cohorts defaultSchema
| 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"
}