Standardise CSV

HTAN.model.csv

@@ -42,9 +42,9 @@ 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,,
-Slide-seq Level 1,"Raw sequencing files for the Slide-seq assay.",,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, Nucleic Acid Source, Library Construction Method, Read Indicator, Spatial Read1, Spatial Read2, End Bias, Reverse Transcription Primer, Spatial Barcode Offset, Spatial Barcode and UMI, Spike In, Sequencing Platform, Run ID, Sequencing Batch ID, Total Number Beads in Puck, Technical Replicate Group, Protocol Link, Spatial Library Construction Method, Library Preparation Days from Index, Sequencing Library Construction Days from Index, Nucleic Acid Capture Days from Index",,FALSE,Spatial Transcriptomics,Biospecimen,,
-Slide-seq Level 2,"Aligned sequencing files and QC for the Slide-seq assay.",,"Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID, Slide-seq Workflow Type, Workflow Version, Slide-seq Workflow Parameter Description, Workflow Link, Genomic Reference, Genomic Reference URL, Genome Annotation URL, Checksum, Spatial Barcode Tag, UMI Tag, Applied Hard Trimming",,FALSE,Spatial Transcriptomics,Slide-seq Level 1,,
-Slide-seq Level 3,"Gene matrices with features and barcodes for Slide-seq as well as spatial information (bead location files).",,"Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID, Data Category, Matrix Type, Slide-seq Workflow Type, Workflow Version, Slide-seq Workflow Parameter Description, Workflow Link, Workflow Version, Beads Total, Median UMI Counts per Spot, Median Number Genes per Spatial Spot, Slide-seq Bead File Type",,FALSE,Spatial Transcriptomics,Slide-seq Level 2,,
+Slide-seq Level 1,Raw sequencing files for the Slide-seq assay.,,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, Nucleic Acid Source, Library Construction Method, Read Indicator, Spatial Read1, Spatial Read2, End Bias, Reverse Transcription Primer, Spatial Barcode Offset, Spatial Barcode and UMI, Spike In, Sequencing Platform, Run ID, Sequencing Batch ID, Total Number Beads in Puck, Technical Replicate Group, Protocol Link, Spatial Library Construction Method, Library Preparation Days from Index, Sequencing Library Construction Days from Index, Nucleic Acid Capture Days from Index",,FALSE,Spatial Transcriptomics,Biospecimen,,
+Slide-seq Level 2,Aligned sequencing files and QC for the Slide-seq assay.,,"Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID, Slide-seq Workflow Type, Workflow Version, Slide-seq Workflow Parameter Description, Workflow Link, Genomic Reference, Genomic Reference URL, Genome Annotation URL, Checksum, Spatial Barcode Tag, UMI Tag, Applied Hard Trimming",,FALSE,Spatial Transcriptomics,Slide-seq Level 1,,
+Slide-seq Level 3,Gene matrices with features and barcodes for Slide-seq as well as spatial information (bead location files).,,"Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID, Data Category, Matrix Type, Slide-seq Workflow Type, Workflow Version, Slide-seq Workflow Parameter Description, Workflow Link, Workflow Version, Beads Total, Median UMI Counts per Spot, Median Number Genes per Spatial Spot, Slide-seq Bead File Type",,FALSE,Spatial Transcriptomics,Slide-seq Level 2,,
 Total Number Beads in Puck,Number of beads in the Slide-seq puck. Integer,,,,TRUE,Spatial Transcriptomics,,,
 Beads Total,Number of sequenced beads. Applies to raw counts matrix only. Integer,,,,FALSE,Spatial Transcriptomics,,,
 Slide-seq Workflow Type,Generic name for the workflow used to analyze the Slide-seq data set. String,,,,TRUE,Spatial Transcriptomics,,,
@@ -878,7 +878,7 @@ RPPA Validation Status,Valid = RPPA and WB correlation > 0.7; Use with Caution =
 Antibody Notes,Notes on antibodies replacements and antibody recognition observations.,,,,FALSE,HTAN RPPA Antibody Table,,,
