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Merged
smgogarten merged 2 commits into from
Jan 24, 2026
Merged

V1.10.1 #44

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7fbfb72
add gene panel to findings method of discovery
smgogarten Dec 1, 2025
0396980
add isogenic cell line to experiment_rna_short_read
smgogarten Dec 8, 2025
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9 changes: 9 additions & 0 deletions CHANGELOG.md
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@@ -1,5 +1,14 @@
# Change log

## 1.10.1

|Table |Field |Change notes |
|:-------------------------|:-------------------|:-----------------------------------------------------------------|
|genetic_findings |method_of_discovery |add enumerated value 'Gene panel' |
|experiment_rna_short_read |rna_sample_type |added as optional field |
|experiment_rna_short_read |analyte_id |make requirement conditional on rna_sample_type = 'GREGoR_sample' |


## 1.10

|Table |Field |Change notes |
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13 changes: 10 additions & 3 deletions GREGoR_data_model.json
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{
"name": "GREGoR Data Model",
"description": "Data model for the GREGoR consortium",
"version": "1.10",
"version": "1.10.1",
"tables": [
{
"table": "participant",
Expand Down Expand Up @@ -594,7 +594,7 @@
"column": "method_of_discovery",
"description": "The method/assay(s) used to identify the candidate",
"data_type": "enumeration",
"enumerations": ["SR-ES", "SR-GS", "LR-GS", "SNP array", "Optical mapping", "Karyotype", "SR RNA-seq", "LR RNA-seq", "SR-ES-reanalysis", "SR-GS-reanalysis", "LR-GS-reanalysis", "SNP array-reanalysis", "Optical mapping-reanalysis", "Karyotype-reanalysis", "SR RNA-seq-reanalysis", "LR RNA-seq-reanalysis"],
"enumerations": ["SR-ES", "SR-GS", "LR-GS", "SNP array", "Optical mapping", "Karyotype", "SR RNA-seq", "LR RNA-seq", "SR-ES-reanalysis", "SR-GS-reanalysis", "LR-GS-reanalysis", "SNP array-reanalysis", "Optical mapping-reanalysis", "Karyotype-reanalysis", "SR RNA-seq-reanalysis", "LR RNA-seq-reanalysis", "Gene panel"],
"multi_value_delimiter": "|",
"examples": "SR-GS",
"notes": "Field to be used to capture method of discovery if experiment not currently supported by data model. (eg. >experiment_table_name.id_in_table)"
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},
{
"column": "analyte_id",
"required": true,
"required": "CONDITIONAL (rna_sample_type = GREGoR_sample)",
"data_type": "string",
"references": "> analyte.analyte_id"
},
Expand All @@ -1096,6 +1096,13 @@
"data_type": "string",
"examples": "12339D-SA"
},
{
"column": "rna_sample_type",
"description": "indicates whether experiment_rna_short_read_id corresponds to study sample with analyte_id or an isogenic cell line",
"data_type": "enumeration",
"enumerations": ["GREGoR_sample", "isogenic_cell_line"],
"examples": "GREGoR_sample"
},
{
"column": "seq_library_prep_kit_method",
"description": "Library prep kit used",
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2 changes: 1 addition & 1 deletion sheets_to_JSON.R
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Expand Up @@ -7,7 +7,7 @@ library(jsonlite)
url <- "https://docs.google.com/spreadsheets/d/1p_0nhKMvKBueSrUAQMCe9cHv16WyhKSX_jnxNCuGFWg"
model_name = "GREGoR Data Model"
model_description = "Data model for the GREGoR consortium"
model_version = "1.10"
model_version = "1.10.1"

# table metadata
meta <- read_sheet(url, sheet="Table overview/status", skip=1)
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