GHL2024.D11.1E71.schema.json

{
  "$schema": "https://json-schema.org/draft-07/schema",
  "$id": "https://raw.githubusercontent.com/globaldothealth/outbreak-schema/GHL2024.D11.1E71.schema.json",
  "title": "Global.health schema for Mpox 2024 outbreak",
  "description": "Day zero outbreak schema",
  "required": ["ID", "Case_status", "Pathogen_name"],
  "properties": {
    "Pathogen_name": {
      "category": "Case Demographics",
      "const": "mpox",
      "description": "Constant, pathogen of interest"
    },
    "ID": {
      "category": "Case Demographics",
      "type": "string",
      "description": "Unique string identifying the case"
    },
    "Case_status": {
      "category": "Case Demographics",
      "enum": ["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."
    },
    "Pathogen_status": {
      "category": "Case Demographics",
      "enum": ["endemic", "emerging", "unknown"],
      "description": "Whether the infection occured in an endemic, or non-endemic region."
    },
    "Location_Admin0": { "type": "string", "description": "Country name" },
    "Location_Admin1": {
      "type": "string",
      "description": "Admin1 level of location, state or province"
    },
    "Location_Admin2": {
      "type": "string",
      "description": "Admin2 level of location"
    },
    "Age": {
      "category": "Case Demographics",
      "type": "string",
      "description": "Age of individual, specified as range, open-ended (<n, >n) or as a range delimited by a hyphen following 5 year increments (m-n)"
    },
    "Sex_at_birth": {
      "category": "Case Demographics",
      "enum": ["male", "female", "other"],
      "description": "Sex at birth of an individual"
    },
    "Sex_at_birth_other": {
      "category": "Case Demographics",
      "type": "string",
      "description": "Free text entry for the sex of an individual, if not covered by 'Sex_at_birth'"
    },
    "Gender": {
      "category": "Case Demographics",
      "enum": ["male", "female", "other"],
      "description": "Gender identity of the individual"
    },
    "Gender_other": {
      "category": "Case Demographics",
      "type": "string",
      "description": "Free text entry for Gender identity if not covered by 'Gender' field"
    },
    "Race": {
      "category": "Case Demographics",
      "type": "array",
      "items": {
        "enum": [
          "Native Hawaiian or Other Pacific Islander",
          "Asian",
          "American Indian or Alaska Native",
          "Black or African American",
          "White",
          "Other"
        ]
      },
      "description": "Race of the individual, can select multiple options"
    },
    "Race_other": {
      "category": "Case Demographics",
      "type": "string",
      "description": "Free response input for the race of the individual"
    },
    "Ethnicity": {
      "category": "Case Demographics",
      "enum": ["Hispanic or Latino", "Not Hispanic or Latino", "other"],
      "description": "Ethnicity of the individual, per the U.S. census definition"
    },
    "Ethnicity_other": {
      "category": "Case Demographics",
      "type": "string",
      "description": "Free response input for the ethnicity of the individual. Input text data as provided by the original data source; do not translate."
    },
    "Nationality": {
      "category": "Case Demographics",
      "type": "array",
      "description": "Nationality of the individual, can select multiple"
    },
    "Nationality_other": {
      "category": "Case Demographics",
      "type": "string",
      "description": "Free response entry for the nationality of the individual, if not covered by the Nationality field."
    },
    "Occupation": {
      "category": "Case Demographics",
      "type": "string",
      "description": "Free response entry describing the individual's occupation"
    },
    "Healthcare_worker": {
      "category": "Case Demographics",
      "enum": ["Y", "N", "NA"],
      "description": "Whether individual is a healthcare worker"
    },
    "Previous_infection": {
      "category": "Medical History",
      "enum": ["Y", "N", "NA"],
      "description": "Did the individual test positive for the infection prior to the most recent diagnosis"
    },
    "Co_infection": {
      "category": "Medical History",
      "type": "array",
      "description": "If the individual tested positive for another pathogen, can select multiple"
    },
    "Pre_existing_condition": {
      "category": "Medical History",
      "enum": ["Y", "N"],
      "description": "If the individual has any pre-existing conditions"
    },
    "Pregnancy_Status": {
      "category": "Medical History",
      "enum": ["Y", "N", "NA"],
      "description": "Is the case pregnant or post-partum?"
