From 54a63e8070596fb69a967f8a8f2a96285d3e6661 Mon Sep 17 00:00:00 2001 From: Christian Busse Date: Sun, 14 Jan 2024 15:26:38 +0100 Subject: [PATCH] Switch references between objects, introduce study_id to ReceptorReactivity --- lang/R/inst/extdata/airr-schema.yaml | 40 ++++++++++++++++--------- lang/python/airr/specs/airr-schema.yaml | 40 ++++++++++++++++--------- specs/airr-schema-openapi3.yaml | 39 ++++++++++++++---------- specs/airr-schema.yaml | 40 ++++++++++++++++--------- 4 files changed, 102 insertions(+), 57 deletions(-) diff --git a/lang/R/inst/extdata/airr-schema.yaml b/lang/R/inst/extdata/airr-schema.yaml index e191ec3eb..3ac46ba97 100644 --- a/lang/R/inst/extdata/airr-schema.yaml +++ b/lang/R/inst/extdata/airr-schema.yaml @@ -4266,7 +4266,7 @@ Cell: title: Cell-associated rearrangements items: type: string - example: [id1, id2] #empty vs NULL? + example: [id1, id2] x-airr: miairr: defined nullable: true @@ -4279,7 +4279,7 @@ Cell: title: Cell-associated receptors items: type: string - example: [id1, id2] #empty vs NULL? + example: [id1, id2] x-airr: miairr: defined nullable: true @@ -4436,7 +4436,7 @@ CellExpression: name: Property value -# The Receptor object hold information about a receptor and its reactivity. +# The Receptor object holds information about a receptor (immunoglobulin or TCR) # Receptor: type: object @@ -4536,22 +4536,15 @@ Receptor: x-airr: nullable: true adc-query-support: true - reactivity_measurements: - type: array - description: > - Array of reactivity measurement identifiers for the ReceptorReactivity objects associated with this Receptor - title: Reactivity measurements - items: - type: string - example: [id1, id2] - x-airr: - nullable: true - adc-query-support: true +# The ReceptorReactivity object holds information about the reactivity exhibited by a given receptor +# ReceptorReactivity: type: object required: - receptor_reactivity_id + - receptor_hash + - study_id - ligand_type - antigen_type - antigen @@ -4568,6 +4561,25 @@ ReceptorReactivity: identifier: true nullable: false adc-query-support: true + receptor_hash: + type: string + description: > + The hash of the receptor that the record refers to, calculated as described for the Receptor.receptor_hash + property. + title: Receptor hash ID + example: aa1c4b77a6f4927611ab39f5267415beaa0ba07a952c233d803b07e52261f026 + x-airr: + nullable: false + adc-query-support: true + study_id: + type: string + description: > + Identifier of the study in the context of which the reactivity measurement was conducted. + title: Study ID + example: PRJNA001 + x-airr: + nullable: false + adc-query-support: true ligand_type: type: string enum: diff --git a/lang/python/airr/specs/airr-schema.yaml b/lang/python/airr/specs/airr-schema.yaml index e191ec3eb..3ac46ba97 100644 --- a/lang/python/airr/specs/airr-schema.yaml +++ b/lang/python/airr/specs/airr-schema.yaml @@ -4266,7 +4266,7 @@ Cell: title: Cell-associated rearrangements items: type: string - example: [id1, id2] #empty vs NULL? + example: [id1, id2] x-airr: miairr: defined nullable: true @@ -4279,7 +4279,7 @@ Cell: title: Cell-associated receptors items: type: string - example: [id1, id2] #empty vs NULL? + example: [id1, id2] x-airr: miairr: defined nullable: true @@ -4436,7 +4436,7 @@ CellExpression: name: Property value -# The Receptor object hold information about a receptor and its reactivity. +# The Receptor object holds information about a receptor (immunoglobulin or TCR) # Receptor: type: object @@ -4536,22 +4536,15 @@ Receptor: x-airr: nullable: true adc-query-support: true - reactivity_measurements: - type: array - description: > - Array of reactivity measurement identifiers for the ReceptorReactivity objects associated with this Receptor - title: Reactivity measurements - items: - type: string - example: [id1, id2] - x-airr: - nullable: true - adc-query-support: true +# The ReceptorReactivity object holds information about the reactivity exhibited by a given receptor +# ReceptorReactivity: type: object required: - receptor_reactivity_id + - receptor_hash + - study_id - ligand_type - antigen_type - antigen @@ -4568,6 +4561,25 @@ ReceptorReactivity: identifier: true nullable: false adc-query-support: true + receptor_hash: + type: string + description: > + The hash of the receptor that the record refers to, calculated as described for the Receptor.receptor_hash + property. + title: Receptor hash ID + example: aa1c4b77a6f4927611ab39f5267415beaa0ba07a952c233d803b07e52261f026 + x-airr: + nullable: false + adc-query-support: true + study_id: + type: string + description: > + Identifier of the study in the context of which the reactivity measurement was conducted. + title: Study ID + example: PRJNA001 + x-airr: + nullable: false + adc-query-support: true ligand_type: type: string enum: diff --git a/specs/airr-schema-openapi3.yaml b/specs/airr-schema-openapi3.yaml index 00cdb250f..03a638611 100644 --- a/specs/airr-schema-openapi3.yaml +++ b/specs/airr-schema-openapi3.yaml @@ -4560,7 +4560,7 @@ Cell: title: Cell-associated rearrangements items: type: string - example: [id1, id2] #empty vs NULL? + example: [id1, id2] x-airr: miairr: defined adc-query-support: true @@ -4573,7 +4573,7 @@ Cell: title: Cell-associated receptors items: type: string - example: [id1, id2] #empty vs NULL? + example: [id1, id2] x-airr: miairr: defined adc-query-support: true @@ -4730,7 +4730,7 @@ CellExpression: name: Property value -# The Receptor object hold information about a receptor and its reactivity. +# The Receptor object holds information about a receptor (immunoglobulin or TCR) # Receptor: type: object @@ -4830,22 +4830,13 @@ Receptor: example: ["IEDB_RECEPTOR:10"] x-airr: adc-query-support: true - reactivity_measurements: - type: array - nullable: true - description: > - Array of reactivity measurement identifiers for the ReceptorReactivity objects associated with this Receptor - title: Reactivity measurements - items: - type: string - example: [id1, id2] - x-airr: - adc-query-support: true ReceptorReactivity: type: object required: - receptor_reactivity_id + - receptor_hash + - study_id - ligand_type - antigen_type - antigen @@ -4862,6 +4853,25 @@ ReceptorReactivity: x-airr: identifier: true adc-query-support: true + receptor_hash: + type: string + nullable: false + description: > + The hash of the receptor that the record refers to, calculated as described for the Receptor.receptor_hash + property. + title: Receptor hash ID + example: aa1c4b77a6f4927611ab39f5267415beaa0ba07a952c233d803b07e52261f026 + x-airr: + adc-query-support: true + study_id: + type: string + nullable: false + description: > + Identifier of the study in the context of which the reactivity measurement was conducted. + title: Study ID + example: PRJNA001 + x-airr: + adc-query-support: true ligand_type: type: string nullable: false @@ -5039,4 +5049,3 @@ ReceptorReactivity: example: pg/ml x-airr: adc-query-support: true - diff --git a/specs/airr-schema.yaml b/specs/airr-schema.yaml index e191ec3eb..3ac46ba97 100644 --- a/specs/airr-schema.yaml +++ b/specs/airr-schema.yaml @@ -4266,7 +4266,7 @@ Cell: title: Cell-associated rearrangements items: type: string - example: [id1, id2] #empty vs NULL? + example: [id1, id2] x-airr: miairr: defined nullable: true @@ -4279,7 +4279,7 @@ Cell: title: Cell-associated receptors items: type: string - example: [id1, id2] #empty vs NULL? + example: [id1, id2] x-airr: miairr: defined nullable: true @@ -4436,7 +4436,7 @@ CellExpression: name: Property value -# The Receptor object hold information about a receptor and its reactivity. +# The Receptor object holds information about a receptor (immunoglobulin or TCR) # Receptor: type: object @@ -4536,22 +4536,15 @@ Receptor: x-airr: nullable: true adc-query-support: true - reactivity_measurements: - type: array - description: > - Array of reactivity measurement identifiers for the ReceptorReactivity objects associated with this Receptor - title: Reactivity measurements - items: - type: string - example: [id1, id2] - x-airr: - nullable: true - adc-query-support: true +# The ReceptorReactivity object holds information about the reactivity exhibited by a given receptor +# ReceptorReactivity: type: object required: - receptor_reactivity_id + - receptor_hash + - study_id - ligand_type - antigen_type - antigen @@ -4568,6 +4561,25 @@ ReceptorReactivity: identifier: true nullable: false adc-query-support: true + receptor_hash: + type: string + description: > + The hash of the receptor that the record refers to, calculated as described for the Receptor.receptor_hash + property. + title: Receptor hash ID + example: aa1c4b77a6f4927611ab39f5267415beaa0ba07a952c233d803b07e52261f026 + x-airr: + nullable: false + adc-query-support: true + study_id: + type: string + description: > + Identifier of the study in the context of which the reactivity measurement was conducted. + title: Study ID + example: PRJNA001 + x-airr: + nullable: false + adc-query-support: true ligand_type: type: string enum: