From 40968d1f80cbae6daf92f8efac37e91261f70958 Mon Sep 17 00:00:00 2001 From: Jason Vander Heiden Date: Mon, 8 Apr 2024 08:11:29 -0700 Subject: [PATCH] Sync specs and update cell_label --- lang/R/inst/extdata/airr-schema.yaml | 112 +++++++++++++----------- lang/python/airr/specs/airr-schema.yaml | 112 +++++++++++++----------- specs/airr-schema-openapi3.yaml | 94 +++++++++++--------- specs/airr-schema.yaml | 16 +++- 4 files changed, 193 insertions(+), 141 deletions(-) diff --git a/lang/R/inst/extdata/airr-schema.yaml b/lang/R/inst/extdata/airr-schema.yaml index a40e5a87..4340faf2 100644 --- a/lang/R/inst/extdata/airr-schema.yaml +++ b/lang/R/inst/extdata/airr-schema.yaml @@ -2526,6 +2526,20 @@ CellProcessing: set: 3 subset: process (cell) name: Cell subset phenotype + cell_label: + type: string + description: > + Free text cell type annotation. Primarily used for annotating cell types that are not + provided in the Cell Ontology. + title: Cell annotation + example: age-associated B cell + x-airr: + miairr: defined + nullable: true + adc-query-support: true + set: 3 + subset: process (cell) + name: Cell annotation cell_species: $ref: '#/Ontology' description: > @@ -4506,7 +4520,6 @@ Cell: type: object required: - cell_id - - rearrangements - repertoire_id - virtual_pairing properties: @@ -4523,32 +4536,6 @@ Cell: nullable: false adc-query-support: true name: Cell index - rearrangements: - type: array - description: > - Array of sequence identifiers defined for the Rearrangement objects associated with this cell - title: Cell-associated rearrangements - items: - type: string - example: [id1, id2] - x-airr: - miairr: defined - nullable: true - adc-query-support: true - name: Cell-associated rearrangements - receptors: - type: array - description: > - Array of receptor identifiers defined for the Receptor objects associated with this cell - title: Cell-associated receptors - items: - type: string - example: [id1, id2] - x-airr: - miairr: defined - nullable: true - adc-query-support: true - name: Cell-associated receptors repertoire_id: type: string description: Identifier to the associated repertoire in study metadata. @@ -4567,34 +4554,59 @@ Cell: nullable: true adc-query-support: true name: Data processing for cell - expression_study_method: - type: string - enum: - - flow_cytometry - - single-cell_transcriptome - - null + receptors: + type: array description: > - Keyword describing the methodology used to assess expression. This values for this field MUST - come from a controlled vocabulary. + Array of receptor identifiers defined for the Receptor objects associated with this cell + title: Cell-associated receptors + items: + type: string + example: [id1, id2] x-airr: miairr: defined nullable: true adc-query-support: true - expression_raw_doi: + name: Cell-associated receptors + cell_subset: + $ref: '#/Ontology' + description: Commonly-used designation of isolated cell population. + title: Cell subset + example: + id: CL:0000972 + label: class switched memory B cell + x-airr: + miairr: important + nullable: true + adc-query-support: true + name: Cell subset + format: ontology + ontology: + draft: false + top_node: + id: CL:0000542 + label: lymphocyte + cell_phenotype: type: string - description: > - DOI of raw data set containing the current event + description: List of cellular markers and their expression levels used to isolate the cell population. + title: Cell subset phenotype + example: CD19+ CD38+ CD27+ IgM- IgD- x-airr: miairr: defined nullable: true adc-query-support: true - expression_index: + name: Cell subset phenotype + cell_label: type: string description: > - Index addressing the current event within the raw data set. + Free text cell type annotation. Primarily used for annotating cell types that are not + provided in the Cell Ontology. + title: Cell annotation + example: age-associated B cell x-airr: miairr: defined nullable: true + adc-query-support: true + name: Cell annotation virtual_pairing: type: boolean description: > @@ -4606,10 +4618,10 @@ Cell: adc-query-support: true name: Virtual pairing -# The CellExpression object acts as a container to hold a single expression level measurement from +# The Expression object acts as a container to hold a single expression level measurement from # an experiment. Expression data is associated with a cell_id and the related repertoire_id and -# data_processing_id -CellExpression: +# data_processing_id +Expression: type: object required: - expression_id @@ -4623,7 +4635,7 @@ CellExpression: expression_id: type: string description: > - Identifier for the CellExpression object. This identifier must be unique within + Identifier for the Expression object. This identifier must be unique within a given study, but it is recommended that it be a universally unique record locator to enable database applications. title: Expression property measurement identifier @@ -4807,12 +4819,12 @@ Receptor: nullable: true adc-query-support: true -# The CellReactivity object holds information about the reactivity exhibited by a given Cell +# The Reactivity object holds information about the reactivity exhibited by a given Cell # -CellReactivity: +Reactivity: type: object required: - - cell_reactivity_id + - reactivity_id - cell_id - ligand_type - antigen_type @@ -4822,13 +4834,13 @@ CellReactivity: - reactivity_value - reactivity_unit properties: - cell_reactivity_id: + reactivity_id: type: string description: > - Identifier for the CellReactivity object. This identifier must be unique within + Identifier for the Reactivity object. This identifier must be unique within a given study, but it is recommended that it be a universally unique record locator to enable database applications. - title: CellReactivity ID + title: Reactivity ID x-airr: identifier: true nullable: false diff --git a/lang/python/airr/specs/airr-schema.yaml b/lang/python/airr/specs/airr-schema.yaml index a40e5a87..4340faf2 100644 --- a/lang/python/airr/specs/airr-schema.yaml +++ b/lang/python/airr/specs/airr-schema.yaml @@ -2526,6 +2526,20 @@ CellProcessing: set: 3 subset: process (cell) name: Cell subset phenotype + cell_label: + type: string + description: > + Free text cell type annotation. Primarily used for annotating cell types that are not + provided in the Cell Ontology. + title: Cell annotation + example: age-associated B cell + x-airr: + miairr: defined + nullable: true + adc-query-support: true + set: 3 + subset: process (cell) + name: Cell annotation cell_species: $ref: '#/Ontology' description: > @@ -4506,7 +4520,6 @@ Cell: type: object required: - cell_id - - rearrangements - repertoire_id - virtual_pairing properties: @@ -4523,32 +4536,6 @@ Cell: nullable: false adc-query-support: true name: Cell index - rearrangements: - type: array - description: > - Array of sequence identifiers defined for the Rearrangement objects associated with this cell - title: Cell-associated rearrangements - items: - type: string - example: [id1, id2] - x-airr: - miairr: defined - nullable: true - adc-query-support: true - name: Cell-associated rearrangements - receptors: - type: array - description: > - Array of receptor identifiers defined for the Receptor objects associated with this cell - title: Cell-associated receptors - items: - type: string - example: [id1, id2] - x-airr: - miairr: defined - nullable: true - adc-query-support: true - name: Cell-associated receptors repertoire_id: type: string description: Identifier to the associated repertoire in study metadata. @@ -4567,34 +4554,59 @@ Cell: nullable: true adc-query-support: true name: Data processing for cell - expression_study_method: - type: string - enum: - - flow_cytometry - - single-cell_transcriptome - - null + receptors: + type: array description: > - Keyword describing the methodology used to assess expression. This values for this field MUST - come from a controlled vocabulary. + Array of receptor identifiers defined for the Receptor objects associated with this cell + title: Cell-associated receptors + items: + type: string + example: [id1, id2] x-airr: miairr: defined nullable: true adc-query-support: true - expression_raw_doi: + name: Cell-associated receptors + cell_subset: + $ref: '#/Ontology' + description: Commonly-used designation of isolated cell population. + title: Cell subset + example: + id: CL:0000972 + label: class switched memory B cell + x-airr: + miairr: important + nullable: true + adc-query-support: true + name: Cell subset + format: ontology + ontology: + draft: false + top_node: + id: CL:0000542 + label: lymphocyte + cell_phenotype: type: string - description: > - DOI of raw data set containing the current event + description: List of cellular markers and their expression levels used to isolate the cell population. + title: Cell subset phenotype + example: CD19+ CD38+ CD27+ IgM- IgD- x-airr: miairr: defined nullable: true adc-query-support: true - expression_index: + name: Cell subset phenotype + cell_label: type: string description: > - Index addressing the current event within the raw data set. + Free text cell type annotation. Primarily used for annotating cell types that are not + provided in the Cell Ontology. + title: Cell annotation + example: age-associated B cell x-airr: miairr: defined nullable: true + adc-query-support: true + name: Cell annotation virtual_pairing: type: boolean description: > @@ -4606,10 +4618,10 @@ Cell: adc-query-support: true name: Virtual pairing -# The CellExpression object acts as a container to hold a single expression level measurement from +# The Expression object acts as a container to hold a single expression level measurement from # an experiment. Expression data is associated with a cell_id and the related repertoire_id and -# data_processing_id -CellExpression: +# data_processing_id +Expression: type: object required: - expression_id @@ -4623,7 +4635,7 @@ CellExpression: expression_id: type: string description: > - Identifier for the CellExpression object. This identifier must be unique within + Identifier for the Expression object. This identifier must be unique within a given study, but it is recommended that it be a universally unique record locator to enable database applications. title: Expression property measurement identifier @@ -4807,12 +4819,12 @@ Receptor: nullable: true adc-query-support: true -# The CellReactivity object holds information about the reactivity exhibited by a given Cell +# The Reactivity object holds information about the reactivity exhibited by a given Cell # -CellReactivity: +Reactivity: