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Merged
smgogarten merged 3 commits into from
Aug 11, 2025
Merged

V1.9.1 #40

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2cd4739
use SNV or INDEL, not SNV/INDEL in gf table
smgogarten Jul 12, 2025
e402af3
update description
smgogarten Jul 25, 2025
9426f7e
update change log
smgogarten Aug 11, 2025
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8 changes: 8 additions & 0 deletions CHANGELOG.md
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@@ -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 |
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8 changes: 4 additions & 4 deletions GREGoR_data_model.json
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{
"name": "GREGoR Data Model",
"description": "Data model for the GREGoR consortium",
"version": "1.9",
"version": "1.9.1",
"tables": [
{
"table": "participant",
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},
{
"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]"]
},
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"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",
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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 = "1.9"
model_version = "1.9.1"

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