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Updates to match openapi3 changes
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@bcorrie
bcorrie authored Feb 8, 2024
1 parent 4b5dfbe commit fe66bfe
Showing 1 changed file with 134 additions and 87 deletions.
221 changes: 134 additions & 87 deletions specs/airr-schema.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -478,12 +478,78 @@ TimePoint:
top_node:
id: UO:0000003
label: time unit

#
# General objects
# TODO: link to global schema with JSON-LD?
#

# A time range or interval
TimeInterval:
discriminator:
propertyName: AIRR
description: Time range or interval for a measurement, observation or action.
type: object
properties:
min:
type: number
description: Lower/minimum value of the time interval
example: 5.0
x-airr:
adc-query-support: true
nullable: true
max:
type: number
description: Upper/maximum value of the time interval
example: 10.0
x-airr:
adc-query-support: true
nullable: true
unit:
$ref: '#/Ontology'
description: Unit of the time interval
example:
id: UO:0000033
label: day
x-airr:
adc-query-support: true
nullable: true
format: ontology
ontology:
draft: false
top_node:
id: UO:0000003
label: time unit

# A physical quantity
PhysicalQuantity:
discriminator:
propertyName: AIRR
description: A physical quantity from a measurement or observation.
type: object
properties:
quantity:
type: number
description: Physical quantity
example: -5.0
x-airr:
adc-query-support: true
nullable: true
unit:
$ref: '#/Ontology'
description: Unit of physical quantity
example:
id: UO:0000024
label: nanogram
x-airr:
nullable: true
format: ontology
ontology:
draft: false
top_node:
id: UO:0000002
label: physical quantity



# An individual
Acknowledgement:
description: Individual whose contribution to this work should be acknowledged
Expand Down Expand Up @@ -1819,52 +1885,29 @@ Subject:
subset: subject
name: Sex
format: controlled_vocabulary
age_min:
type: number
description: Specific age or lower boundary of age range.
title: Age minimum
example: 60
x-airr:
miairr: important
nullable: true
adc-query-support: true
set: 1
subset: subject
name: Age minimum
age_max:
type: number
age:
$ref: '#/TimeInterval'
description: >
Upper boundary of age range or equal to age_min for specific age.
This field should only be null if age_min is null.
title: Age maximum
example: 80
Age of subject expressed as a time interval. If singular time point then
min == max in the time interval.
examples:
- min: 50
max: 50
unit:
id: UO:0000036
label: year
- min: 5
max: 10
unit:
id: UO:0000034
label: week
x-airr:
miairr: important
nullable: true
adc-query-support: true
set: 1
subset: subject
name: Age maximum
age_unit:
$ref: '#/Ontology'
description: Unit of age range
title: Age unit
example:
id: UO:0000036
label: year
x-airr:
miairr: important
nullable: true
adc-query-support: true
set: 1
subset: subject
name: Age unit
format: ontology
ontology:
draft: false
top_node:
id: UO:0000003
label: time unit
name: Age
age_event:
type: string
description: >
Expand All @@ -1880,15 +1923,33 @@ Subject:
set: 1
subset: subject
name: Age event
age:
type: string



age_min:
type: number
x-airr:
nullable: true
deprecated: true
deprecated-description: Combined into single age field.
deprecated-replaced-by:
- age
age_max:
type: number
x-airr:
nullable: true
deprecated: true
deprecated-description: Combined into single age field.
deprecated-replaced-by:
- age
age_unit:
$ref: '#/Ontology'
x-airr:
nullable: true
deprecated: true
deprecated-description: Split into two fields to specify as an age range.
deprecated-description: Combined into single age field.
deprecated-replaced-by:
- age_min
- age_max
- age_unit
- age
ancestry_population:
$ref: '#/Ontology'
description: Broad geographic origin of ancestry (continent)
Expand Down Expand Up @@ -2046,10 +2107,14 @@ Diagnosis:
id: DOID:4
label: disease
disease_length:
type: string
$ref: '#/PhysicalQuantity'
description: Time duration between initial diagnosis and current intervention
title: Length of disease
example: 23 months
example:
quantity: 23
unit:
id: UO:0000035
label: month
x-airr:
miairr: important
nullable: true
Expand Down Expand Up @@ -2130,7 +2195,6 @@ Sample:
- anatomic_site
- disease_state_sample
- collection_time_point_relative
- collection_time_point_relative_unit
- collection_time_point_reference
- biomaterial_provider
properties:
Expand Down Expand Up @@ -2206,10 +2270,14 @@ Sample:
subset: sample
name: Disease state of sample
collection_time_point_relative:
type: number
$ref: '#/PhysicalQuantity'
description: Time point at which sample was taken, relative to `Collection time event`
title: Sample collection time
example: 14
example:
quantity: 14
unit:
id: UO:0000033
label: day
x-airr:
miairr: important
nullable: true
Expand All @@ -2219,24 +2287,12 @@ Sample:
name: Sample collection time
collection_time_point_relative_unit:
$ref: '#/Ontology'
description: Unit of Sample collection time
title: Sample collection time unit
example:
id: UO:0000033
label: day
x-airr:
miairr: important
nullable: true
adc-query-support: true
set: 2
subset: sample
name: Sample collection time unit
format: ontology
ontology:
draft: false
top_node:
id: UO:0000003
label: time unit
deprecated: true
deprecated-description: Field has been merged with collection_time_point_relative.
deprecated-replaced-by:
- collection_time_point_relative
collection_time_point_reference:
type: string
description: Event in the study schedule to which `Sample collection time` relates to
Expand Down Expand Up @@ -2518,7 +2574,6 @@ NucleicAcidProcessing:
- template_class
- template_quality
- template_amount
- template_amount_unit
- library_generation_method
- library_generation_protocol
- library_generation_kit_version
Expand Down Expand Up @@ -2555,10 +2610,14 @@ NucleicAcidProcessing:
subset: process (nucleic acid)
name: Target substrate quality
template_amount:
type: number
$ref: '#/PhysicalQuantity'
description: Amount of template that went into the process
title: Template amount
example: 1000
example:
quantity: 1000
unit:
id: UO:0000024
label: nanogram
x-airr:
miairr: important
nullable: true
Expand All @@ -2568,24 +2627,12 @@ NucleicAcidProcessing:
name: Template amount
template_amount_unit:
$ref: '#/Ontology'
description: Unit of template amount
title: Template amount time unit
example:
id: UO:0000024
label: nanogram
x-airr:
miairr: important
nullable: true
adc-query-support: true
set: 3
subset: process (nucleic acid)
name: Template amount time unit
format: ontology
ontology:
draft: false
top_node:
id: UO:0000002
label: physical quantity
deprecated: true
deprecated-description: Field has been merged with template_amount.
deprecated-replaced-by:
- template_amount
library_generation_method:
type: string
enum:
Expand Down

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