From a85a9dc5eac72cca7ed6cd0d719e6368339e9613 Mon Sep 17 00:00:00 2001 From: "Stephanie M. Gogarten" Date: Fri, 9 May 2025 12:06:13 -0700 Subject: [PATCH] updates for fiberseq --- CHANGELOG.md | 18 ++++++++++++++++++ GREGoR_data_model.json | 22 ++++++++++++++++++---- sheets_to_JSON.R | 2 +- 3 files changed, 37 insertions(+), 5 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 80dde23..44b6fed 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,23 @@ # Change log +## 1.8.1 + +|Table |Field |Change notes | +|:-------------------|:------------------|:-----------------------------------------------------------------------------------| +|experiment_pac_bio |experiment_type |enumerated value 'fiberseq' replaced with 'fiberseq-genome' and 'fiberseq-targeted' | +|aligned_pac_bio |methylation_called |updated description | +|aligned_pac_bio |fiberseq_format |added as optional field | +|experiment_nanopore |experiment_type |add enumerated values 'fiberseq-genome' and 'fiberseq-targeted' | +|aligned_nanopore |fiberseq_format |added as optional field | + + +## 1.8 + +|Table |Field |Change notes | +|:-----|:-----|:-------------------------------------------------------------------| +|NA |NA |incrementing major version number for next Consortium Upload Cycle. | + + ## 1.7.1 |Table |Field |Change notes | diff --git a/GREGoR_data_model.json b/GREGoR_data_model.json index 079d9f1..10f5853 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": "1.8", + "version": "1.8.1", "tables": [ { "table": "participant", @@ -1502,7 +1502,7 @@ "column": "experiment_type", "required": true, "data_type": "enumeration", - "enumerations": ["targeted", "genome"], + "enumerations": ["targeted", "genome", "fiberseq-genome", "fiberseq-targeted"], "examples": "targeted", "notes": "While the most common use of ONT is whole-genome sequencing, targeted sequencing is possible and may be of interest to the consortium." }, @@ -1713,6 +1713,13 @@ "column": "quality_issues", "description": "describe if there are any QC issues that would be important to note", "data_type": "string" + }, + { + "column": "fiberseq_format", + "description": "Indicates if BAM file has been formatted using fibertools to include nucleosome and methyltransferase-sensitive patch (MSP) calls", + "data_type": "boolean", + "examples": true, + "notes": "See https://fiberseq.github.io/index.html for details on methods and Fiber-seq BAM specific tags" } ] }, @@ -1850,7 +1857,7 @@ "column": "experiment_type", "required": true, "data_type": "enumeration", - "enumerations": ["targeted", "genome", "fiberseq", "isoseq", "masseq"], + "enumerations": ["targeted", "genome", "fiberseq-genome", "fiberseq-targeted", "isoseq", "masseq"], "examples": "targeted", "notes": "While the most common use of PacBio is whole-genome sequencing, targeted sequencing is possible and may be of interest to the consortium." }, @@ -2134,7 +2141,7 @@ { "column": "methylation_called", "required": true, - "description": "Indicates whether 5mC methylation has been called and annotated in the BAM file's MM and ML tags", + "description": "Indicates whether 5mC and 6mA methylation has been called and annotated in the BAM file's MM and ML tags", "data_type": "boolean", "examples": true }, @@ -2142,6 +2149,13 @@ "column": "quality_issues", "description": "describe if there are any QC issues that would be important to note", "data_type": "string" + }, + { + "column": "fiberseq_format", + "description": "Indicates if BAM file has been formatted using fibertools to include nucleosome and methyltransferase-sensitive patch (MSP) calls", + "data_type": "boolean", + "examples": true, + "notes": "See https://fiberseq.github.io/index.html for details on methods and Fiber-seq BAM specific tags" } ] }, diff --git a/sheets_to_JSON.R b/sheets_to_JSON.R index 88041cb..866aee8 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 = "1.8" +model_version = "1.8.1" # table metadata meta <- read_sheet(url, sheet="Table overview/status", skip=1)