From 7fbfb72f8f121767f1078f0ebc091064a9256ce9 Mon Sep 17 00:00:00 2001 From: "Stephanie M. Gogarten" Date: Mon, 1 Dec 2025 13:43:03 -0800 Subject: [PATCH 1/2] add gene panel to findings method of discovery --- CHANGELOG.md | 7 +++++++ GREGoR_data_model.json | 4 ++-- sheets_to_JSON.R | 2 +- 3 files changed, 10 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 218e3b2..6cb3404 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,12 @@ # Change log +## 1.10.1 + +|Table |Field |Change notes | +|:----------------|:-------------------|:---------------------------------| +|genetic_findings |method_of_discovery |add enumerated value 'Gene panel' | + + ## 1.10 |Table |Field |Change notes | diff --git a/GREGoR_data_model.json b/GREGoR_data_model.json index e1b76c0..97eaf7d 100644 --- a/GREGoR_data_model.json +++ b/GREGoR_data_model.json @@ -1,7 +1,7 @@ { "name": "GREGoR Data Model", "description": "Data model for the GREGoR consortium", - "version": "1.10", + "version": "1.10.1", "tables": [ { "table": "participant", @@ -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)" diff --git a/sheets_to_JSON.R b/sheets_to_JSON.R index 8a56cb1..0c40336 100644 --- a/sheets_to_JSON.R +++ b/sheets_to_JSON.R @@ -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) From 03969801fc590701e2be64049711ff05ec7ca1c5 Mon Sep 17 00:00:00 2001 From: "Stephanie M. Gogarten" Date: Mon, 8 Dec 2025 14:01:38 -0800 Subject: [PATCH 2/2] add isogenic cell line to experiment_rna_short_read --- CHANGELOG.md | 8 +++++--- GREGoR_data_model.json | 9 ++++++++- 2 files changed, 13 insertions(+), 4 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 6cb3404..f821996 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,9 +2,11 @@ ## 1.10.1 -|Table |Field |Change notes | -|:----------------|:-------------------|:---------------------------------| -|genetic_findings |method_of_discovery |add enumerated value 'Gene panel' | +|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 diff --git a/GREGoR_data_model.json b/GREGoR_data_model.json index 97eaf7d..99b31ef 100644 --- a/GREGoR_data_model.json +++ b/GREGoR_data_model.json @@ -1086,7 +1086,7 @@ }, { "column": "analyte_id", - "required": true, + "required": "CONDITIONAL (rna_sample_type = GREGoR_sample)", "data_type": "string", "references": "> analyte.analyte_id" }, @@ -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",