From 2cd473942bdb5aeb373c2358771d7a744a52c1ca Mon Sep 17 00:00:00 2001 From: "Stephanie M. Gogarten" Date: Fri, 11 Jul 2025 19:26:19 -0700 Subject: [PATCH 1/3] use SNV or INDEL, not SNV/INDEL in gf table --- GREGoR_data_model.json | 6 +++--- sheets_to_JSON.R | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/GREGoR_data_model.json b/GREGoR_data_model.json index b6476d5..2f22c60 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": "1.9", + "version": "1.9.1", "tables": [ { "table": "participant", @@ -343,10 +343,10 @@ "column": "variant_type", "required": true, "data_type": "enumeration", - "enumerations": ["SNV/INDEL", "SV", "RE", "SNV", "INDEL", "CNV", "MEI", "STR"], + "enumerations": ["SNV", "INDEL", "SV", "RE", "CNV", "MEI", "STR"], "multi_value_delimiter": "|", "examples": "SNV|CNV", - "notes": "SNV/INDEL: single nucelotide variants or short insertion/deletions (<50bp)\nRE: repeat elements\nSV: structural variants, including copy number variants and mobile element insertions" + "notes": "SNV: single nucelotide variants\nINDEL: short insertion/deletions (<50bp)\nSV: structural variants\nRE: repeat elements\nCNV: copy number variants\nMEI: mobile element insertions\nSTR: short tandem repeats" }, { "column": "sv_type", diff --git a/sheets_to_JSON.R b/sheets_to_JSON.R index 3a423de..d683a2e 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 = "1.9" +model_version = "1.9.1" # table metadata meta <- read_sheet(url, sheet="Table overview/status", skip=1) From e402af3ff0a4d3a3aeceb63c3e811182bbda2d88 Mon Sep 17 00:00:00 2001 From: "Stephanie M. Gogarten" Date: Fri, 25 Jul 2025 13:52:14 -0700 Subject: [PATCH 2/3] update description --- GREGoR_data_model.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/GREGoR_data_model.json b/GREGoR_data_model.json index 2f22c60..8c7de03 100644 --- a/GREGoR_data_model.json +++ b/GREGoR_data_model.json @@ -116,7 +116,7 @@ }, { "column": "sex_detail", - "description": "Optional free-text field to describe known discrepancies between 'sex' value (female=>XX, male=>XY) and actual sex chromosome karyotype", + "description": "Optional free-text field to describe known discrepancies between 'sex' value (female=>XX, male=>XY) and actual sex chromosome karyotype or other relevant details", "data_type": "string", "examples": ["XXY expected", "XY expected [for someone assigned female at birth with XY DSD]"] }, From 9426f7e2aac112460d23258c7cec56d5ebee6475 Mon Sep 17 00:00:00 2001 From: "Stephanie M. Gogarten" Date: Mon, 11 Aug 2025 12:06:31 -0700 Subject: [PATCH 3/3] update change log --- CHANGELOG.md | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index aa1c306..5715fae 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,13 @@ # Change log +## 1.9.1 + +|Table |Field |Change notes | +|:-------------------------|:---------------|:---------------------------------------------------------------| +|genetic_findings |variant_type |removed SNV/INDEL as enumerated value; use SNV or INDEL instead | +|participant |sex_detail |updated description | + + ## 1.9 |Table |Field |Change notes |