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Cohorts

Term Description Type Properties Example Enum
cohortDataTypes Type of information. Preferably values from Genomics Cohorts Knowledge Ontology (GeCKO) or others when GeCKO is not applicable. array id, label [{"id": "OGMS:0000015", "label": "clinical history"}, {"id": "OBI:0000070", "label": "genotyping assay"}, {"id": "OMIABIS:0000060", "label": "survey data"}] NA
cohortDesign Definition of an ontology term. object id, label NA NA
cohortSize Count of unique Individuals in cohort (individuals meeting criteria for ´user-defined´ cohorts). If not previously known, it could be calculated by counting the individuals in the cohort. integer NA 14765, 20000 NA
cohortType Cohort type by its definition. If a cohort is declared ´study-defined´ or ´beacon-defined´ criteria are to be entered in cohort_inclusion_criteria; if a cohort is declared ‘user-defined' cohort_inclusion_criteria could be automatically populated from the parameters used to perform the query. string NA NA study-defined, beacon-defined, user-defined
collectionEvents TBD array eventAgeRange, eventCases, eventControls, eventDataTypes, eventDate, eventDiseases, eventEthnicities, eventGenders, eventLocations, eventNum, eventPhenotypes, eventSize, eventTimeline NA NA
exclusionCriteria Criteria used for defining the cohort. It is assumed that all cohort participants will match or NOT match such criteria. object ageRange, diseaseConditions, ethnicities, genders, locations, phenotypicConditions NA NA
id Cohort identifier. For ´study-defined´ or ´beacon-defined´cohorts this field is set by the implementer. For ´user-defined´ this unique identifier could be generated upon the query that defined the cohort, but could be later edited by the user. string NA cohort-T2D-2010 NA
inclusionCriteria Criteria used for defining the cohort. It is assumed that all cohort participants will match or NOT match such criteria. object ageRange, diseaseConditions, ethnicities, genders, locations, phenotypicConditions NA NA
name Name of the cohort. For ´user-defined´ this field could be generated upon the query, e.g. a value that is a concatenationor some representation of the user query. string NA Wellcome Trust Case Control Consortium, GCAT Genomes for Life NA

Examples

These are examples extracted directly from the GitHub repository.

{
    "$schema": "https://json-schema.org/draft/2020-12/schema",
    "cohortType": "study-defined",
    "id": "cohort0001",
    "name": "GCAT Genomes for Life"
}
{
    "$schema": "https://json-schema.org/draft/2020-12/schema",
    "cohortDataTypes": [
        {
            "id": "OGMS:0000015",
            "label": "clinical history"
        },
        {
            "id": "OBI:0000070",
            "label": "genotyping assay"
        },
        {
            "id": "OMIABIS:0000060",
            "label": "survey data"
        }
    ],
    "cohortDesign": {
        "id": "OMIABIS:0001019",
        "label": "longitudinal study design"
    },
    "cohortSize": 20000,
    "cohortType": "study-defined",
    "id": "cohort0001",
    "inclusionCriteria": {
        "ageRange": {
            "end": {
                "iso8601duration": "P40Y"
            },
            "start": {
                "iso8601duration": "P18Y"
            }
        },
        "genders": [
            {
                "id": "NCIT:C16576",
                "label": "female"
            },
            {
                "id": "NCIT:C20197",
                "label": "male"
            }
        ],
        "locations": [
            {
                "id": "GAZ:00004501",
                "label": "Catalonia Autonomous Community"
            }
        ]
    },
    "name": "GCAT Genomes for Life"
}
{
    "$schema": "https://json-schema.org/draft/2020-12/schema",
    "cohortDataTypes": [
        {
            "id": "OGMS:0000015",
            "label": "clinical history"
        },
        {
            "id": "OBI:0000070",
            "label": "genotyping assay"
        },
        {
            "id": "OMIABIS:0000060",
            "label": "survey data"
        }
    ],
    "cohortDesign": {
        "id": "OMIABIS:0001019",
        "label": "longitudinal study design"
    },
    "cohortSize": 20000,
    "cohortType": "study-defined",
    "collectionEvents": [
        {
            "eventDataTypes": {
                "availability": true,
                "distribution": {
                    "dataTypes": {
                        "blood collected from fasting subject": 51,
                        "survey data": 98
                    }
                }
            },
            "eventDate": "2019-04-23",
            "eventEthnicities": {
                "availability": true,
                "availabilityCount": 101,
                "distribution": {
                    "ethnicities": {
                        "African": 3,
                        "European": 90,
                        "Latin American": 8
                    }
                }
            },
            "eventGenders": {
                "availability": true,
                "availabilityCount": 101,
                "distribution": {
                    "genders": {
                        "female": 51,
                        "male": 50
                    }
                }
            },
            "eventNum": 1,
            "eventSize": 101
        }
    ],
    "id": "cohort0001",
    "inclusionCriteria": {
        "ageRange": {
            "end": {
                "iso8601duration": "P40Y"
            },
            "start": {
                "iso8601duration": "P18Y"
            }
        },
        "genders": [
            {
                "id": "NCIT:C16576",
                "label": "female"
            },
            {
                "id": "NCIT:C20197",
                "label": "male"
            }
        ],
        "locations": [
            {
                "id": "GAZ:00004501",
                "label": "Catalonia Autonomous Community"
            }
        ]
    },
    "name": "GCAT Genomes for Life"
}