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Merged
smgogarten merged 1 commit into from
May 13, 2026
Merged

v1.12: consolidate enumerations for variant types #48

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11 changes: 11 additions & 0 deletions CHANGELOG.md
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# 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 |
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20 changes: 10 additions & 10 deletions GREGoR_data_model.json
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{
"name": "GREGoR Data Model",
"description": "Data model for the GREGoR consortium",
"version": "1.11.1",
"version": "1.12",
"tables": [
{
"table": "participant",
Expand Down Expand Up @@ -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",
Expand Down Expand Up @@ -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"
},
{
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"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"
Expand Down Expand Up @@ -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"
Expand Down Expand Up @@ -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"
},
{
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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 = "1.11.1"
model_version = "1.12"

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