 Pre-processing Completed,Pre-processing steps completed to convert level 1 raw data to a single level 2 image,"Illumination correction, Tile Stitching, Channel/Cycle Registration, TMA de-arraying, None, Other",,,TRUE,Imaging,,https://www.miti-consortium.org/,
 Pre-processing Required,Pre-processing steps required to convert level 1 raw data to a single level 2 image,"Illumination correction, Tile Stitching, Channel/Cycle Registration, TMA de-arraying, None, Other",,,TRUE,Imaging,,https://www.miti-consortium.org/,
-Publication,"An empty parent attribute for publications",,,,FALSE,,,,
+Publication,An empty parent attribute for publications,,,,FALSE,,,,
 Publication Manifest,Publication specific attributes.,,"Component,Publication-associated HTAN Parent Data File ID, HTAN Grant ID, HTAN Center ID, Publication Content Type, DOI, Title, Authors, Corresponding Author, Corresponding Author ORCID, Year of Publication, Location of Publication, Publication Abstract, License, PMID, Publication contains HTAN ID, Data Type, Tool, Supporting Link, Supporting Link Description",,FALSE,Publication,Publication,,
 Publication-associated HTAN Parent Data File ID,HTAN Data File Identifier(s) of the files associated with the content presented/published. Should be comma-separated lists.,,,,TRUE,Publication,,,list like
 HTAN Grant ID,HTAN grant number(s) (i.e. CA------ format) associated with the content presented/published.,,,,TRUE,Publication,,,list like
@@ -984,23 +984,23 @@ DMC data file format,Format of the data files,"BED, bedGraph",,,TRUE,Bulk Methyl
 DMR data file Format,Format of the data files.,"BED, bedGraph",,,TRUE,Bulk Methylation-seq Level 3,,,
 MS Assay Category,Type of Mass Spectrometry performed.,,,,TRUE,Mass Spectrometry Level 2,,,
 Publication contains HTAN ID,HTAN IDs are used in the publication.,"Yes, No",,,TRUE,Publication,,,
-Electron Microscopy Level 1,"Raw electron microscopy data as one TIFF file per plane for a 3D image stack or per tile for a 2D large area montage",,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, EM method, EM signal or contrast mech, EM instrument, Protocol Link, Software and Version, SizeX, SizeY, SizeC, SizeZ, PhysicalSizeX, PhysicalSizeY, PhysicalSizeZ, EM dwell or exposure time,EM voltage, EM beam current, EM spot size, EM stage tilt, EM signal processing, EM contrast type",,FALSE,Assay,Biospecimen,,
-Electron Microscopy Level 2,"Processed electron microscopy data as one OME-TIFF image per plane or montage",,"Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID,Tile overlap X, Tile overlap Y,EM contrast type",,FALSE,Assay,Electron Microscopy Level 1,,
-Electron Microscopy Level 3,"Segmented electron microscopy data as .am or .tiff formats",,"Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID, Imaging Object Class",,FALSE,Assay,Electron Microscopy Level 2,,
-Electron Microscopy Level 4,"Movies or other derived files from electron microscopy data",,"Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID, Comment",,FALSE,Assay,Electron Microscopy Level 3,,
-EM instrument,"Make and model of the EM instrument used",,,,TRUE,Electron Microscopy Level 1,,,str
-EM method,"Electron microscopy method used","SEM, FIB-SEM, SBF-SEM, AT, TEM, ET, cryo ET, ssTEM",,,TRUE,Electron Microscopy Level 1,,,
-EM signal or contrast mech,"How the electron microscopy signal is generated from the sample","BSE, SE, phase, bright-field, dark-field",,,TRUE,Electron Microscopy Level 1,,,
-EM dwell or exposure time,"Duration in microseconds (µs) of electron beam data collection per pixel or frame",,,,FALSE,Electron Microscopy Level 1,,,num
-EM voltage,"Accelerating voltage in kiloelectronvolts (keV)",,,,FALSE,Electron Microscopy Level 1,,,num
-EM beam current,"Beam current in nanoamps (nA)",,,,FALSE,Electron Microscopy Level 1,,,num 
-EM spot size,"Beam spot size in micrometers (µm)",,,,FALSE,Electron Microscopy Level 1,,,num 
-EM stage tilt,"Physical stage tilt in degrees with respect to the electron beam",,,,FALSE,Electron Microscopy Level 1,,,num
