Partial resolution of #50

modules/Assay/Sequencing/Single_Cell_Sequencing/scATAC-seq/scATAC-seq_Level_1.csv

@@ -1,5 +1,5 @@
 Attribute,Description,Valid Values,DependsOn,Properties,Required,Parent,DependsOn Component,Source,Validation Rules
-scATAC-seq Level 1,"scATAC-seq files containing sequence read information, with or without alignment, as FASTQ or BAM files",,"Component, Filename, File Format, Lab ID, Nucleic Acid Source, Dissociation Method, Single Nucleus Buffer, Single Cell Isolation Method, Transposition Reaction, scATACseq Library Layout, Nucleus Identifier, Nuclei Barcode Length, Nuclei Barcode Read, scATACseq Read1, scATACseq Read2, scATACseq Read3, Library Construction Method, Sequencing Platform, Threshold for Minimum Passing Reads, Total Number of Passing Nuclei, Median Fraction of Reads in Peaks, Median Fraction of Reads in Annotated cis DNA Elements, Median Passing Read Percentage, Median Percentage of Mitochondrial Reads per Nucleus,Technical Replicate Group, Total Reads, Protocol Link",,FALSE,Single_Cell_Sequencing,,,
+scATAC-seq Level 1,"scATAC-seq files containing sequence read information, with or without alignment, as FASTQ or BAM files",,"Component, Filename, File Format, Participant ID, Sample ID, Detailed Sample ID,Nucleic Acid Source, Dissociation Method, Single Nucleus Buffer, Single Cell Isolation Method, Transposition Reaction, scATACseq Library Layout, Nucleus Identifier, Nuclei Barcode Length, Nuclei Barcode Read, scATACseq Read1, scATACseq Read2, scATACseq Read3, Library Construction Method, Sequencing Platform, Threshold for Minimum Passing Reads, Total Number of Passing Nuclei, Median Fraction of Reads in Peaks, Median Fraction of Reads in Annotated cis DNA Elements, Median Passing Read Percentage, Median Percentage of Mitochondrial Reads per Nucleus,Technical Replicate Group, Total Reads, Protocol Link",,FALSE,Single_Cell_Sequencing,,,
 Transposition Reaction,"Name of the transposase, transposon sequences","Tn5, EZ-Tn5, Tn5-059, Nextera Tn5, Diagenode-unloaded Apex-Bio, Diagenode-loaded Apex-Bio, In-House",,,TRUE,scATAC-seq Level 1,,,
 Single Nucleus Buffer,Nuclei isolation buffer,"NIB, 10x, Omni",,,TRUE,scATAC-seq Level 1,,,
 scATACseq Library Layout,Sequencing read type,scATACseq Paired End,,,TRUE,scATAC-seq Level 1,,,

modules/Assay/Sequencing/Single_Cell_Sequencing/scRNA-seq/scRNA-seq_Level_1.csv

@@ -1,5 +1,5 @@
 Attribute,Description,Valid Values,DependsOn,Properties,Required,Parent,DependsOn Component,Source,Validation Rules
-scRNA-seq Level 1,Single-cell RNA-seq [EFO_0008913],,"Component, Filename, File Format, Lab ID, Cryopreserved Cells in Sample, Single Cell Isolation Method, Dissociation Method, Library Construction Method, Read Indicator, Read1, Read2, End Bias, Reverse Transcription Primer, Spike In, Sequencing Platform, Total Number of Input Cells, Input Cells and Nuclei,Protocol Link, Technical Replicate Group",,FALSE,Single_Cell_Sequencing,Biospecimen,http://www.ebi.ac.uk/efo/EFO_0008913,
+scRNA-seq Level 1,Single-cell RNA-seq [EFO_0008913],,"Component, Filename, File Format, Participant ID, Sample ID, Detailed Sample ID, Cryopreserved Cells in Sample, Single Cell Isolation Method, Dissociation Method, Library Construction Method, Read Indicator, Read1, Read2, End Bias, Reverse Transcription Primer, Spike In, Sequencing Platform, Total Number of Input Cells, Input Cells and Nuclei,Protocol Link, Technical Replicate Group",,FALSE,Single_Cell_Sequencing,Biospecimen,http://www.ebi.ac.uk/efo/EFO_0008913,
 Cell Barcode and UMI,Cell and transcript identifiers,"","UMI Barcode Offset, UMI Barcode Length, Median UMIs per Cell Number, Cell Barcode Offset, Cell Barcode Length, Valid Barcodes Cell Number","",FALSE,scRNA-seq Level 1,"","",""
 Cell Barcode Offset,Offset in sequence for cell barcode read (in bp): number,"","","",TRUE,scRNA-seq Level 1,"","",""
 Cell Barcode Length,Length of cell barcode read (in bp): number,"","","",TRUE,scRNA-seq Level 1,"","",""

