data_dictionary.yml

dictionary_last_modified: 2022-11-04
fields:
  - name: ID
    type: string
    description: >
      Unique ID of the case 
    required: true

  - name: Pathogen
    type: string
    description: >
      Constant, pre-filled value, pathogen of interest 
    required: true

  - name: Case_status
    type: confirmed | suspected | discarded | omit_error
    description: >
      Status of a case. Cases which are discarded were previously
      suspected but have now been confirmed negative, and should
      be excluded from case counts. Cases which are omit_error were
      incorrectly added and should be dismissed from any data
      interpretation.
    required: true

  - name: Location
    type: string
    description: Country subdivision where case was reported
    examples: [Islington, Croydon]

  - name: City
    type: string
    description: City where case was reported
    examples: [London, Madrid, Sydney, Boston]

  - name: Country
    type: string
    description: Country where case was reported
    required: true
    examples: [England, United States, Spain, Australia]

  - name: Country_ISO3
    type: string
    description: ISO 3166-1 alpha-3, three letter country codes
    required: true
    examples: [ITA, GBR, ESP, BOL]

  - name: Age
    type: integer-range
    description: Age of the individual, specified as a range, either open-ended (<n, >n) or as a range delimited by a hyphen (m-n) following 5-year age increments (m-n)

  - name: Gender
    type: male | female | other
    description: Gender of the individual

  - name: Occupation
    type: string
    description: Free response entry describing the individual's occupation

  - name: Healthcare_worker
    type: Y | N | NA
    description: Is the individual a healthcare worker (Y=Yes, N=No, NA=Not applicable)?

  - name: Symptoms
    type: string
    description: Comma separated list of symptoms
    examples:
      - rash
      - vesicular rash
      - skin lesions
      - ulcerative lesions
      - oral and genital ulcers
      - fever

  - name: Date_onset
    type: iso8601date
    description: Date of onset of symptoms

  - name: Date_confirmation
    type: iso8601date
    description: Date when case was confirmed

  - name: Confirmation_method
    type: string
    description: Test used to confirm diagnosis 
    examples: ["RT-PCR"]

  - name: Previous_infection
    type: Y | N | NA
    description: Did the individual test positive for the infection prior to the most recent diagnosis (Y=Yes, N=No, NA=Not applicable)?

  - name: Co_infection
    type: string
    description: If the individual tested positive for another pathogen

  - name: Pre_existing_condition
    type: string
    description: If the individual has any pre-existing medical conditions 

  - name: Pregnancy_status
    type: Y | N | NA
    description: Is the case pregnant or post-partum? 

  - name: Vaccination
    type: Y | N | NA
    description: Has the individual received a dose of vaccine (Y=Yes, N=No, NA=Not applicable)? 

  - name: Vaccine_name
    type: string
    description: Name of the first vaccine 

  - name: Vaccine_date
    type: iso8601date
    Description: Date of first vaccination

  - name: Vaccine_side_effects
    type: string
    description: Comma separated list of symptoms experienced after receiving the vaccine (i.e. cough, sore throat, etc.) 

  - name: Date_of_first_consult
    type: iso8601date
    Description: Date that the individual received first clinical consultation

  - name: Hospitalised (Y/N/NA)
    type: Y | N | NA
    description: Whether individual was hospitalised (Y=Yes, N=No, NA=Not applicable)

  - name: Reason for hospitalisation
    type: monitoring | treatment | unknown
    Description: Reason why the individual was hospitalised; can list multiple, comma separated 

  - name: Date_hospitalisation
    type: iso8601date
    Description: Date individual was hospitalised 

  - name: Date_discharge_hospital
    type: iso8601date
    Description: > 
        Date that the individual was discharged from the hospital. Note: there is a separate field for ICU discharge.
  
