Skip to content

Commit

Permalink
Merge pull request #270 from ncihtan/pick-seq-model-addition
Browse files Browse the repository at this point in the history 
Adding Pick-Seq attributes to the data model.
  • Loading branch information
@adamjtaylor
adamjtaylor authored Jul 31, 2023
2 parents b9dbcbb + cee72a5 commit d84d729
Show file tree
Hide file tree
Showing 2 changed files with 106 additions and 2 deletions.
6 changes: 4 additions & 2 deletions HTAN.model.csv
View file
Original file line number Diff line number Diff line change
Expand Up @@ -45,7 +45,7 @@ scRNA-seq Level 1,Single-cell RNA-seq [EFO_0008913],,"Component, Filename, File
scRNA-seq Level 2,Alignment workflows downstream of scRNA-seq Level 1,,"Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID, scRNAseq Workflow Type, Workflow Version, scRNAseq Workflow Parameters Description, Workflow Link, Genomic Reference, Genomic Reference URL, Genome Annotation URL, Checksum, Whitelist Cell Barcode File Link, Cell Barcode Tag, UMI Tag, Applied Hard Trimming",,FALSE,Sequencing,scRNA-seq Level 1,,
scRNA-seq Level 3,Gene and Isoform expression files,,"Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID, Data Category, Matrix Type, Linked Matrices, Cell Median Number Reads, Cell Median Number Genes, Cell Total, scRNAseq Workflow Type, scRNAseq Workflow Parameters Description, Workflow Link, Workflow Version",,FALSE,Sequencing,scRNA-seq Level 2,,
scRNA-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, scRNAseq Workflow Type, scRNAseq Workflow Parameters Description, Workflow Version, Workflow Link",,FALSE,Sequencing,scRNA-seq Level 3,,
Bulk RNA-seq Level 1,Bulk RNA-seq [EFO_0003738],,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, Library Layout, Read Indicator, Nucleic Acid Source, Sequencing Platform, Sequencing Batch ID, Read Length, Library Selection Method, Library Preparation Kit Name, Library Preparation Kit Vendor, Library Preparation Kit Version, Library Preparation Days from Index, Spike In, 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, Transcript Integrity Number, RIN, DV200, 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,http://www.ebi.ac.uk/efo/EFO_0003738,
Bulk RNA-seq Level 1,Bulk RNA-seq [EFO_0003738],,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, Library Layout, Read Indicator, Nucleic Acid Source, Micro-region Seq Platform, ROI Tag, Sequencing Platform, Sequencing Batch ID, Read Length, Library Selection Method, Library Preparation Kit Name, Library Preparation Kit Vendor, Library Preparation Kit Version, Library Preparation Days from Index, Spike In, 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, Transcript Integrity Number, RIN, DV200, 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,http://www.ebi.ac.uk/efo/EFO_0003738,
Bulk RNA-seq Level 2,Bulk RNA-seq alignment protocol description,,"Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID, HTAN Parent 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, Contamination, Contamination Error, Mean Coverage, MSI Workflow Link, MSI Score, MSI Status, 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, Is lowest level",,FALSE,Sequencing,Bulk RNA-seq Level 1,,
Bulk RNA-seq Level 3,Bulk RNA-seq gene expression matrices,,"Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID, Pseudo Alignment Used, Data Category, Expression Units, Matrix Type, Fusion Gene Detected, Fusion Gene Identity",,FALSE,Sequencing,Bulk RNA-seq Level 2,,
Bulk WES Level 1,Bulk Whole Exome Sequencing raw files,,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, Sequencing Batch ID, Library Layout, Read Indicator, Library Selection Method, Read Length, Target Capture Kit, Library Preparation Kit Name, Library Preparation Kit Vendor, Library Preparation Kit Version, Sequencing Platform, 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, Multiplex Barcode, Library Preparation Days from Index, Size Selection Range, Target Depth, To Trim Adapter Sequence",,FALSE,Sequencing,Biospecimen,,
Expand Down Expand Up @@ -197,7 +197,9 @@ Imaging Object Class Description,Free text description of object class [string],