-EM signal processing,"SNR improvement strategies used","None, line integration, frame integration, frame averaging",,,FALSE,Electron Microscopy Level 1,,,
-EM contrast type,"Does the image use standard SEM contrast or TEM contrast","SEM,TEM",,,FALSE,Electron Microscopy Level 1,,,
-Tile overlap X,"Percentage of image overlap to allow tile stitching in x direction",,,,TRUE,Electron Microscopy Level 1,,,num
-Tile overlap Y,"Percentage of image overlap to allow tile stitching in x direction",,,,TRUE,Electron Microscopy Level 1,,,num
-Barretts Esophagus Goblet Cells Present,"Presence or absennce of Barretts esophagus goblet cells.","Yes, No",,,FALSE,Follow Up,,,
-Pancreatitis Onset Year,"Date of onset of pancreatitis.",,,,FALSE,Follow Up,,,num
-HTAN Parent Channel Metadata ID,"HTAN ID for a level 3 channels table.",,,,TRUE, Imaging Level 4,,,
+Electron Microscopy Level 1,Raw electron microscopy data as one TIFF file per plane for a 3D image stack or per tile for a 2D large area montage,,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, EM method, EM signal or contrast mech, EM instrument, Protocol Link, Software and Version, SizeX, SizeY, SizeC, SizeZ, PhysicalSizeX, PhysicalSizeY, PhysicalSizeZ, EM dwell or exposure time,EM voltage, EM beam current, EM spot size, EM stage tilt, EM signal processing, EM contrast type",,FALSE,Assay,Biospecimen,,
+Electron Microscopy Level 2,Processed electron microscopy data as one OME-TIFF image per plane or montage,,"Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID,Tile overlap X, Tile overlap Y,EM contrast type",,FALSE,Assay,Electron Microscopy Level 1,,
+Electron Microscopy Level 3,Segmented electron microscopy data as .am or .tiff formats,,"Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID, Imaging Object Class",,FALSE,Assay,Electron Microscopy Level 2,,
+Electron Microscopy Level 4,Movies or other derived files from electron microscopy data,,"Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID, Comment",,FALSE,Assay,Electron Microscopy Level 3,,
+EM instrument,Make and model of the EM instrument used,,,,TRUE,Electron Microscopy Level 1,,,str
+EM method,Electron microscopy method used,"SEM, FIB-SEM, SBF-SEM, AT, TEM, ET, cryo ET, ssTEM",,,TRUE,Electron Microscopy Level 1,,,
+EM signal or contrast mech,How the electron microscopy signal is generated from the sample,"BSE, SE, phase, bright-field, dark-field",,,TRUE,Electron Microscopy Level 1,,,
+EM dwell or exposure time,Duration in microseconds (µs) of electron beam data collection per pixel or frame,,,,FALSE,Electron Microscopy Level 1,,,num
+EM voltage,Accelerating voltage in kiloelectronvolts (keV),,,,FALSE,Electron Microscopy Level 1,,,num
+EM beam current,Beam current in nanoamps (nA),,,,FALSE,Electron Microscopy Level 1,,,num 
+EM spot size,Beam spot size in micrometers (µm),,,,FALSE,Electron Microscopy Level 1,,,num 
+EM stage tilt,Physical stage tilt in degrees with respect to the electron beam,,,,FALSE,Electron Microscopy Level 1,,,num
+EM signal processing,SNR improvement strategies used,"None, line integration, frame integration, frame averaging",,,FALSE,Electron Microscopy Level 1,,,
+EM contrast type,Does the image use standard SEM contrast or TEM contrast,"SEM,TEM",,,FALSE,Electron Microscopy Level 1,,,
+Tile overlap X,Percentage of image overlap to allow tile stitching in x direction,,,,TRUE,Electron Microscopy Level 1,,,num
+Tile overlap Y,Percentage of image overlap to allow tile stitching in x direction,,,,TRUE,Electron Microscopy Level 1,,,num
+Barretts Esophagus Goblet Cells Present,Presence or absennce of Barretts esophagus goblet cells.,"Yes, No",,,FALSE,Follow Up,,,
+Pancreatitis Onset Year,Date of onset of pancreatitis.,,,,FALSE,Follow Up,,,num
+HTAN Parent Channel Metadata ID,HTAN ID for a level 3 channels table.,,,,TRUE, Imaging Level 4,,,
 Single Nucleus Capture, Nuclei isolation method,"Plates, 10x, droplet",,,FALSE,scmC-seq Level 1,,,