individuals defaultSchema

Term	Description	Type	Properties	Example	Enum
diseases	Diseases diagnosed e.g. to an individual, defined by diseaseID, age of onset, stage, level of severity, outcome and the presence of family history. Similarities to GA4GH Phenopackets v2 Disease	array	ageOfOnset, diseaseCode, familyHistory, notes, severity, stage	NA	NA
ethnicity	Ethnic background of the individual. Value from NCIT Race (NCIT:C17049) ontology term descendants, e.g. NCIT:C126531 (Latin American). A geographic ancestral origin category that is assigned to a population group based mainly on physical characteristics that are thought to be distinct and inherent. [ NCI ]	object	id, label	[{"id": "NCIT:C42331", "label": "African"}, {"id": "NCIT:C41260", "label": "Asian"}, {"id": "NCIT:C126535", "label": "Australian"}, {"id": "NCIT:C43851", "label": "European"}, {"id": "NCIT:C77812", "label": "North American"}, {"id": "NCIT:C126531", "label": "Latin American"}, {"id": "NCIT:C104495", "label": "Other race"}]	NA
exposures	Exposures (lifestyle, behavioural exposures) occurred to individual, defined by exposure ID, date and age of onset, dose, and duration.	array	ageAtExposure, date, duration, exposureCode, unit, value	NA	NA
geographicOrigin	Individual's country or region of origin (birthplace or residence place regardless of ethnic origin). Value from GAZ Geographic Location ontology (GAZ:00000448), e.g. GAZ:00002459 (United States of America).	object	id, label	[{"id": "GAZ:00002955", "label": "Slovenia"}, {"id": "GAZ:00002459", "label": "United States of America"}, {"id": "GAZ:00316959", "label": "Municipality of El Masnou"}, {"id": "GAZ:00000460", "label": "Eurasia"}]	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	Class describing a clinical procedure or intervention. Provenance: GA4GH Phenopackets v2 Procedure	array	ageAtProcedure, bodySite, dateOfProcedure, procedureCode	NA	NA
karyotypicSex	The chromosomal sex of an individual represented from a selection of options.	string	NA	NA	UNKNOWN_KARYOTYPE, XX, XY, XO, XXY, XXX, XXYY, XXXY, XXXX, XYY, OTHER_KARYOTYPE
measures	Definition of a measurement class. Provenance: GA4GH Phenopackets v2 Measurement	array	assayCode, date, measurementValue, notes, observationMoment, procedure	NA	NA
pedigrees	Pedigree studies in which the individual is part of.	array	disease, id, members, numSubjects	NA	NA
phenotypicFeatures	Used to describe a phenotype that characterizes the subject or biosample.	array	evidence, excluded, featureType, modifiers, notes, onset, resolution, severity	NA	NA
sex	Sex of the individual. Value from NCIT General Qualifier (NCIT:C27993): 'unknown' (not assessed or not available) (NCIT:C17998), 'female' (NCIT:C16576), or 'male', (NCIT:C20197).	object	id, label	[{"id": "NCIT:C16576", "label": "female"}, {"id": "NCIT:C20197", "label": "male"}, {"id": "NCIT:C1799", "label": "unknown"}]	NA
treatments	Treatment(s) prescribed/administered, defined by treatment ID, date and age of onset, dose, schedule and duration.	array	ageAtOnset, cumulativeDose, doseIntervals, routeOfAdministration, treatmentCode	NA	NA

Examples

These are examples extracted directly from the GitHub repository.

MINMID

{
    "$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"
    }
}