Number of Objects,The number of objects (eg cells) described,,,,TRUE,Imaging,,https://www.miti-consortium.org/,int
Number of Features,The number of features (eg channels) described,,,,TRUE,Imaging,,https://www.miti-consortium.org/,int
Imaging Summary Statistic,Function used to summarize object/feature intensity,"Mean,Median,Not Specified",,,FALSE,Imaging,,https://www.miti-consortium.org/,
Nucleic Acid Source,The source of the input nucleic molecule,"Single Cell, Bulk Whole Cell, Single Nucleus, Bulk Nuclei",,,TRUE,Sequencing,,,
Nucleic Acid Source,The source of the input nucleic molecule,"Single Cell, Bulk Whole Cell, Single Nucleus, Bulk Nuclei, Micro-region",,,TRUE,Sequencing,,,
Micro-region Seq Platform,The platform used for micro-regional RNA sequencing (if applicable),"Rarecyte Pick-Seq, Laser Capture Microdissection",,,FALSE,Sequencing,,,
ROI Tag,The tag or grouping used to identify the ROI in micro-regional RNA sequencing (if applicable). Must match the ROI tag within the count matrix in level 3.,,,,FALSE,Sequencing,,,
Single Cell Isolation Method,"The method by which cells are isolated into individual reaction containers at a single cell resolution (e.g. wells, micro-droplets)","Microfluidics Chip, Droplets, FACS, Plates, 10x, Nuclei Isolation",,,TRUE,scRNA-seq Level 1,,,
Dissociation Method,The tissue dissociation method used for scRNASeq or scATAC-seq assays,"gentleMACS, Dounce, Enzymatic Digestion, Not Applicable",,,TRUE,scRNA-seq Level 1,,,
Library Layout,Sequencing read type,"Paired End, Single Read, Mid-length, Long Read",,,TRUE,Sequencing,,,
Expand Down
102 changes: 102 additions & 0 deletions HTAN.model.jsonld
View file
Original file line number Diff line number Diff line change
Expand Up @@ -5371,6 +5371,12 @@
{
"@id": "bts:NucleicAcidSource"
},
{
"@id": "bts:Micro-regionSeqPlatform"
},
{
"@id": "bts:ROITag"
},
{
"@id": "bts:SequencingPlatform"
},
Expand Down Expand Up @@ -11847,12 +11853,57 @@
},
{
"@id": "bts:BulkNuclei"
},
{
"@id": "bts:Micro-region"
}
],
"sms:displayName": "Nucleic Acid Source",
"sms:required": "sms:true",
"sms:validationRules": []
},
{
"@id": "bts:Micro-regionSeqPlatform",
"@type": "rdfs:Class",
"rdfs:comment": "The platform used for micro-regional RNA sequencing (if applicable)",
"rdfs:label": "Micro-regionSeqPlatform",
"rdfs:subClassOf": [
{
"@id": "bts:Sequencing"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"schema:rangeIncludes": [
{
"@id": "bts:RarecytePick-Seq"
},
{
"@id": "bts:LaserCaptureMicrodissection"
}
],
"sms:displayName": "Micro-region Seq Platform",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:ROITag",
"@type": "rdfs:Class",
"rdfs:comment": "The tag or grouping used to identify the ROI in micro-regional RNA sequencing (if applicable). Must match the ROI tag within the count matrix in level 3.",
"rdfs:label": "ROITag",
"rdfs:subClassOf": [
{
"@id": "bts:Sequencing"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "ROI Tag",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:SingleCellIsolationMethod",
"@type": "rdfs:Class",
Expand Down Expand Up @@ -55875,6 +55926,57 @@
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:Micro-region",
"@type": "rdfs:Class",
"rdfs:comment": "TBD",
"rdfs:label": "Micro-region",
"rdfs:subClassOf": [
{
"@id": "bts:NucleicAcidSource"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "Micro-region",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:RarecytePick-Seq",
"@type": "rdfs:Class",
"rdfs:comment": "TBD",
"rdfs:label": "RarecytePick-Seq",
"rdfs:subClassOf": [
{
"@id": "bts:Micro-regionSeqPlatform"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "Rarecyte Pick-Seq",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:LaserCaptureMicrodissection",
"@type": "rdfs:Class",
"rdfs:comment": "TBD",
"rdfs:label": "LaserCaptureMicrodissection",
"rdfs:subClassOf": [
{
"@id": "bts:Micro-regionSeqPlatform"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "Laser Capture Microdissection",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:MicrofluidicsChip",
"@type": "rdfs:Class",
Expand Down

0 comments on commit d84d729

Please sign in to comment.