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AKC updates to v1.5 #814

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AKC updates to v1.5 #814

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dc0615b
add ontology info
schristley Nov 26, 2024
4642032
add ontology info
schristley Nov 26, 2024
f52ea07
set to integer
schristley Nov 26, 2024
3b4bf86
define object for repertoires array
schristley Nov 26, 2024
c075adc
make field names unique
schristley Dec 10, 2024
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71 changes: 43 additions & 28 deletions specs/airr-schema-openapi3.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -429,21 +429,21 @@ TimePoint:
description: Time point at which an observation or other action was performed.
type: object
properties:
label:
time_point_label:
type: string
nullable: true
description: Informative label for the time point
example: Pre-operative sampling of cancer tissue
x-airr:
adc-query-support: true
value:
time_point_value:
type: number
nullable: true
description: Value of the time point
example: -5.0
x-airr:
adc-query-support: true
unit:
time_point_unit:
$ref: '#/Ontology'
nullable: true
description: Unit of the time point
Expand Down Expand Up @@ -480,7 +480,7 @@ Acknowledgement:
identifier: true
miairr: important
nullable: true
name:
individual_full_name:
type: string
nullable: true
description: Full name of individual
Expand Down Expand Up @@ -944,6 +944,12 @@ AlleleDescription:
label: Homo sapiens
x-airr:
miairr: essential
format: ontology
ontology:
draft: false
top_node:
id: NCBITAXON:7776
label: Gnathostomata
species_subgroup:
type: string
nullable: true
Expand Down Expand Up @@ -1172,7 +1178,7 @@ GermlineSet:
items:
$ref: '#/Acknowledgement'
release_version:
type: number
type: integer
nullable: true
x-airr:
miairr: important
Expand Down Expand Up @@ -1213,13 +1219,19 @@ GermlineSet:
species:
$ref: '#/Ontology'
nullable: false
x-airr:
miairr: essential
description: Binomial designation of subject's species
title: Organism
example:
id: NCBITAXON:9606
label: Homo sapiens
x-airr:
miairr: essential
format: ontology
ontology:
draft: false
top_node:
id: NCBITAXON:7776
label: Gnathostomata
species_subgroup:
type: string
nullable: true
Expand Down Expand Up @@ -3233,6 +3245,28 @@ Repertoire:
adc-query-support: true

# A collection of repertoires for analysis purposes, includes optional time course
RepertoireGroupDetail:
type: object
properties:
repertoire_id:
type: string
nullable: false
description: Identifier to the repertoire
x-airr:
adc-query-support: true
repertoire_description:
type: string
nullable: true
description: Description of this repertoire within the group
x-airr:
adc-query-support: true
time_point:
$ref: '#/TimePoint'
nullable: true
description: Time point designation for this repertoire within the group
x-airr:
adc-query-support: true

RepertoireGroup:
type: object
required:
Expand All @@ -3259,26 +3293,7 @@ RepertoireGroup:
description: >
List of repertoires in this collection with an associated description and time point designation
items:
type: object
properties:
repertoire_id:
type: string
nullable: false
description: Identifier to the repertoire
x-airr:
adc-query-support: true
repertoire_description:
type: string
nullable: true
description: Description of this repertoire within the group
x-airr:
adc-query-support: true
time_point:
$ref: '#/TimePoint'
nullable: true
description: Time point designation for this repertoire within the group
x-airr:
adc-query-support: true
$ref: '#/RepertoireGroupDetail'

Alignment:
type: object
Expand Down Expand Up @@ -4732,7 +4747,7 @@ CellExpression:
adc-query-support: true
format: ontology
name: Property information
value:
property_value:
type: number
description: Level at which the property was observed in the experiment (non-normalized).
title: Property value
Expand Down
57 changes: 36 additions & 21 deletions specs/airr-schema.yaml
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -905,6 +905,12 @@ AlleleDescription:
x-airr:
miairr: essential
nullable: false
format: ontology
ontology:
draft: false
top_node:
id: NCBITAXON:7776
label: Gnathostomata
species_subgroup:
type: string
description: Race, strain or other species subgroup to which this subject belongs
Expand Down Expand Up @@ -1103,7 +1109,7 @@ GermlineSet:
items:
$ref: '#/Acknowledgement'
release_version:
type: number
type: integer
description: Version number of this record, allocated automatically
x-airr:
miairr: important
Expand Down Expand Up @@ -1145,6 +1151,12 @@ GermlineSet:
x-airr:
miairr: essential
nullable: false
format: ontology
ontology:
draft: false
top_node:
id: NCBITAXON:7776
label: Gnathostomata
species_subgroup:
type: string
description: Race, strain or other species subgroup to which this subject belongs
Expand Down Expand Up @@ -3131,6 +3143,28 @@ Repertoire:
adc-query-support: true

# A collection of repertoires for analysis purposes, includes optional time course
RepertoireGroupDetail:
type: object
properties:
repertoire_id:
type: string
description: Identifier to the repertoire
x-airr:
nullable: false
adc-query-support: true
repertoire_description:
type: string
description: Description of this repertoire within the group
x-airr:
nullable: true
adc-query-support: true
time_point:
$ref: '#/TimePoint'
description: Time point designation for this repertoire within the group
x-airr:
nullable: true
adc-query-support: true

RepertoireGroup:
type: object
required:
Expand All @@ -3153,26 +3187,7 @@ RepertoireGroup:
description: >
List of repertoires in this collection with an associated description and time point designation
items:
type: object
properties:
repertoire_id:
type: string
description: Identifier to the repertoire
x-airr:
nullable: false
adc-query-support: true
repertoire_description:
type: string
description: Description of this repertoire within the group
x-airr:
nullable: true
adc-query-support: true
time_point:
$ref: '#/TimePoint'
description: Time point designation for this repertoire within the group
x-airr:
nullable: true
adc-query-support: true
$ref: '#/RepertoireGroupDetail'


Alignment:
Expand Down
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