From 2c9a9ece3c3fe3de344e878bac58e63f4b2e8daa Mon Sep 17 00:00:00 2001 From: "Stephanie M. Gogarten" Date: Fri, 5 Sep 2025 13:14:01 -0700 Subject: [PATCH 1/4] add enumerated values to seq_library_prep_kit_method --- 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 8c7de03..a234d64 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": "1.9.1", + "version": "1.9.2", "tables": [ { "table": "participant", @@ -1844,7 +1844,7 @@ "required": true, "description": "Library prep kit used", "data_type": "enumeration", - "enumerations": ["SMRTbell prep kit 3.0", "SMRTbell prep kit - Revio 1.0", "HiFI express template prep kit 2.0"], + "enumerations": ["SMRTbell prep kit 3.0", "SMRTbell prep kit - Revio 1.0", "HiFI express template prep kit 2.0", "Kinnex Full-Length RNA kit", "MAS-Seq for 10x Single Cell 3’ kit"], "examples": "SMRTbell prep kit 3.0", "notes": "Can be missing if RC receives external data" }, @@ -1901,7 +1901,7 @@ { "column": "barcode_kit", "description": "Barcode kit used", - "data_type": "string", + "data_type": "enumeration", "enumerations": ["SMRTbell barcoded adapter plate 3.0", "Barcoded M13 primer plate", "Barcoded overhang adapter kit - 8A/8B"], "examples": "SMRTbell barcoded adapter plate 3.0" }, diff --git a/sheets_to_JSON.R b/sheets_to_JSON.R index d683a2e..0e45367 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 = "1.9.1" +model_version = "1.9.2" # table metadata meta <- read_sheet(url, sheet="Table overview/status", skip=1) From 8fcd6627bbfbed050d97e0de478e6daadcc05677 Mon Sep 17 00:00:00 2001 From: "Stephanie M. Gogarten" Date: Wed, 24 Sep 2025 08:51:54 -0700 Subject: [PATCH 2/4] replace special character with single quote --- 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 a234d64..3f012ca 100644 --- a/GREGoR_data_model.json +++ b/GREGoR_data_model.json @@ -1844,7 +1844,7 @@ "required": true, "description": "Library prep kit used", "data_type": "enumeration", - "enumerations": ["SMRTbell prep kit 3.0", "SMRTbell prep kit - Revio 1.0", "HiFI express template prep kit 2.0", "Kinnex Full-Length RNA kit", "MAS-Seq for 10x Single Cell 3’ kit"], + "enumerations": ["SMRTbell prep kit 3.0", "SMRTbell prep kit - Revio 1.0", "HiFI express template prep kit 2.0", "Kinnex Full-Length RNA kit", "MAS-Seq for 10x Single Cell 3' kit"], "examples": "SMRTbell prep kit 3.0", "notes": "Can be missing if RC receives external data" }, From e1bee55ad0f6bb9fb16bbd8f0b683dd9761b5f6b Mon Sep 17 00:00:00 2001 From: "Stephanie M. Gogarten" Date: Tue, 14 Oct 2025 12:20:38 -0700 Subject: [PATCH 3/4] added enumeration for barcode_kit --- 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 3f012ca..0ca04d3 100644 --- a/GREGoR_data_model.json +++ b/GREGoR_data_model.json @@ -1902,7 +1902,7 @@ "column": "barcode_kit", "description": "Barcode kit used", "data_type": "enumeration", - "enumerations": ["SMRTbell barcoded adapter plate 3.0", "Barcoded M13 primer plate", "Barcoded overhang adapter kit - 8A/8B"], + "enumerations": ["SMRTbell barcoded adapter plate 3.0", "Barcoded M13 primer plate", "Barcoded overhang adapter kit - 8A/8B", "SMRTbell adapter index plate 96A"], "examples": "SMRTbell barcoded adapter plate 3.0" }, { From faed817d6a75971d06f4636e14e78b3c2779f846 Mon Sep 17 00:00:00 2001 From: "Stephanie M. Gogarten" Date: Wed, 15 Oct 2025 10:23:21 -0700 Subject: [PATCH 4/4] change log for v1.9.2 --- CHANGELOG.md | 16 ++++++++++++---- 1 file changed, 12 insertions(+), 4 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 5715fae..1721c10 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,11 +1,19 @@ # Change log +## 1.9.2 + +|Table |Field |Change notes | +|:------------------|:---------------------------|:-------------------------------------------------------------------------------------------| +|experiment_pac_bio |seq_library_prep_kit_method |add enumerated values 'Kinnex Full-Length RNA kit' and 'MAS-Seq for 10x Single Cell 3’ kit' | +|experiment_pac_bio |barcode_kit |change type to enumerated; add value 'SMRTbell adapter index plate 96A' | + + ## 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 | +|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