modules/Assay/Sequencing/Single_Cell_Sequencing/scRNA-seq/scRNA-seq_Level_2.csv

@@ -1,2 +1,2 @@
 Attribute,Description,Valid Values,DependsOn,Properties,Required,Parent,DependsOn Component,Source,Validation Rules
-scRNA-seq Level 2,Alignment workflows downstream of scRNA-seq Level 1,,"Component, Filename, File Format, Parent File ID, scRNAseq Workflow Type, Workflow Version, scRNAseq Workflow Parameters Description, Workflow Link, Genomic Reference, Genomic Reference URL, Genome Annotation URL, Whitelist Cell Barcode File Link, Cell Barcode Tag, UMI Tag, Applied Hard Trimming",,FALSE,Single_Cell_Sequencing,scRNA-seq Level 1,,
+scRNA-seq Level 2,Alignment workflows downstream of scRNA-seq Level 1,,"Component, Filename, File Format, Participant ID, Sample ID, Detailed Sample ID, scRNAseq Workflow Type, Workflow Version, scRNAseq Workflow Parameters Description, Workflow Link, Genomic Reference, Genomic Reference URL, Genome Annotation URL, Whitelist Cell Barcode File Link, Cell Barcode Tag, UMI Tag, Applied Hard Trimming",,FALSE,Single_Cell_Sequencing,scRNA-seq Level 1,,

modules/Assay/Sequencing/Single_Cell_Sequencing/scRNA-seq/scRNA-seq_Level_3.csv

@@ -1,5 +1,5 @@
 Attribute,Description,Valid Values,DependsOn,Properties,Required,Parent,DependsOn Component,Source,Validation Rules
-scRNA-seq Level 3,Gene and Isoform expression files,,"Component, Filename, File Format, 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,Single_Cell_Sequencing,,,
+scRNA-seq Level 3,Gene and Isoform expression files,,"Component, Filename, File Format, Participant ID, Sample ID, Detailed Sample 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,Single_Cell_Sequencing,,,
 Cell Median Number Reads,Median number of reads per cell. Number,"","","",TRUE,scRNA-seq Level 3,"","",""
 Cell Median Number Genes,Median number of genes detected per cell. Number,"","","",TRUE,scRNA-seq Level 3,"","",""
 Cell Total,Number of sequenced  cells. Applies to raw counts matrix only.,"","","",TRUE,scRNA-seq Level 3,"","",""

modules/Assay/Sequencing/Single_Cell_Sequencing/scRNA-seq/scRNA-seq_Level_4.csv

@@ -1,2 +1,2 @@
 Attribute,Description,Valid Values,DependsOn,Properties,Required,Parent,DependsOn Component,Source,Validation Rules
-scRNA-seq Level 4,"Gene and Isoform expression files",,"Component, Filename, File Format, 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,Single_Cell_Sequencing,,,
+scRNA-seq Level 4,"Gene and Isoform expression files",,"Component, Filename, File Format, Participant ID, Sample ID, Detailed Sample 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,Single_Cell_Sequencing,,,

modules/Biospecimen/Biospecimen.csv

@@ -1,6 +1,7 @@
 Attribute,Description,Valid Values,DependsOn,Properties,Required,Parent,DependsOn Component,Source,Validation Rules
 Biospecimen,"Biological entity; this can be tissue, blood, analyte and subsamples of those","","Biospecimen ID, Parent ID, Parent Biospecimen ID, Adjacent Biospecimen IDs,Biospecimen Type,Timepoint Label,Specimen Laterality","",FALSE,Patient,"","",""
 Sample ID, ID associated with a biosample,"","","",TRUE,Biospecimen,"",,""
+Biospecimen ID, Alias for Sample ID,"","","",TRUE,Biospecimen,"",,""
 Detailed Sample ID, Additional alternative ID associated with a biosample,"","","",TRUE,Biospecimen,"",,""
 Parent ID, ID of parent biospecimen,"","","",TRUE,Biospecimen,"",https://docs.google.com/document/d/1podtPP8L1UNvVxx9_c_szlDcU1f8n7bige6XA_GoRVM/edit?usp=sharing,""
 Parent Biospecimen ID, Biospecimen identifier indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,"","","",TRUE,Biospecimen,"",https://docs.google.com/document/d/1podtPP8L1UNvVxx9_c_szlDcU1f8n7bige6XA_GoRVM/edit?usp=sharing,""