From 14dfa1175094e6ecb4fcd06d06b3e358692b2057 Mon Sep 17 00:00:00 2001 From: Jason Vander Heiden Date: Tue, 5 Mar 2024 17:01:32 -0800 Subject: [PATCH 1/8] Initial restructuring of Cell --- specs/airr-schema.yaml | 96 +++++++++++++++++++++--------------------- 1 file changed, 47 insertions(+), 49 deletions(-) diff --git a/specs/airr-schema.yaml b/specs/airr-schema.yaml index a40e5a87..4a0b30cb 100644 --- a/specs/airr-schema.yaml +++ b/specs/airr-schema.yaml @@ -4506,7 +4506,6 @@ Cell: type: object required: - cell_id - - rearrangements - repertoire_id - virtual_pairing properties: @@ -4523,32 +4522,6 @@ 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 +4540,59 @@ 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 + 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: defined nullable: true adc-query-support: true - expression_raw_doi: + 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 +4604,10 @@ 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 +4621,7 @@ 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 +4805,12 @@ 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 +4820,13 @@ 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 From 40968d1f80cbae6daf92f8efac37e91261f70958 Mon Sep 17 00:00:00 2001 From: Jason Vander Heiden Date: Mon, 8 Apr 2024 08:11:29 -0700 Subject: [PATCH 2/8] 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 From 259755c1843b899a915ac11874092ab6b73d7a90 Mon Sep 17 00:00:00 2001 From: Jason Vander Heiden Date: Mon, 8 Apr 2024 08:14:59 -0700 Subject: [PATCH 3/8] punctuation!?...,;) --- lang/R/inst/extdata/airr-schema.yaml | 6 ++++-- lang/python/airr/specs/airr-schema.yaml | 6 ++++-- specs/airr-schema-openapi3.yaml | 2 +- specs/airr-schema.yaml | 6 ++++-- 4 files changed, 13 insertions(+), 7 deletions(-) diff --git a/lang/R/inst/extdata/airr-schema.yaml b/lang/R/inst/extdata/airr-schema.yaml index 4340faf2..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: @@ -4587,7 +4588,8 @@ Cell: 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: diff --git a/lang/python/airr/specs/airr-schema.yaml b/lang/python/airr/specs/airr-schema.yaml index 4340faf2..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: @@ -4587,7 +4588,8 @@ Cell: 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: diff --git a/specs/airr-schema-openapi3.yaml b/specs/airr-schema-openapi3.yaml index 2e62d281..a16c0a9d 100644 --- a/specs/airr-schema-openapi3.yaml +++ b/specs/airr-schema-openapi3.yaml @@ -2611,7 +2611,7 @@ CellProcessing: type: string nullable: true description: > - List of cellular markers and their expression levels used to isolate the cell population + 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: diff --git a/specs/airr-schema.yaml b/specs/airr-schema.yaml index cdc69097..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: @@ -4587,7 +4588,8 @@ Cell: 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: From 020afc1388b2b283548f609840214d9cf78053aa Mon Sep 17 00:00:00 2001 From: Jason Vander Heiden Date: Mon, 8 Apr 2024 08:20:55 -0700 Subject: [PATCH 4/8] Sync Expression and Reactivity --- specs/airr-schema-openapi3.yaml | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/specs/airr-schema-openapi3.yaml b/specs/airr-schema-openapi3.yaml index a16c0a9d..29c6b983 100644 --- a/specs/airr-schema-openapi3.yaml +++ b/specs/airr-schema-openapi3.yaml @@ -4904,10 +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 @@ -4921,7 +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 @@ -5106,10 +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 @@ -5119,14 +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 From 2e6300ae9a739cdc0e3990ca77f6622c614ac1bc Mon Sep 17 00:00:00 2001 From: Jason Vander Heiden Date: Mon, 8 Apr 2024 08:28:18 -0700 Subject: [PATCH 5/8] Add Cell.cell_label to test data --- lang/R/tests/data-tests/good_repertoire.yaml | 1 + lang/python/tests/data/good_repertoire.yaml | 1 + 2 files changed, 2 insertions(+) diff --git a/lang/R/tests/data-tests/good_repertoire.yaml b/lang/R/tests/data-tests/good_repertoire.yaml index 3f294b6b..5bd9a7cf 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" diff --git a/lang/python/tests/data/good_repertoire.yaml b/lang/python/tests/data/good_repertoire.yaml index 3f294b6b..5bd9a7cf 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" From 05a6477c894b3389f93ddb0be774d11276aa17f4 Mon Sep 17 00:00:00 2001 From: Jason Vander Heiden Date: Mon, 8 Apr 2024 08:31:23 -0700 Subject: [PATCH 6/8] Missed some --- lang/R/tests/data-tests/good_repertoire.yaml | 4 +++- lang/python/tests/data/good_repertoire.yaml | 2 ++ 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/lang/R/tests/data-tests/good_repertoire.yaml b/lang/R/tests/data-tests/good_repertoire.yaml index 5bd9a7cf..ce83f55f 100644 --- a/lang/R/tests/data-tests/good_repertoire.yaml +++ b/lang/R/tests/data-tests/good_repertoire.yaml @@ -255,6 +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" @@ -382,7 +383,7 @@ Repertoire: link_type: twin diagnosis: - study_group_description: null - diagnosis_timepoint: + diagnosis_timepoint: label: Study enrollment value: 60 unit: @@ -410,6 +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/tests/data/good_repertoire.yaml b/lang/python/tests/data/good_repertoire.yaml index 5bd9a7cf..7ac0ae57 100644 --- a/lang/python/tests/data/good_repertoire.yaml +++ b/lang/python/tests/data/good_repertoire.yaml @@ -255,6 +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" @@ -410,6 +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" From b9c4795723ec1c4dc1ecd67aaa441d234b49be0d Mon Sep 17 00:00:00 2001 From: Jason Vander Heiden Date: Mon, 8 Apr 2024 08:46:24 -0700 Subject: [PATCH 7/8] sync combined repertoire test data --- lang/R/tests/data-tests/good_combined_airr.json | 3 +++ lang/R/tests/data-tests/good_combined_airr.yaml | 3 +++ lang/python/tests/data/good_combined_airr.json | 3 +++ lang/python/tests/data/good_combined_airr.yaml | 3 +++ 4 files changed, 12 insertions(+) diff --git a/lang/R/tests/data-tests/good_combined_airr.json b/lang/R/tests/data-tests/good_combined_airr.json index fdbbeedc..19fafb5e 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..4ec21b01 100644 --- a/lang/R/tests/data-tests/good_combined_airr.yaml +++ b/lang/R/tests/data-tests/good_combined_airr.yaml @@ -145,6 +145,7 @@ Repertoire: cell_species: id: NCBITAXON:9606 label: Homo sapiens + cell_label: naive B cell single_cell: false cell_isolation: FACS template_class: RNA @@ -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_combined_airr.json b/lang/python/tests/data/good_combined_airr.json index fdbbeedc..19fafb5e 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..4ec21b01 100644 --- a/lang/python/tests/data/good_combined_airr.yaml +++ b/lang/python/tests/data/good_combined_airr.yaml @@ -145,6 +145,7 @@ Repertoire: cell_species: id: NCBITAXON:9606 label: Homo sapiens + cell_label: naive B cell single_cell: false cell_isolation: FACS template_class: RNA @@ -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 From 4fd1bf904cb3d930ba8f9334c694241fc9c4a51e Mon Sep 17 00:00:00 2001 From: Jason Vander Heiden Date: Mon, 8 Apr 2024 08:58:14 -0700 Subject: [PATCH 8/8] fix field order in test data --- lang/R/tests/data-tests/good_combined_airr.json | 2 +- lang/R/tests/data-tests/good_combined_airr.yaml | 4 ++-- lang/python/tests/data/good_combined_airr.json | 2 +- lang/python/tests/data/good_combined_airr.yaml | 4 ++-- 4 files changed, 6 insertions(+), 6 deletions(-) diff --git a/lang/R/tests/data-tests/good_combined_airr.json b/lang/R/tests/data-tests/good_combined_airr.json index 19fafb5e..fbea0271 100644 --- a/lang/R/tests/data-tests/good_combined_airr.json +++ b/lang/R/tests/data-tests/good_combined_airr.json @@ -589,7 +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_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 4ec21b01..b04fcb42 100644 --- a/lang/R/tests/data-tests/good_combined_airr.yaml +++ b/lang/R/tests/data-tests/good_combined_airr.yaml @@ -142,10 +142,10 @@ 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 - cell_label: naive B cell single_cell: false cell_isolation: FACS template_class: RNA @@ -474,7 +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_label: naive CD4 aB T cell cell_species: id: NCBITAXON:9606 label: Homo sapiens diff --git a/lang/python/tests/data/good_combined_airr.json b/lang/python/tests/data/good_combined_airr.json index 19fafb5e..fbea0271 100644 --- a/lang/python/tests/data/good_combined_airr.json +++ b/lang/python/tests/data/good_combined_airr.json @@ -589,7 +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_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 4ec21b01..b04fcb42 100644 --- a/lang/python/tests/data/good_combined_airr.yaml +++ b/lang/python/tests/data/good_combined_airr.yaml @@ -142,10 +142,10 @@ 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 - cell_label: naive B cell single_cell: false cell_isolation: FACS template_class: RNA @@ -474,7 +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_label: naive CD4 aB T cell cell_species: id: NCBITAXON:9606 label: Homo sapiens