schema=http://json-schema.org/draft-07/schema
definitions:
  assays:
    enum:
    - RdRp_SARSr
    - ORF1ab
    - 2019-nCoV_N1
    - PowerChek-E
    - E_Sarbeco
    - CCDC-ORF1ab
    - HKU-N
    - S
    - '?'
    type: string
properties:
  assay:
    description: assay or primer/probe set used to quantify RNA
    oneOf:
    - $ref: '#/definitions/assays'
    - items:
        $ref: '#/definitions/assays'
      type: array
  doi:
    description: digital object identifier to retrieve the publication or dataste
    type: string
  key:
    description: unique identifier for a dataset (typically the same as a publication)
    type: string
  loads:
    items:
      additionalProperties: false
      properties:
        day:
          description: day as reported by the study (often since symptom onset or
            hospital admission)
          type: integer
        err:
          description: optional error estimate for the viral load value
          type:
          - number
          - 'null'
        patient:
          description: zero-based unique patient identifier
          type: integer
        severity: {}
        stage: {}
        threshold:
          description: semi-quantitative qPCR cycle threshold
          type: number
        value:
          description: viral load as log10 copies per mL
          type:
          - number
          - 'null'
      required:
      - value
      type: object
    type: array
  loq:
    description: level of quantification, i.e. the smallest possible concentration
      that can be measured, or `null` if not available
    type:
    - number
    - 'null'
  patients:
    additionalProperties: false
    properties:
      details:
        description: details about individual patients
        type: array
      n:
        description: number of patients in the study
        type: integer
      negative:
        description: number of patients without any positive stool samples
        type: integer
      positive:
        description: number of patients with at least one positive stool sample
        type: integer
    type: object
  samples:
    additionalProperties: false
    properties:
      n:
        description: number of samples analysed in the study
        type: integer
      negative:
        description: number of negative samples
        type: integer
      positive:
        description: number of positive samples
        type: integer
    type: object
  temporal:
    description: reference for reporting of temporal information, if available
    enum:
    - symptoms
    - admission
    type: string
  title:
    description: title of the publication
    type: string
required:
- key
- doi
- assay
- title
- patients
- samples
- loq
type: object