    },
    "Vaccination": {
      "category": "Medical History",
      "enum": ["Y", "N", "NA"],
      "description": "Has the individual received a dose of vaccine"
    },
    "Vaccine_name": {
      "category": "Medical History",
      "type": "string",
      "description": "Name of the first vaccine"
    },
    "Vaccine_date": {
      "category": "Medical History",
      "type": "string",
      "format": "date",
      "description": "Date of first vaccination"
    },
    "Vaccine_side_effects": {
      "category": "Medical History",
      "type": "array",
      "description": "List of symptoms experienced after receiving the vaccine"
    },
    "Symptoms": {
      "category": "Clinical Presentation",
      "type": "string",
      "description": "List of symptoms (i.e. cough, sore throat, etc.)."
    },
    "Date_report": {
      "category": "Clinical Presentation",
      "type": "string",
      "format": "date",
      "description": "Date case was first reported. Suggest adding the date of first report, such as the date first included in a situation report or other official communication"
    },
    "Date_report_source_I": {
      "category": "Clinical Presentation",
      "type": "string",
      "format": "date",
      "description": "Date of report of source I"
    },
    "Date_onset": {
      "category": "Clinical Presentation",
      "type": "string",
      "format": "date",
      "description": "Date of onset of symptoms. May be difficult to infer from aggregate date reporting"
    },
    "Date_confirmation": {
      "category": "Clinical Presentation",
      "type": "string",
      "format": "date",
      "description": "Date when case was confirmed"
    },
    "Confirmation_method": {
      "category": "Clinical Presentation",
      "type": "string",
      "description": "Test used to perform diagnosis. Dependent on pathogen, and often already included in the definition"
    },
    "Date_of_first_consultation": {
      "category": "Clinical Presentation",
      "type": "string",
      "format": "date",
      "description": "Date that the individual received first clinical consultation"
    },
    "Hospitalised": {
      "category": "Clinical Presentation",
      "enum": ["Y", "N", "NA"],
      "description": "Whether individual was hospitalised"
    },
    "Reason_for_hospitalisation": {
      "category": "Clinical Presentation",
      "type": "array",
      "items": {
        "enum": ["monitoring", "treatment"]
      },
      "description": "Reason why the individual was hospitalised, can select multiple"
    },
    "Date_hospitalisation": {
      "category": "Clinical Presentation",
      "type": "string",
      "format": "date",
      "description": "Date individual was hospitalised"
    },
    "Date_discharge_hospital": {
      "category": "Clinical Presentation",
      "type": "string",
      "format": "date",
      "description": "Date that the individual was discharged from the hospital. Note: there is a separate field for ICU discharge"
    },
    "Intensive_care": {
      "category": "Clinical Presentation",
      "enum": ["Y", "N", "NA"],
      "description": "Whether individual admitted to an intensive care unit or high dependency unit at hospital"
    },
    "Date_admission_ICU": {
      "category": "Clinical Presentation",
      "type": "string",
      "format": "date",
      "description": "Date individual entered intensive care unit"
    },
    "Date_discharge_ICU": {
      "category": "Clinical Presentation",
      "type": "string",
      "format": "date",
      "description": "Date that the individual was discharged from the ICU"
    },
    "Home_monitoring": {
      "category": "Clinical Presentation",
      "enum": ["Y", "N", "NA"],
      "description": "Whether individual is being remotely monitored by health officials at home without hospital admission"
    },
    "Isolated": {
      "category": "Clinical Presentation",
      "enum": ["Y", "N", "NA"],
      "description": "Whether individual was isolated at home or in hospital. Dependent on context/pathogen"
    },
    "Date_isolation": {
      "category": "Clinical Presentation",
      "type": "string",
      "format": "date",
      "description": "Date individual entered isolation"
    },
    "Outcome": {
      "category": "Clinical Presentation",
      "enum": ["recovered", "death", "ongoing post-acute condition"],
      "description": "Outcome of the disease, recovered includes inactive case counts"
    },
    "Date_death": {
      "category": "Clinical Presentation",
      "type": "string",
      "format": "date",
      "description": "Date individual died"
    },
    "Date_recovered": {
      "category": "Clinical Presentation",
