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Merged
anu-shiva merged 6 commits into from
May 14, 2025
Merged

Develop #82

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2f62979
expression alteration phenotype changed alongwith description changes
anu-shiva Apr 24, 2025
49db303
updated versions.json
anu-shiva Apr 24, 2025
b09b723
Merge pull request #81 from morphic-bio/test_develop_as
anu-shiva May 2, 2025
1e69806
Update versions.json
anu-shiva May 8, 2025
e31ef0f
Update versions.json
anu-shiva May 8, 2025
e06f9ab
New test schema generated
anu-shiva May 14, 2025
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12 changes: 6 additions & 6 deletions json_schema/type/biomaterial/clonal_cell_line.json
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Expand Up @@ -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"
Expand All @@ -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"
]
Expand Down Expand Up @@ -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",
Expand Down Expand Up @@ -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",
Expand Down
2 changes: 1 addition & 1 deletion json_schema/type/biomaterial/differentiated_product.json
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Expand Up @@ -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",
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2 changes: 1 addition & 1 deletion json_schema/type/biomaterial/undifferentiated_product.json
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Expand Up @@ -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",
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25 changes: 19 additions & 6 deletions json_schema/type/protocol/expression_alteration.json
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Expand Up @@ -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",
Expand All @@ -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": {
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8 changes: 4 additions & 4 deletions json_schema/versions.json
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Expand Up @@ -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"
}
}
}
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12 changes: 6 additions & 6 deletions tests/test_schemas/clonal_cell_line.json
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Expand Up @@ -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"
Expand All @@ -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"
]
Expand Down Expand Up @@ -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",
Expand Down Expand Up @@ -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",
Expand Down
2 changes: 1 addition & 1 deletion tests/test_schemas/differentiated_product.json
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Expand Up @@ -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",
Expand Down
25 changes: 19 additions & 6 deletions tests/test_schemas/expression_alteration.json
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Original file line number Diff line number Diff line change
Expand Up @@ -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",
Expand All @@ -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": {
Expand Down
2 changes: 1 addition & 1 deletion tests/test_schemas/undifferentiated_product.json
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Expand Up @@ -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",
Expand Down