From 2f62979c0ebfd0de2c2900fecef0fa5a11fdb048 Mon Sep 17 00:00:00 2001 From: Anu Shivalikanjli Date: Thu, 24 Apr 2025 15:25:30 +0100 Subject: [PATCH 1/5] expression alteration phenotype changed alongwith description changes --- .../type/biomaterial/clonal_cell_line.json | 12 ++++----- .../biomaterial/differentiated_product.json | 2 +- .../biomaterial/undifferentiated_product.json | 2 +- .../type/protocol/expression_alteration.json | 25 ++++++++++++++----- 4 files changed, 27 insertions(+), 14 deletions(-) diff --git a/json_schema/type/biomaterial/clonal_cell_line.json b/json_schema/type/biomaterial/clonal_cell_line.json index 64fc436..f7862e6 100644 --- a/json_schema/type/biomaterial/clonal_cell_line.json +++ b/json_schema/type/biomaterial/clonal_cell_line.json @@ -63,7 +63,7 @@ "pattern": "^[a-zA-Z0-9_]*$", "minLength": 1, "description": "A unique label for the cell line. No spaces allowed.", - "title": "Cell line ID", + "title": "Clonal cell line ID", "examples": [ "PRMT5_C-terminal_AID_DMSO", "OCM_108_Auxin_24h" @@ -72,8 +72,8 @@ "description": { "type": "string", "minLength": 1, - "description": "A general description of the cell line.", - "title": "Cell line description", + "description": "A general description of the clonal cell line.", + "title": "Clonal cell line description", "examples": [ "KOLF2.2J derived knockout cell line, PAX6/STL2 DKO" ] @@ -207,8 +207,8 @@ "type": { "type": "string", "minLength": 1, - "description": "The type of cell line.", - "title": "Cell line type", + "description": "The type of clonal cell line.", + "title": "Clonal cell line type", "enum": [ "iPSC", "embryoid", @@ -341,7 +341,7 @@ "treatment_condition": { "type": "string", "minLength": 1, - "description": "Protocol for generating cell line. e.g. condition or multiple conditions used to generate the cell line (if applicable).", + "description": "Condition or multiple conditions used to generate the cell line (if applicable).", "title": "Treatment/Condition", "examples": [ "DMSO", diff --git a/json_schema/type/biomaterial/differentiated_product.json b/json_schema/type/biomaterial/differentiated_product.json index b866089..5c80c87 100644 --- a/json_schema/type/biomaterial/differentiated_product.json +++ b/json_schema/type/biomaterial/differentiated_product.json @@ -147,7 +147,7 @@ "treatment_condition": { "type": "string", "minLength": 1, - "description": "Protocol for generating cell line. e.g. condition or multiple conditions used to generate the cell line. (if applicable)", + "description": "Condition or multiple conditions used to generate the cell line. (if applicable)", "title": "Treatment/Condition", "examples": [ "DMSO", diff --git a/json_schema/type/biomaterial/undifferentiated_product.json b/json_schema/type/biomaterial/undifferentiated_product.json index 0efc160..109bd72 100644 --- a/json_schema/type/biomaterial/undifferentiated_product.json +++ b/json_schema/type/biomaterial/undifferentiated_product.json @@ -104,7 +104,7 @@ "treatment_condition": { "type": "string", "minLength": 1, - "description": "Protocol for generating cell line. e.g. condition or multiple conditions used to generate the cell line. (if applicable)", + "description": "Condition or multiple conditions used to generate the cell line. (if applicable)", "title": "Treatment/Condition", "examples": [ "DMSO", diff --git a/json_schema/type/protocol/expression_alteration.json b/json_schema/type/protocol/expression_alteration.json index 6cba3d9..9adf7d8 100644 --- a/json_schema/type/protocol/expression_alteration.json +++ b/json_schema/type/protocol/expression_alteration.json @@ -133,10 +133,10 @@ "exon" ] }, - "expected_alteration_type": { + "expected_rna_alteration_phenotype": { "type": "string", - "description": "How the expression for the gene(s) or protein(s) was altered.", - "title": "Expected alteration type", + "description": "How the expression for the RNA was altered.", + "title": "Expected RNA alteration phenotype", "enum": [ "RNA down-regulation", "RNA up-regulation", @@ -147,9 +147,22 @@ "examples": [ "RNA down-regulation", "RNA up-regulation", - "gene silencing", - "protein downregulation", - "protein upregulation" + "not applicable" + ] + }, + "expected_protein_alteration_phenotype": { + "type": "string", + "description": "How the expression for the protein(s) was altered.", + "title": "Expected protein alteration phenotype", + "enum": [ + "protein down-regulation", + "protein up-regulation", + "not applicable" + ], + "examples": [ + "RNA down-regulation", + "RNA up-regulation", + "not applicable" ] }, "editing_strategy": { From 49db303cf2543f8214abf1a81844f96260f17eed Mon Sep 17 00:00:00 2001 From: Anu Shivalikanjli Date: Thu, 24 Apr 2025 15:33:29 +0100 Subject: [PATCH 2/5] updated versions.json --- json_schema/versions.json | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/json_schema/versions.json b/json_schema/versions.json index 8046837..93b7536 100644 --- a/json_schema/versions.json +++ b/json_schema/versions.json @@ -9,17 +9,17 @@ "study": "1.0.0" }, "biomaterial": { - "clonal_cell_line": "1.0.0", - "differentiated_product": "2.0.0", + "clonal_cell_line": "1.0.1", + "differentiated_product": "2.0.1", "library_preparation": "2.0.0", - "undifferentiated_product": "1.0.0" + "undifferentiated_product": "1.0.1" }, "file": { "analysis_file": "1.0.0", "sequence_file": "1.1.0" }, "protocol": { - "expression_alteration": "1.0.0" + "expression_alteration": "2.0.0" } } } From 1e69806c4836247f59c876ed8d13eb3e6217a703 Mon Sep 17 00:00:00 2001 From: Anu Shivalikanjli <120177925+anu-shiva@users.noreply.github.com> Date: Thu, 8 May 2025 11:06:31 +0100 Subject: [PATCH 3/5] Update versions.json added a comment line --- json_schema/versions.json | 1 + 1 file changed, 1 insertion(+) diff --git a/json_schema/versions.json b/json_schema/versions.json index 93b7536..177ebf7 100644 --- a/json_schema/versions.json +++ b/json_schema/versions.json @@ -20,6 +20,7 @@ }, "protocol": { "expression_alteration": "2.0.0" + #current versions updated } } } From e31ef0ffc38d616d14cbbbae4b249bca6e01f2b6 Mon Sep 17 00:00:00 2001 From: Anu Shivalikanjli <120177925+anu-shiva@users.noreply.github.com> Date: Thu, 8 May 2025 13:17:47 +0100 Subject: [PATCH 4/5] Update versions.json Removed comment --- json_schema/versions.json | 1 - 1 file changed, 1 deletion(-) diff --git a/json_schema/versions.json b/json_schema/versions.json index 177ebf7..93b7536 100644 --- a/json_schema/versions.json +++ b/json_schema/versions.json @@ -20,7 +20,6 @@ }, "protocol": { "expression_alteration": "2.0.0" - #current versions updated } } } From e06f9abc934ef0d4b95f1bf98885a1e326ed3418 Mon Sep 17 00:00:00 2001 From: anu-shiva <120177925+anu-shiva@users.noreply.github.com> Date: Wed, 14 May 2025 14:36:36 +0000 Subject: [PATCH 5/5] New test schema generated --- tests/test_schemas/clonal_cell_line.json | 12 ++++----- .../test_schemas/differentiated_product.json | 2 +- tests/test_schemas/expression_alteration.json | 25 ++++++++++++++----- .../undifferentiated_product.json | 2 +- 4 files changed, 27 insertions(+), 14 deletions(-) diff --git a/tests/test_schemas/clonal_cell_line.json b/tests/test_schemas/clonal_cell_line.json index 7fb7316..e223a4d 100644 --- a/tests/test_schemas/clonal_cell_line.json +++ b/tests/test_schemas/clonal_cell_line.json @@ -134,7 +134,7 @@ "pattern": "^[a-zA-Z0-9_]*$", "minLength": 1, "description": "A unique label for the cell line. No spaces allowed.", - "title": "Cell line ID", + "title": "Clonal cell line ID", "examples": [ "PRMT5_C-terminal_AID_DMSO", "OCM_108_Auxin_24h" @@ -143,8 +143,8 @@ "description": { "type": "string", "minLength": 1, - "description": "A general description of the cell line.", - "title": "Cell line description", + "description": "A general description of the clonal cell line.", + "title": "Clonal cell line description", "examples": [ "KOLF2.2J derived knockout cell line, PAX6/STL2 DKO" ] @@ -278,8 +278,8 @@ "type": { "type": "string", "minLength": 1, - "description": "The type of cell line.", - "title": "Cell line type", + "description": "The type of clonal cell line.", + "title": "Clonal cell line type", "enum": [ "iPSC", "embryoid", @@ -412,7 +412,7 @@ "treatment_condition": { "type": "string", "minLength": 1, - "description": "Protocol for generating cell line. e.g. condition or multiple conditions used to generate the cell line (if applicable).", + "description": "Condition or multiple conditions used to generate the cell line (if applicable).", "title": "Treatment/Condition", "examples": [ "DMSO", diff --git a/tests/test_schemas/differentiated_product.json b/tests/test_schemas/differentiated_product.json index d400825..656cc50 100644 --- a/tests/test_schemas/differentiated_product.json +++ b/tests/test_schemas/differentiated_product.json @@ -218,7 +218,7 @@ "treatment_condition": { "type": "string", "minLength": 1, - "description": "Protocol for generating cell line. e.g. condition or multiple conditions used to generate the cell line. (if applicable)", + "description": "Condition or multiple conditions used to generate the cell line. (if applicable)", "title": "Treatment/Condition", "examples": [ "DMSO", diff --git a/tests/test_schemas/expression_alteration.json b/tests/test_schemas/expression_alteration.json index 245d13e..bf87c12 100644 --- a/tests/test_schemas/expression_alteration.json +++ b/tests/test_schemas/expression_alteration.json @@ -210,10 +210,10 @@ "exon" ] }, - "expected_alteration_type": { + "expected_rna_alteration_phenotype": { "type": "string", - "description": "How the expression for the gene(s) or protein(s) was altered.", - "title": "Expected alteration type", + "description": "How the expression for the RNA was altered.", + "title": "Expected RNA alteration phenotype", "enum": [ "RNA down-regulation", "RNA up-regulation", @@ -224,9 +224,22 @@ "examples": [ "RNA down-regulation", "RNA up-regulation", - "gene silencing", - "protein downregulation", - "protein upregulation" + "not applicable" + ] + }, + "expected_protein_alteration_phenotype": { + "type": "string", + "description": "How the expression for the protein(s) was altered.", + "title": "Expected protein alteration phenotype", + "enum": [ + "protein down-regulation", + "protein up-regulation", + "not applicable" + ], + "examples": [ + "RNA down-regulation", + "RNA up-regulation", + "not applicable" ] }, "editing_strategy": { diff --git a/tests/test_schemas/undifferentiated_product.json b/tests/test_schemas/undifferentiated_product.json index 0beee0b..74d8050 100644 --- a/tests/test_schemas/undifferentiated_product.json +++ b/tests/test_schemas/undifferentiated_product.json @@ -179,7 +179,7 @@ "treatment_condition": { "type": "string", "minLength": 1, - "description": "Protocol for generating cell line. e.g. condition or multiple conditions used to generate the cell line. (if applicable)", + "description": "Condition or multiple conditions used to generate the cell line. (if applicable)", "title": "Treatment/Condition", "examples": [ "DMSO",