      "type": "string",
      "format": "date",
      "description": "Date individual recovered, inactive case status"
    },
    "Contact_with_case": {
      "category": "Exposure",
      "enum": ["Y", "N", "NA"],
      "description": "Has the individual had contact with a confirmed or suspected case"
    },
    "Treatment_antiviral": {
      "enum": ["Y", "N"],
      "description": "Whether antiviral treatment was administered"
    },
    "Treatment_antiviral_name": {
      "type": "string",
      "description": "Antiviral name"
    },
    "Contact_ID": {
      "category": "Exposure",
      "type": "string",
      "description": "If specified, the ID of the confirmed or suspected contact"
    },
    "Contact_setting": {
      "category": "Exposure",
      "enum": [
        "HOUSE",
        "WORK",
        "SCHOOL",
        "HEALTH",
        "PARTY",
        "BAR",
        "LARGE",
        "LARGECONTACT",
        "OTHER",
        "UNK"
      ],
      "description": "Setting where contact occurred. HEALTH=healthcare, including laboratory exposure, PARTY=Sexual contact at night club/private party/sauna or similar setting, BAR=bar/restaurant/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, UNK=unknown"
    },
    "Contact_setting_other": {
      "category": "Exposure",
      "type": "string",
      "description": "Contact setting not covered by Contact_setting"
    },
    "Contact_animal": {
      "category": "Exposure",
      "enum": ["PET", "PETRODENTS", "WILD", "WILDRODENTS", "OTHER"],
      "description": "Whether the individual has known contact with animals. PET=household pets excluding rodents, PETRODENTS=rodent pets, WILD=wild animals excluding rodents, WILDRODENTS=wild rodents"
    },
    "Contact_comment": {
      "category": "Exposure",
      "type": "string",
      "description": "Free text describing any additional contact information"
    },
    "Transmission": {
      "category": "Exposure",
      "enum": [
        "ANIMAL",
        "HAI",
        "LAB",
        "MTCT",
        "OTHER",
        "FOMITE",
        "PTP",
        "SEX",
        "TRANSFU",
        "UNK"
      ],
      "description": "Most likely mode of transmission. 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"
    },
    "Travel_history": {
      "category": "Exposure",
      "enum": ["Y", "N", "NA"],
      "description": "Whether individual has travel history, domestic and/or international"
    },
    "Travel_history_entry": {
      "category": "Exposure",
      "type": "string",
      "format": "date",
      "description": "Date when individual entered the country"
    },
    "Travel_history_start": {
      "category": "Exposure",
      "type": "string",
      "format": "date",
      "description": "Date when individual began travel"
    },
    "Travel_history_location": {
      "category": "Exposure",
      "type": "string",
      "description": "Location of travel obtained from geocoding API such as Mapbox"
    },
    "Genomics_Metadata": {
      "category": "Laboratory Information",
      "type": "string",
      "description": "Which clade the viral strain belongs to"
    },
    "Accession_Number": {
      "category": "Laboratory Information",
      "type": "string",
      "description": "Accession number of the sequence uploaded to public database"
    },
    "Source_I": {
      "category": "Source Information",
      "type": "string",
      "pattern": "^https?://",
      "description": "URL of news story or government source where this case was confirmed"
    },
    "Source_I_Government": {
      "enum": ["Yes", "No"],
      "description": "Whether source I is a government source"
    },
    "Source_II": {
      "category": "Source Information",
      "type": "string",
      "pattern": "^https?://",
      "description": "URL of news story or government source where this case was confirmed"
    },
    "Source_III": {
      "category": "Source Information",
      "type": "string",
      "pattern": "^https?://",
      "description": "URL of news story or government source where this case was confirmed"
    },
    "Source_IV": {
      "category": "Source Information",
      "type": "string",
      "pattern": "^https?://",
      "description": "URL of news story or government source where this case was confirmed"
    },
    "Date_entry": {
      "category": "Source Information",
      "type": "string",
      "format": "date",
      "description": "Date case was entered into line list"
    },
    "Date_last_modified": {
      "category": "Source Information",
      "type": "string",
      "format": "date",
      "description": "Last date when case was modified in line list"
    }
  }
}