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updates for fiberseq #38

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Merged
smgogarten merged 1 commit into from
Jul 11, 2025
Merged

updates for fiberseq #38

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18 changes: 18 additions & 0 deletions CHANGELOG.md
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# 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 |
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22 changes: 18 additions & 4 deletions GREGoR_data_model.json
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{
"name": "GREGoR Data Model",
"description": "Data model for the GREGoR consortium",
"version": "1.8",
"version": "1.8.1",
"tables": [
{
"table": "participant",
Expand Down Expand Up @@ -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."
},
Expand Down Expand Up @@ -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"
}
]
},
Expand Down Expand Up @@ -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."
},
Expand Down Expand Up @@ -2134,14 +2141,21 @@
{
"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
},
{
"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"
}
]
},
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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 = "1.8"
model_version = "1.8.1"

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