diff --git a/lang/R/inst/extdata/airr-schema.yaml b/lang/R/inst/extdata/airr-schema.yaml index a40e5a87..3eeca443 100644 --- a/lang/R/inst/extdata/airr-schema.yaml +++ b/lang/R/inst/extdata/airr-schema.yaml @@ -2516,7 +2516,8 @@ CellProcessing: label: lymphocyte cell_phenotype: type: string - 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: @@ -2526,6 +2527,20 @@ 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 +4521,6 @@ Cell: type: object required: - cell_id - - rearrangements - repertoire_id - virtual_pairing properties: @@ -4523,32 +4537,6 @@ 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 +4555,60 @@ 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 + 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 +4620,10 @@ 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 +4637,7 @@ 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 +4821,12 @@ 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 +4836,13 @@ 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/R/tests/data-tests/good_combined_airr.json b/lang/R/tests/data-tests/good_combined_airr.json index fdbbeedc..fbea0271 100644 --- a/lang/R/tests/data-tests/good_combined_airr.json +++ b/lang/R/tests/data-tests/good_combined_airr.json @@ -189,6 +189,7 @@ "label": "naive B cell" }, "cell_phenotype": "expression of CD20 and the absence of CD27", + "cell_label": "naive B cell", "cell_species": { "id": "NCBITAXON:9606", "label": "Homo sapiens" @@ -388,6 +389,7 @@ "label": "memory B cell" }, "cell_phenotype": "expression of CD20 and CD27", + "cell_label": "memory B cell", "cell_species": { "id": "NCBITAXON:9606", "label": "Homo sapiens" @@ -587,6 +589,7 @@ "label": "naive thymus-derived CD4-positive, alpha-beta T cell" }, "cell_phenotype": "expression of CD8 and absence of CD4 and CD45RO", + "cell_label": "naive CD4 aB T cell", "cell_species": { "id": "NCBITAXON:9606", "label": "Homo sapiens" diff --git a/lang/R/tests/data-tests/good_combined_airr.yaml b/lang/R/tests/data-tests/good_combined_airr.yaml index 8bb8e755..b04fcb42 100644 --- a/lang/R/tests/data-tests/good_combined_airr.yaml +++ b/lang/R/tests/data-tests/good_combined_airr.yaml @@ -142,6 +142,7 @@ Repertoire: id: CL:0000788 label: naive B cell cell_phenotype: expression of CD20 and the absence of CD27 + cell_label: naive B cell cell_species: id: NCBITAXON:9606 label: Homo sapiens @@ -307,6 +308,7 @@ Repertoire: id: CL:0000787 label: memory B cell cell_phenotype: expression of CD20 and CD27 + cell_label: memory B cell cell_species: id: NCBITAXON:9606 label: Homo sapiens @@ -472,6 +474,7 @@ Repertoire: id: CL:0000895 label: naive thymus-derived CD4-positive, alpha-beta T cell cell_phenotype: expression of CD8 and absence of CD4 and CD45RO + cell_label: naive CD4 aB T cell cell_species: id: NCBITAXON:9606 label: Homo sapiens diff --git a/lang/R/tests/data-tests/good_repertoire.yaml b/lang/R/tests/data-tests/good_repertoire.yaml index 3f294b6b..ce83f55f 100644 --- a/lang/R/tests/data-tests/good_repertoire.yaml +++ b/lang/R/tests/data-tests/good_repertoire.yaml @@ -99,6 +99,7 @@ Repertoire: id: "CL:0000788" label: "naive B cell" cell_phenotype: "expression of CD20 and the absence of CD27" + cell_label: "naive B cell" cell_species: id: "NCBITAXON:9606" label: "Homo sapiens" @@ -254,6 +255,7 @@ Repertoire: id: "CL:0000787" label: "memory B cell" cell_phenotype: "expression of CD20 and CD27" + cell_label: "memory B cell" cell_species: id: "NCBITAXON:9606" label: "Homo sapiens" @@ -381,7 +383,7 @@ Repertoire: link_type: twin diagnosis: - study_group_description: null - diagnosis_timepoint: + diagnosis_timepoint: label: Study enrollment value: 60 unit: @@ -409,6 +411,7 @@ Repertoire: id: "CL:0000895" label: "naive thymus-derived CD4-positive, alpha-beta T cell" cell_phenotype: "expression of CD8 and absence of CD4 and CD45RO" + cell_label: "naive CD4+ aB T cell" cell_species: id: "NCBITAXON:9606" label: "Homo sapiens" diff --git a/lang/python/airr/specs/airr-schema.yaml b/lang/python/airr/specs/airr-schema.yaml index a40e5a87..3eeca443 100644 --- a/lang/python/airr/specs/airr-schema.yaml +++ b/lang/python/airr/specs/airr-schema.yaml @@ -2516,7 +2516,8 @@ CellProcessing: label: lymphocyte cell_phenotype: type: string - 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: @@ -2526,6 +2527,20 @@ 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 +4521,6 @@ Cell: type: object required: - cell_id - - rearrangements - repertoire_id - virtual_pairing properties: @@ -4523,32 +4537,6 @@ 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 +4555,60 @@ 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 + 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 +4620,10 @@ 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 +4637,7 @@ 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 +4821,12 @@ 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 +4836,13 @@ 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/tests/data/good_combined_airr.json b/lang/python/tests/data/good_combined_airr.json index fdbbeedc..fbea0271 100644 --- a/lang/python/tests/data/good_combined_airr.json +++ b/lang/python/tests/data/good_combined_airr.json @@ -189,6 +189,7 @@ "label": "naive B cell" }, "cell_phenotype": "expression of CD20 and the absence of CD27", + "cell_label": "naive B cell", "cell_species": { "id": "NCBITAXON:9606", "label": "Homo sapiens" @@ -388,6 +389,7 @@ "label": "memory B cell" }, "cell_phenotype": "expression of CD20 and CD27", + "cell_label": "memory B cell", "cell_species": { "id": "NCBITAXON:9606", "label": "Homo sapiens" @@ -587,6 +589,7 @@ "label": "naive thymus-derived CD4-positive, alpha-beta T cell" }, "cell_phenotype": "expression of CD8 and absence of CD4 and CD45RO", + "cell_label": "naive CD4 aB T cell", "cell_species": { "id": "NCBITAXON:9606", "label": "Homo sapiens" diff --git a/lang/python/tests/data/good_combined_airr.yaml b/lang/python/tests/data/good_combined_airr.yaml index 8bb8e755..b04fcb42 100644 --- a/lang/python/tests/data/good_combined_airr.yaml +++ b/lang/python/tests/data/good_combined_airr.yaml @@ -142,6 +142,7 @@ Repertoire: id: CL:0000788 label: naive B cell cell_phenotype: expression of CD20 and the absence of CD27 + cell_label: naive B cell cell_species: id: NCBITAXON:9606 label: Homo sapiens @@ -307,6 +308,7 @@ Repertoire: id: CL:0000787 label: memory B cell cell_phenotype: expression of CD20 and CD27 + cell_label: memory B cell cell_species: id: NCBITAXON:9606 label: Homo sapiens @@ -472,6 +474,7 @@ Repertoire: id: CL:0000895 label: naive thymus-derived CD4-positive, alpha-beta T cell cell_phenotype: expression of CD8 and absence of CD4 and CD45RO + cell_label: naive CD4 aB T cell cell_species: id: NCBITAXON:9606 label: Homo sapiens diff --git a/lang/python/tests/data/good_repertoire.yaml b/lang/python/tests/data/good_repertoire.yaml index 3f294b6b..7ac0ae57 100644 --- a/lang/python/tests/data/good_repertoire.yaml +++ b/lang/python/tests/data/good_repertoire.yaml @@ -99,6 +99,7 @@ Repertoire: id: "CL:0000788" label: "naive B cell" cell_phenotype: "expression of CD20 and the absence of CD27" + cell_label: "naive B cell" cell_species: id: "NCBITAXON:9606" label: "Homo sapiens" @@ -254,6 +255,7 @@ Repertoire: id: "CL:0000787" label: "memory B cell" cell_phenotype: "expression of CD20 and CD27" + cell_label: "memory B cell" cell_species: id: "NCBITAXON:9606" label: "Homo sapiens" @@ -409,6 +411,7 @@ Repertoire: id: "CL:0000895" label: "naive thymus-derived CD4-positive, alpha-beta T cell" cell_phenotype: "expression of CD8 and absence of CD4 and CD45RO" + cell_label: "naive CD4+ aB T cell" cell_species: id: "NCBITAXON:9606" label: "Homo sapiens" diff --git a/specs/airr-schema-openapi3.yaml b/specs/airr-schema-openapi3.yaml index e833ff93..29c6b983 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 @@ -4890,10 +4904,10 @@ 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: +Expression: type: object required: - expression_id @@ -4907,7 +4921,7 @@ 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 @@ -5092,10 +5106,10 @@ Receptor: x-airr: adc-query-support: true -CellReactivity: +Reactivity: type: object required: - - cell_reactivity_id + - reactivity_id - cell_id - ligand_type - antigen_type @@ -5105,14 +5119,14 @@ CellReactivity: - reactivity_value - reactivity_unit properties: - cell_reactivity_id: + reactivity_id: type: string nullable: false 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 adc-query-support: true diff --git a/specs/airr-schema.yaml b/specs/airr-schema.yaml index a40e5a87..13a542c3 100644 --- a/specs/airr-schema.yaml +++ b/specs/airr-schema.yaml @@ -2516,7 +2516,8 @@ CellProcessing: label: lymphocyte cell_phenotype: type: string - 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: @@ -2526,6 +2527,20 @@ 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 +4521,6 @@ Cell: type: object required: - cell_id - - rearrangements - repertoire_id - virtual_pairing properties: @@ -4523,32 +4537,6 @@ 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 +4555,60 @@ 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 + 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 +4620,10 @@ 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: +Expression: type: object required: - expression_id @@ -4623,7 +4637,7 @@ 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 +4821,12 @@ 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 +4836,13 @@ 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