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Merged
smgogarten merged 1 commit into from
Nov 3, 2025
Merged

version 1.10 #42

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9 changes: 9 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -247,6 +247,15 @@
|called_variants_nanopore |all |DCC added 'Is Unique' column to data model document to support validation - no impact to data submitters. |


## 1.10

|Table |Field |Change notes |
|:----------------|:---------------|:-----------------------|
|participant |sex |updated description |
|aligned_pac_bio |read_length_n50 |added as optional field |
|aligned_nanopore |read_length_n50 |added as optional field |


## 1.1

|Table |Field |Change notes |
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16 changes: 14 additions & 2 deletions GREGoR_data_model.json
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@@ -1,7 +1,7 @@
{
"name": "GREGoR Data Model",
"description": "Data model for the GREGoR consortium",
"version": "1.9.2",
"version": "1.10",
"tables": [
{
"table": "participant",
Expand Down Expand Up @@ -110,7 +110,7 @@
{
"column": "sex",
"required": true,
"description": "Biological sex assigned at birth (aligned with All of Us). If individual has a known DSD / not expected sex chromosome karyotype, this can be noted in the phenotype information section.",
"description": "Biological sex assigned at birth (aligned with All of Us). If individual has a known DSD / not expected sex chromosome karyotype, this can be noted in the sex_detail field.",
"data_type": "enumeration",
"enumerations": ["Female", "Male", "Unknown"]
},
Expand Down Expand Up @@ -1721,6 +1721,12 @@
"data_type": "boolean",
"examples": true,
"notes": "See https://fiberseq.github.io/index.html for details on methods and Fiber-seq BAM specific tags"
},
{
"column": "read_length_n50",
"description": "N50 is the shortest read length that, when all reads are sorted by length from longest to shortest, covers 50% of the total sequence data (longer is better). Value in kilobases",
"data_type": "float",
"examples": "15"
}
]
},
Expand Down Expand Up @@ -2157,6 +2163,12 @@
"data_type": "boolean",
"examples": true,
"notes": "See https://fiberseq.github.io/index.html for details on methods and Fiber-seq BAM specific tags"
},
{
"column": "read_length_n50",
"description": "N50 is the shortest read length that, when all reads are sorted by length from longest to shortest, covers 50% of the total sequence data (longer is better). Value in kilobases",
"data_type": "float",
"examples": "15"
}
]
},
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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 = "1.9.2"
model_version = "1.10"

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