diff --git a/CHANGELOG.md b/CHANGELOG.md index 1721c10..94e359b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -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 | diff --git a/GREGoR_data_model.json b/GREGoR_data_model.json index 0ca04d3..e1b76c0 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": "1.9.2", + "version": "1.10", "tables": [ { "table": "participant", @@ -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"] }, @@ -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" } ] }, @@ -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" } ] }, diff --git a/sheets_to_JSON.R b/sheets_to_JSON.R index 0e45367..8a56cb1 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 = "1.9.2" +model_version = "1.10" # table metadata meta <- read_sheet(url, sheet="Table overview/status", skip=1)