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Merge pull request #244 from ncihtan/238-drop-biospecimen-preparation…
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…-attribute-from-bulk-methyl-seq

Remove Biospecimen preparation from BulkMCseq L1
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@adamjtaylor
adamjtaylor authored Jun 22, 2023
2 parents 67ff658 + acdedf6 commit 212d687
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Showing 2 changed files with 1 addition and 64 deletions.
3 changes: 1 addition & 2 deletions HTAN.model.csv
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Original file line number Diff line number Diff line change
Expand Up @@ -59,7 +59,7 @@ scmC-seq Level 2,"Files contain scmC-seq files containing aligned sequence data,
scATAC-seq Level 4,"Data represents the relationships between cells derived from Level 3 expression data and shown as tSNE or UMAP coordinates per cell, plus all other cell-specific meta information (e.g., cell type)",,"Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID, scATACseq Workflow Type, scATACseq Workflow Parameters Description, Workflow Version, Workflow Link",,FALSE,Sequencing,scATAC-seq Level 3,,
scDNA-seq Level 1,Single-cell DNA-seq,,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, Sequencing Batch ID, Library Layout, Nucleic Acid Source, Library Selection Method, Read Length, Library Preparation Kit Name, Library Preparation Kit Vendor, Library Preparation Kit Version, Adapter Name, Adapter Sequence, Base Caller Name, Base Caller Version, Flow Cell Barcode, Fragment Maximum Length, Fragment Mean Length, Fragment Minimum Length, Fragment Standard Deviation Length, Lane Number, Library Strand, Multiplex Barcode, Size Selection Range, Target Depth, To Trim Adapter Sequence, Adapter Content, Basic Statistics, Encoding, Kmer Content, Overrepresented Sequences, Per Base N Content, Per Base Sequence Content, Per Base Sequence Quality, Per Sequence GC Content, Per Sequence Quality Score, Per Tile Sequence Quality, Percent GC Content, Sequence Duplication Levels, Sequence Length Distribution, Total Reads, QC Workflow Type, QC Workflow Version, QC Workflow Link",,FALSE,Sequencing,Biospecimen,,
scDNA-seq Level 2,Alignment workflows downstream of scDNA-seq Level 1,,"Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID, Alignment Workflow Url, Alignment Workflow Type, Genomic Reference, Genomic Reference URL, Index File Name, Average Base Quality, Average Insert Size, Average Read Length, Mean Coverage, Pairs On Diff CHR, Total Reads, Proportion Reads Mapped, MapQ30, Total Uniquely Mapped, Total Unmapped reads,Proportion Reads Duplicated, Short Reads, Proportion Coverage 10X, Proportion Coverage 30X, Proportion Targets No Coverage, Proportion Base Mismatch, Proportion Mitochondrial Reads, Contamination, Contamination Error",,FALSE,Sequencing,scDNA-seq Level 1,,
Bulk Methylation-seq Level 1,"Raw data for bulk methylation sequencing, such as FASTQs and unaligned BAMs",,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, Biospecimen Preparation, Nucleic Acid Source, Bisulfite Conversion, Sequencing Platform, Replicate Type, Bulk Methylation Assay Type, Total DNA Input",,FALSE,Sequencing,Biospecimen,,
Bulk Methylation-seq Level 1,"Raw data for bulk methylation sequencing, such as FASTQs and unaligned BAMs",,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, Nucleic Acid Source, Bisulfite Conversion, Sequencing Platform, Replicate Type, Bulk Methylation Assay Type, Total DNA Input",,FALSE,Sequencing,Biospecimen,,
Bulk Methylation-seq Level 2,"Aligned primary data for bulk methylation sequencing, such as gene expression matrix files, VCFs, etc.",,"Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID, Alignment Workflow Url, Trimmer, Bulk Methylation Genomic Reference, Genomic Reference URL, Index File Name, Alignment Workflow Type, Duplicate Removal Software, Mean Coverage, Library Layout, Average Base Quality, Average Insert Size, Average Read Length, Contamination, Contamination Error, Pairs On Diff CHR, Total Reads, Total Uniquely Mapped, Total Unmapped reads, Proportion Reads Duplicated, Proportion Reads Mapped, Proportion Targets No Coverage, Proportion Base Mismatch, Short Reads, Proportion of Minimum CpG Coverage 10X, Proportion Coverage 30X, Proportion Reads Duplicated, Proportion Targets No Coverage",,FALSE,Sequencing,"Bulk Methylation-seq Level 1, Biospecimen",,
Bulk Methylation-seq Level 3,"Sample level summary data for bulk methylation sequencing, such as t-SNE plot coordinates, etc.",,"Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID,DMC Calling Tool, DMC Calling Workflow URL, DMR Calling Tool, DMR Calling Workflow URL, pUC19 methylation ratio, Lambda methylation ratio, DMC data file format, DMR data file Format",,FALSE,Sequencing,"Bulk Methylation-seq Level 2, Biospecimen",,
Imaging Level 1,Raw imaging data,,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, Imaging Assay Type, Protocol Link, Software and Version, Commit SHA, Pre-processing Completed, Pre-processing Required, Comment",,FALSE,Assay,Biospecimen,,
Expand Down Expand Up @@ -923,7 +923,6 @@ LC Gradient,The program dictates the mobile phase solvent composition over the c
LC Mobile Phase A,Composition of mobile phase A,,,,TRUE,Mass Spectrometry Level 1,,,
LC Mobile Phase B,Composition of mobile phase B,,,,TRUE,Mass Spectrometry Level 1,,,
MS Instrument Metadata File,Additional file containing instrument metadata details. Use either synapse_path or entity_Id,,,,TRUE,Mass Spectrometry Level 1,,,
Biospecimen Preparation,The way tissue is processed after collection,"Fresh Frozen, FFPE",,,TRUE,Bulk Methylation-seq Level 1,,,
Bisulfite Conversion,Name of the kit used in bisulfite conversion.,"Zimo EZ DNA Methylation Kit, Zimo EZ-96 DNA Methylation Shallow Kit, Zimo EZ-96 DNA Methylation Deep Kit, NEBNext Enzymatic Methyl-seq Kit, Agilent SureSelectXT Methyl-Seq",,,TRUE,Bulk Methylation-seq Level 1,,,
Replicate Type,A common term for all files belonging to the same sample. We suggest using a stable sample accession from a biosample archive like BioSamples.,"Technical replicate, Biological replicate, Not Applicable",,,TRUE,Sequencing,,,
Bulk Methylation Assay Type,Assay types normally determine genomic coverage,"Whole genome, Targeted Genome, Beadchip Array ","Targeted Genome, Beadchip Array",,TRUE,Bulk Methylation-seq Level 1,,,
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62 changes: 0 additions & 62 deletions HTAN.model.jsonld
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Original file line number Diff line number Diff line change
Expand Up @@ -6976,9 +6976,6 @@
{
"@id": "bts:HTANDataFileID"
},
{
"@id": "bts:BiospecimenPreparation"
},
{
"@id": "bts:NucleicAcidSource"
},
Expand Down Expand Up @@ -49028,31 +49025,6 @@
"sms:required": "sms:true",
"sms:validationRules": []
},
{
"@id": "bts:BiospecimenPreparation",
"@type": "rdfs:Class",
"rdfs:comment": "The way tissue is processed after collection",
"rdfs:label": "BiospecimenPreparation",
"rdfs:subClassOf": [
{
"@id": "bts:BulkMethylation-seqLevel1"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"schema:rangeIncludes": [
{
"@id": "bts:FreshFrozen"
},
{
"@id": "bts:FFPE"
}
],
"sms:displayName": "Biospecimen Preparation",
"sms:required": "sms:true",
"sms:validationRules": []
},
{
"@id": "bts:BisulfiteConversion",
"@type": "rdfs:Class",
Expand Down Expand Up @@ -143051,40 +143023,6 @@
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:FreshFrozen",
"@type": "rdfs:Class",
"rdfs:comment": "TBD",
"rdfs:label": "FreshFrozen",
"rdfs:subClassOf": [
{
"@id": "bts:BiospecimenPreparation"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "Fresh Frozen",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:FFPE",
"@type": "rdfs:Class",
"rdfs:comment": "TBD",
"rdfs:label": "FFPE",
"rdfs:subClassOf": [
{
"@id": "bts:BiospecimenPreparation"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "FFPE",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:ZimoEZDNAMethylationKit",
"@type": "rdfs:Class",
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