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Individuals

Term Description Type Properties Example Enum
diseases List of disease(s) been diagnosed to the individual, defined by disease ontology ID(s), age of onset, stage and the presence of family history. array ageOfOnset, diseaseCode, familyHistory, notes, severity, stage NA NA
ethnicity Definition of an ontology term. object id, label NA NA
exposures NA array ageAtExposure, date, duration, exposureCode, unit, value NA NA
geographicOrigin Definition of an ontology term. object id, label NA NA
id Individual identifier (internal ID). string NA P0001 NA
info Placeholder to allow the Beacon to return any additional information that is necessary or could be of interest in relation to the query or the entry returned. It is recommended to encapsulate additional informations in this attribute instead of directly adding attributes at the same level than the others in order to avoid collision in the names of attributes in future versions of the specification. object NA NA NA
interventionsOrProcedures NA array ageAtProcedure, bodySite, dateOfProcedure, procedureCode NA NA
karyotypicSex The chromosomal sex of an individual represented from a selection of options. The values correspond to the ordinal values in the Phenopackets schema where: 0 - UNKNOWN_KARYOTYPE (Untyped or inconclusive karyotyping); 1 - XX (Female); 2 - XY (Male); 3 - XO (Single X chromosome only); 4 - XXY (Two X and one Y chromosome); 5 - XXX (Three X chromosomes); 6 - XXYY (Two X chromosomes and two Y chromosomes); 7 - XXXY (Three X chromosomes and one Y chromosome); 8 - XXXX (Four X chromosomes); 9 - XYY (One X and two Y chromosomes); 10 - OTHER_KARYOTYPE (None of the above types) string NA NA UNKNOWN_KARYOTYPE, XX, XY, XO, XXY, XXX, XXYY, XXXY, XXXX, XYY, OTHER_KARYOTYPE
measures NA array assayCode, date, measurementValue, notes, observationMoment, procedure NA NA
pedigrees NA array disease, id, members, numSubjects NA NA
phenotypicFeatures NA array evidence, excluded, featureType, modifiers, notes, onset, resolution, severity NA NA
sex Definition of an ontology term. object id, label NA NA
treatments NA array ageAtOnset, cumulativeDose, doseIntervals, routeOfAdministration, treatmentCode NA NA

Examples

These are examples extracted directly from the GitHub repository.

{
    "$schema": "https://json-schema.org/draft/2020-12/schema",
    "id": "Ind001",
    "sex": {
        "id": "NCIT:C16576",
        "label": "female"
    }
}
{
    "$schema": "https://json-schema.org/draft/2020-12/schema",
    "diseases": [
        {
            "ageOfOnset": {
                "ageGroup": {
                    "id": "NCIT:C49685",
                    "label": "Adult 18-65 Years Old"
                }
            },
            "diseaseCode": {
                "id": "OMIM:164400",
                "label": "Spinocerebellar ataxia 1"
            },
            "familyHistory": false,
            "severity": {
                "id": "HP:0012829",
                "label": "Profound"
            },
            "stage": {
                "id": "OGMS:0000119",
                "label": "acute onset"
            }
        }
    ],
    "ethnicity": {
        "id": "NCIT:C43851",
        "label": "European"
    },
    "geographicOrigin": {
        "id": "GAZ:00002955",
        "label": "Slovenia"
    },
    "id": "Ind001",
    "measures": [
        {
            "assayCode": {
                "id": "LOINC:26515-7",
                "label": "Platelets [#/volume] in Blood"
            },
            "date": "2017-05-03",
            "measurementValue": {
                "units": {
                    "id": "NCIT:C103452",
                    "label": "Per Milliliter"
                },
                "value": 55345
            },
            "observationMoment": {
                "age": {
                    "iso8601duration": "P55Y8M12D"
                }
            }
        }
    ],
    "sex": {
        "id": "NCIT:C16576",
        "label": "female"
    }
}