type: object required: - - cell_reactivity_id + - reactivity_id - cell_id - ligand_type - antigen_type @@ -4822,13 +4834,13 @@ CellReactivity: - reactivity_value - reactivity_unit properties: - cell_reactivity_id: + reactivity_id: type: string description: > - Identifier for the CellReactivity object. This identifier must be unique within + Identifier for the Reactivity object. This identifier must be unique within a given study, but it is recommended that it be a universally unique record locator to enable database applications. - title: CellReactivity ID + title: Reactivity ID x-airr: identifier: true nullable: false diff --git a/specs/airr-schema-openapi3.yaml b/specs/airr-schema-openapi3.yaml index e833ff93..2e62d281 100644 --- a/specs/airr-schema-openapi3.yaml +++ b/specs/airr-schema-openapi3.yaml @@ -2610,7 +2610,8 @@ CellProcessing: cell_phenotype: type: string nullable: true - description: List of cellular markers and their expression levels used to isolate the cell population + description: > + List of cellular markers and their expression levels used to isolate the cell population title: Cell subset phenotype example: CD19+ CD38+ CD27+ IgM- IgD- x-airr: @@ -2619,6 +2620,20 @@ CellProcessing: set: 3 subset: process (cell) name: Cell subset phenotype + cell_label: + type: string + nullable: true + description: > + Free text cell type annotation. Primarily used for annotating cell types that are not + provided in the Cell Ontology. + title: Cell annotation + example: age-associated B cell + x-airr: + miairr: defined + adc-query-support: true + set: 3 + subset: process (cell) + name: Cell annotation cell_species: $ref: '#/Ontology' nullable: true @@ -4790,7 +4805,6 @@ Cell: type: object required: - cell_id - - rearrangements - repertoire_id - virtual_pairing properties: @@ -4807,32 +4821,6 @@ Cell: miairr: defined adc-query-support: true name: Cell index - rearrangements: - type: array - nullable: true - description: > - Array of sequence identifiers defined for the Rearrangement objects associated with this cell - title: Cell-associated rearrangements - items: - type: string - example: [id1, id2] - x-airr: - miairr: defined - adc-query-support: true - name: Cell-associated rearrangements - receptors: - type: array - nullable: true - description: > - Array of receptor identifiers defined for the Receptor objects associated with this cell - title: Cell-associated receptors - items: - type: string - example: [id1, id2] - x-airr: - miairr: defined - adc-query-support: true - name: Cell-associated receptors repertoire_id: type: string nullable: true @@ -4851,34 +4839,60 @@ Cell: miairr: defined adc-query-support: true name: Data processing for cell - expression_study_method: - type: string - enum: - - flow_cytometry - - single-cell_transcriptome - - null + receptors: + type: array nullable: true description: > - Keyword describing the methodology used to assess expression. This values for this field MUST - come from a controlled vocabulary. + Array of receptor identifiers defined for the Receptor objects associated with this cell + title: Cell-associated receptors + items: + type: string + example: [id1, id2] x-airr: miairr: defined adc-query-support: true - expression_raw_doi: + name: Cell-associated receptors + cell_subset: + $ref: '#/Ontology' + nullable: true + description: Commonly-used designation of isolated cell population. + title: Cell subset + example: + id: CL:0000972 + label: class switched memory B cell + x-airr: + miairr: important + adc-query-support: true + name: Cell subset + format: ontology + ontology: + draft: false + top_node: + id: CL:0000542 + label: lymphocyte + cell_phenotype: type: string nullable: true description: > - DOI of raw data set containing the current event + List of cellular markers and their expression levels used to isolate the cell population. + title: Cell subset phenotype + example: CD19+ CD38+ CD27+ IgM- IgD- x-airr: miairr: defined adc-query-support: true - expression_index: + name: Cell subset phenotype + cell_label: type: string nullable: true description: > - Index addressing the current event within the raw data set. + Free text cell type annotation. Primarily used for annotating cell types that are not + provided in the Cell Ontology. + title: Cell annotation + example: age-associated B cell x-airr: miairr: defined + adc-query-support: true + name: Cell annotation virtual_pairing: type: boolean nullable: true diff --git a/specs/airr-schema.yaml b/specs/airr-schema.yaml index 4a0b30cb..cdc69097 100644 --- a/specs/airr-schema.yaml +++ b/specs/airr-schema.yaml @@ -2526,6 +2526,20 @@ CellProcessing: set: 3 subset: process (cell) name: Cell subset phenotype + cell_label: + type: string + description: > + Free text cell type annotation. Primarily used for annotating cell types that are not + provided in the Cell Ontology. + title: Cell annotation + example: age-associated B cell + x-airr: + miairr: defined + nullable: true + adc-query-support: true + set: 3 + subset: process (cell) + name: Cell annotation cell_species: $ref: '#/Ontology' description: > @@ -4561,7 +4575,7 @@ Cell: id: CL:0000972 label: class switched memory B cell x-airr: - miairr: defined + miairr: important nullable: true adc-query-support: true name: Cell subset