  - name: Intensive_care (Y/N/NA)
    type: Y | N | NA
    description: Whether individual admitted to an intensive care unit or high dependency unit at hospital (Y=Yes, N=No, NA=Not applicable)

  - name: Date_admission_ICU 
    type: Y | N | NA
    description: Date individual entered intensive care unit

  - name: Date_discharge_ICU 
    type: Y | N | NA
    description: Date that the individual was discharged from the ICU

  - name: Home_monitoring 
    type: Y | N | NA
    description: Whether individual is being remotely monitored by health officials at home without hospital admission (Y=Yes, N=No, NA=Not applicable)

  - name: Isolated (Y/N/NA)
    type: Y | N | NA
    description: Whether individual was isolated at home or in hospital (Y=Yes, N=No, NA=Not applicable)

  - name: Date_isolation
    type: iso8601date
    description: Date individual entered isolation

  - name: Outcome
    type: recovered | death
    description: Optional field that specifies outcome of the disease

  - name: Date_death
    type: iso8601date
    description: Date of death

  - name: Date_recovered
    type: iso8601date
    description: Date of recovery

  - name: Contact_with_case
    type: Y | N | NA
    Description: Has the individual had contact with a confirmed/ probable/ suspected case (Y=Yes, N=No, NA=Not applicable)?
    
  - name: Contact_ID
    type: integer
    description: If specified, is the case ID from which this patient contracted the virus

  - name: Contact_setting
    type: string
    description: Setting where contact occurred that led to transmission
    examples: >
        Dictionary of possible entries:
            HOUSE= household 
            WORK= workplace
            SCHOOL= school/nursery
            HEALTH= healthcare (including laboratory exposure)
            PARTY= Sexual contact at night club/private party/sauna or similar setting
            BAR= Bar/restaurant/ or other small event where there was no sexual contact
            LARGE = Large event with no sexual contact (e.g., festival or sports event) 
            LARGECONTACT = Large event with sexual contact
            OTHER
            UNK= Unknown

  - name: Contact_animal
    description: Whether the individual has known contact with animals
    examples: >
        Dictionary of possible entries:
            PET = Household pets excluding rodents
        PETRODENTS = Rodent pets
        WILD = Wild animals excluding rodent
        WILDRODENTS = Wild rodents
        Other (specify)

  - name: Contact_comment
    type: string
    description: Free text describing any additional contact information.

  - name: Transmission
    type: string
    description: Setting where contact occurred that led to transmission
    examples: >
        Dictionary of possible entries:
            ANIMAL = Animal to human transmission
            HAI = Healthcare-associated
            LAB = Transmission in a laboratory due to occupational exposure
            MTCT = Transmission from mother to child during pregnancy or at birth
            OTHER = Other transmission
            FOMITE = Contact with contaminated material (e.g bedding, clothing, objects)
            PTP = Person-to-person (excluding: mother-to-child, healthcare-associated or sexual transmission)
            SEX = Sexual transmission
            TRANSFU = parenteral transmission including intravenous drug use and transfusion
            UNK = Unknown

  - name: Travel_history (Y/N/NA)
    type: Y | N | NA
    description: Whether individual has travel history, domestic and/or international (Y=Yes, N=No, NA=Not applicable)

  - name: Travel_history_entry
    type: string
    description: Date when individual entered the country

  - name: Travel_history_start
    type: string
    description: Free text describing travel

  - name: Travel_history_location
    type: string
    description: Last known location where individual had travelled from
    example: [Europe] 

  - name: Travel_history_country
    type: string
    description: Last known country where individual had travelled from
    example: [Spain] 

  - name: Genomics_Metadata
    type: string
    description: Which clade the viral strain belongs to
    examples:
      - West African Clade
      - North African Clade

  - name: Accession Number
    type: string
    description: Accession number of the sequence uploaded to public database

  - name: Source
    type: url
    description: URL of news story or government source where this case was confirmed
    required: true

  - name: Source_II
    type: url
    description: URL of news story or government source where this case was confirmed (archived or secondary source)

  - name: Source_III
    type: url
    description: URL of news story or government source where this case was confirmed (archived or secondary source)

  - name: Source_IV
    type: url
    description: URL of news story or government source where this case was confirmed (archived or secondary source)

  - name: Source_V
    type: url
    description: URL of news story or government source where this case was confirmed (archived or secondary source)

  - name: Source_VI
    type: url
    description: URL of news story or government source where this case was confirmed (archived or secondary source)

  - name: Source_VII
    type: url
    description: URL of news story or government source where this case was confirmed (archived or secondary source)

  - name: Date_entry
    type: iso8601date
    description: Date case was entered into line list
    required: true

  - name: Date_last_modified
    type: iso8601date
    description: Last date when case was modified in line list
    required: true