From 425f5920ce2887148ebb877b537e44b5bc5ba2ed Mon Sep 17 00:00:00 2001 From: "Stephanie M. Gogarten" Date: Tue, 12 May 2026 17:46:32 -0700 Subject: [PATCH] consolidate enumerations for variant types --- CHANGELOG.md | 11 +++++++++++ GREGoR_data_model.json | 20 ++++++++++---------- sheets_to_JSON.R | 2 +- 3 files changed, 22 insertions(+), 11 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index d041630..d840b02 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,16 @@ # Change log +## 1.12 + +|Table |Field |Change notes | +|:------------------------------|:-------------|:---------------------------------------| +|genetic_findings |variant_type |removed enumerated values CNV, MEI, STR | +|called_variants_dna_short_read |variant_types |removed enumerated values CNV, MEI, STR | +|called_variants_nanopore |variant_types |removed enumerated values CNV, MEI, STR | +|called_variants_pac_bio |variant_types |removed enumerated values CNV, MEI, STR | +|called_variants_iclr |variant_types |removed enumerated values CNV, MEI, STR | + + ## 1.11.1 |Table |Field |Change notes | diff --git a/GREGoR_data_model.json b/GREGoR_data_model.json index a267580..eb16126 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": "1.11.1", + "version": "1.12", "tables": [ { "table": "participant", @@ -348,10 +348,10 @@ "column": "variant_type", "required": true, "data_type": "enumeration", - "enumerations": ["SNV", "INDEL", "SV", "RE", "CNV", "MEI", "STR"], + "enumerations": ["SNV", "INDEL", "SV", "RE"], "multi_value_delimiter": "|", - "examples": "SNV|CNV", - "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" + "examples": "SNV|SV", + "notes": "SNV: single nucelotide variants\nINDEL: short insertion/deletions (<50bp)\nSV: structural variants\nRE: repeat elements" }, { "column": "sv_type", @@ -1062,9 +1062,9 @@ "required": true, "description": "types of variants called", "data_type": "enumeration", - "enumerations": ["SNV", "INDEL", "SV", "CNV", "RE", "MEI", "STR"], + "enumerations": ["SNV", "INDEL", "SV", "RE"], "multi_value_delimiter": "|", - "examples": ["RE = Repeat Expansion", "MEI = Mobile Element Insertion"], + "examples": "SNV|INDEL", "notes": "can add more values as the need arises\nif there are two VCFs for SNV and Indels, there would be two different lines in this table; if combined in one VCF, a |-delimited entry" }, { @@ -1833,7 +1833,7 @@ "required": true, "description": "types of variants called", "data_type": "string", - "enumerations": ["SNV", "INDEL", "SV", "CNV", "RE", "MEI", "STR"], + "enumerations": ["SNV", "INDEL", "SV", "RE"], "multi_value_delimiter": "|", "examples": "SNV|INDEL", "notes": "can add more values as the need arises\nif there are two VCFs for SNV and Indels, there would be two different lines in this table; if combined in one VCF, a |-delimited entry" @@ -2275,7 +2275,7 @@ "required": true, "description": "types of variants called", "data_type": "string", - "enumerations": ["SNV", "INDEL", "SV", "CNV", "RE", "MEI", "STR"], + "enumerations": ["SNV", "INDEL", "SV", "RE"], "multi_value_delimiter": "|", "examples": "SNV|INDEL", "notes": "can add more values as the need arises\nif there are two VCFs for SNV and Indels, there would be two different lines in this table; if combined in one VCF, a |-delimited entry" @@ -3398,9 +3398,9 @@ "required": true, "description": "types of variants called", "data_type": "enumeration", - "enumerations": ["SNV", "INDEL", "SV", "CNV", "RE", "MEI", "STR"], + "enumerations": ["SNV", "INDEL", "SV", "RE"], "multi_value_delimiter": "|", - "examples": ["RE = Repeat Expansion", "MEI = Mobile Element Insertion"], + "examples": "SNV|INDEL", "notes": "can add more values as the need arises\nif there are two VCFs for SNV and Indels, there would be two different lines in this table; if combined in one VCF, a |-delimited entry" }, { diff --git a/sheets_to_JSON.R b/sheets_to_JSON.R index d433e14..ce10f65 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 = "1.11.1" +model_version = "1.12" # table metadata meta <- read_sheet(url, sheet="Table overview/status", skip=1)