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Cohorts

Term Description Type Properties Example Enum
cohortDataTypes NA array id, label [{"id": "OGMS:0000015", "label": "clinical history"}, {"id": "OBI:0000070", "label": "genotyping assay"}, {"id": "OMIABIS:0000060", "label": "survey data"}] NA
cohortDesign Cohort type by its design. A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution. Value from Ontologized MIABIS (OMIABIS) Study design ontology term tree (OBI:0500000). object id, label [{"id": "OMIABIS:0001017", "label": "case control study design"}, {"id": "OMIABIS:0001019", "label": "longitudinal study design"}, {"id": "OMIABIS:0001024", "label": "twin study design"}] 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 Exclusion criteria used for defining the cohort. It is assumed that NONE of the cohort participants will 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 Inclusion criteria used for defining the cohort. It is assumed that all cohort participants will 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"
}