outbreak.schema.json

{
    "$schema": "https://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/globaldothealth/outbreak-schema/main/outbreak.schema.json",
    "title": "Global.health Day zero outbreak schema",
    "description": "Day zero outbreak schema",
    "required": [
        "ID",
        "Case_status",
        "Pathogen"
    ],
    "properties": {
        "Pathogen": {
            "category": "Case Demographics",
            "type": "string",
            "description": "Constant, pathogen of interest"
        },
        "ID": {
            "category": "Case Demographics",
            "type": "string",
            "description": "Unique string identifying the case"
        },
        "Case_status": {
            "category": "Case Demographics",
            "enum": [
                "confirmed",
                "probable",
                "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_information": {
            "category": "Case Demographics",
            "type": "object",
            "description": "(GeoJSON) Curators input an initial location where the case was reported from. This query results in a location structure returned from a geocoding API, such as Mapbox"
        },
        "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": [
                "man",
                "woman",
                "transgender",
                "non-binary",
                "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",
            "type": "array",
            "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"
        },
        "Vaccination_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": "array",
            "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_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"
        },
        "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": "object",
            "description": "(GeoJSON) 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": {
            "category": "Source Information",
            "type": "string",
            "format": "uri",
            "description": "URL of news story or government source where this case was confirmed"
        },
        "Source_II": {
            "category": "Source Information",
            "type": "string",
            "format": "uri",
            "description": "URL of news story or government source where this case was confirmed"
        },
        "Source_III": {
            "category": "Source Information",
            "type": "string",
            "format": "uri",
            "description": "URL of news story or government source where this case was confirmed"
        },
        "Source_IV": {
            "category": "Source Information",
            "type": "string",
            "format": "uri",
            "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"
        }
    }
}