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default_cohort_schema.yaml
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default_cohort_schema.yaml
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openapi: 3.0.2
servers: []
info:
version: "draft.3"
title: GA4GH Beacon Cohort Default Schema
description: |
Schema for cohorts to be used as default by the Beacon.
This object contains info from a set of persons who satisfy one or more
inclusion criteria for a duration of time.
contact:
email: [email protected]
license:
name: Apache 2.0
url: 'http://www.apache.org/licenses/LICENSE-2.0.html'
externalDocs:
description: |
Beacon project
url: 'http://beacon-project.io/'
paths: {}
components:
schemas:
CollectionEvent:
description: TBD # TBD
type: object
properties:
eventNum:
description: cardinality of the collection event / data point in a series
type: integer
eventDate:
description: date of collection event/data point
type: string
format: datetime
eventTimeline:
description: |
Aggregated information of dates of visit/diagnostic/inclusion in study obtained from individual level
info in database. Will coincide with collection event date for multi-time
type: object
properties:
start:
description: earliest date of visit
type: string
format: datetime
end:
description: latest date of visit
type: string
format: datetime
eventSize:
description: |
Count of individuals in cohort at data point (for ´user-defined´ cohorts, this is individuals
meeting criteria) obtained from individual level info in database.
type: integer
eventCases:
description: count of cases
type: integer
eventControls:
description: count of controls
type: integer
eventLocations:
description: Aggregated information of geographic location obtained from individual level info in database.
type: object
properties:
availability:
description: data availability
type: boolean
availabilityCount:
description: count of individuals with data available
type: integer
distribution:
description: TBD # TBD
type: array
items:
type: integer
eventGenders:
description: Aggregated information of gender(s) obtained from individual level info in the database.
type: object
properties:
availability:
description: data availability
type: boolean
availabilityCount:
description: count of individuals with data available
type: integer
distribution:
description: TBD # TBD
type: array
items:
type: integer
eventEthnicities:
description: Aggregated information of ethnicity obtained from individual level info in database.
type: object
properties:
availability:
description: data availability
type: boolean
availabilityCount:
description: count of individuals with data available
type: integer
distribution:
description: TBD # TBD
type: array
items:
type: integer
eventAgeRange:
description: Individual age range, obtained from individual level info in database.
type: object
properties:
start:
description: min age in collection event
type: string
format: datetime
end:
description: max age in collection event
type: string
format: datetime
eventDiseases:
description: Aggregated information of disease/condition(s) obtained from individual level info in the database.
type: object
properties:
availability:
description: data availability
type: boolean
availabilityCount:
description: count of individuals with data available
type: integer
distribution:
description: TBD # TBD
type: array
items:
type: integer
eventPhenotypes:
description: Aggregated information of phenotype(s) obtained from individual level info in the database.
type: object
properties:
availability:
description: data availability
type: boolean
availabilityCount:
description: count of individuals with data available
type: integer
distribution:
description: TBD # TBD
type: array
items:
type: integer
eventDataTypes:
description: Aggregated data type information available for each cohort data type as declared in cohort_data types, and obtained from individual level info.
type: object
properties:
availability:
description: data availability
type: boolean
availabilityCount:
description: count of individuals with data available
type: integer
distribution:
description: TBD # TBD
type: array
items:
type: integer
Cohort:
description: |
Level/severity ontology when and as applicable to phenotype observed. Value from TBD, e.g "mild"
type: object
properties:
cohortType:
description: |
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.
type: string
enum:
- study-defined
- beacon-defined
- user-defined
cohortDesign:
description: Cohort type by its design.
type: string
enum:
- TBD # TBD
cohortId:
description: |
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.
type: string
cohortName:
description: |
For ´user-defined´ this field could be generated upon the query, e.g. a value that is a concatenation
or some representation of the user query.
type: string
cohortInclusionCriteria:
description: |
None or any number of these criteria can be filled. (For ´beacon-defined´cohorts, cohorts matching
the whole dataset wont apply criteria for if cohorts are subsets of Datasets the criteria used to
defined them can be added in these fields)
type: object
properties:
cohortLocations:
description: Geographic location(s) in cohort inclusion criteria
type: string
cohortGenders:
description: Gender(s) in cohort inclusion criteria
type: string
cohortConditions:
description: Condition(s) in cohort inclusion criteria
type: string
cohortAgeRange:
description: Individual age range in cohort inclusion criteria
type: object
properties:
start:
description: min age accepted in cohort criteria.
type: string
format: datetime
end:
description: max age accepted in cohort criteria.
type: string
format: datetime
cohortExclusionCriteria:
description: TBD # TBD
type: object
properties:
cohortLocations:
description: Geographic location(s) in cohort inclusion criteria
type: string
cohortGenders:
description: Gender(s) in cohort inclusion criteria
type: string
cohortConditions:
description: Condition(s) in cohort inclusion criteria
type: string
cohortAgeRange:
description: Individual age range in cohort inclusion criteria
type: object
properties:
start:
description: min age accepted in cohort criteria.
type: string
format: datetime
end:
description: max age accepted in cohort criteria.
type: string
format: datetime
cohortLicense:
description: TBD # TBD
type: array
items:
type: string
cohortContact:
description: TBD # TBD
type: string
cohortRights:
description: TBD # TBD
type: array
items:
type: string
cohortSize:
description: |
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.
type: integer
cohortDataTypes:
description: TBD # TBD
type: array
items:
type: string
enum:
- data
- num
collectionEvents:
description: TBD # TBD
type: array
items:
$ref: '#/components/schemas/CollectionEvent'