Merge branch 'main' into 364-update-enumerated-values-in-publication-…

…data-type-field-to-include-all-assay-types

HTAN.model.csv

@@ -84,7 +84,7 @@ Visium File Type,The file type generated for the visium experiment.,"reference p
 Run ID,A unique identifier for this individual run (typically associated with a single slide) of the spatial transcriptomic processing workflow.,,,,TRUE,Spatial Transcriptomics,,,
 Capture Area,"Area (or Capture Area) - One of the either four or two active regions where tissue can be placed on a Visium slide. Each area is intended to contain only one tissue sample. Slide areas are named consecutively from top to bottom: A1, B1, C1, D1 for Visium slides with 6.5 mm Capture Area and A, B for CytAssist slides with 11 mm Capture Area. Both CytAssist slides with 6.5 mm Capture Area and Gateway Slides contain only two slide areas, A1 and D1.","A, B, C, D, A1, B1, C1, D1",,,FALSE,Spatial Transcriptomics,,,
 Slide Version,Version of imaging slide used. Slide version is critical for the analysis of the sequencing data as different slides have different capture area layouts.,"V1, V2, V3, V4",,,FALSE,Spatial Transcriptomics,,,
-Slide ID,"The unique identifier printed on the label of each Visium slide. The serial number starts with V followed by a number which can range between one through five and ends with a dash and a three digit number, such as 123.",,,,FALSE,Spatial Transcriptomics,,,
+Slide ID,"For Visium, it is the unique identifier printed on the label of each Visium slide. The serial number starts with V followed by a number which can range between one through five and ends with a dash and a three digit number, such as 123. For CosMx, this refers to the loaded Flow Cell ID. For Xenium, this ID indicates the slide orientation, as it matches the relative location of the ID on the physical Xenium slide.",,,,FALSE,Spatial Transcriptomics,,,
 Image Re-orientation,"To ensure good fiducial alignment and tissue spots detection, it is important to correct for this shift in orientation.","TRUE, FALSE",,,FALSE,Spatial Transcriptomics,,,
 Permeabilization Time,Fixed and stained tissue sections are permeabilized for different times. Each Capture Area captures polyadenylated mRNA from the attached tissue section. Measure is provided in minutes.,,,,FALSE,Spatial Transcriptomics,,,
 Whitelist Spatial Barcode File Link,Link to file listing all possible spatial barcodes. URL,,,,TRUE,Spatial Transcriptomics,,,
@@ -122,7 +122,7 @@ GeoMx DSP Workflow Parameter Description,Parameters used to run the GeoMx DSP wo
 GeoMx DSP Workflow Link,Link to workflow or command. DockStore.org recommended. URL,,,,FALSE,Spatial Transcriptomics,,,
 NanoString GeoMx DSP ROI RCC Segment Annotation Metadata,GeoMx ROI and Segment Metadata Attributes. The assayed biospecimen should be reported one per row with the associated ROI coordinates. ,,"HTAN Parent Biospecimen ID, Scan name, ROI name, Segment name, ROI X Coordinate,ROI Y Coordinate, Tags, QC status, Scan Height, Scan Width, Scan Offset X, Scan Offset Y, Binding Density, Positive norm factor, Surface area, Nuclei count, Tissue Stain",,FALSE,Assay,,,
 Scan name,GeoMx Scan name (as appears in Segment Summary),,,,TRUE,"NanoString GeoMx DSP ROI RCC Segment Annotation Metadata, NanoString GeoMx DSP ROI DCC Segment Annotation Metadata",,,
-ROI name,ROI name (application generated),,,,TRUE,"NanoString GeoMx DSP ROI RCC Segment Annotation Metadata, NanoString GeoMx DSP ROI DCC Segment Annotation Metadata",,,
+ROI name,"ROI name (application generated). For Xenium this is referred to as the “region name”",,,,TRUE,"NanoString GeoMx DSP ROI RCC Segment Annotation Metadata, NanoString GeoMx DSP ROI DCC Segment Annotation Metadata",,,
 Segment name,Name given to segment at time of generation,,,,TRUE,"NanoString GeoMx DSP ROI RCC Segment Annotation Metadata, NanoString GeoMx DSP ROI DCC Segment Annotation Metadata",,,
 Tags,Unique descriptor of a variable group (ie. MAPK+),,,,TRUE,"NanoString GeoMx DSP ROI RCC Segment Annotation Metadata, NanoString GeoMx DSP ROI DCC Segment Annotation Metadata",,,
 ROI X Coordinate,X location within the image,,,,TRUE,"NanoString GeoMx DSP ROI RCC Segment Annotation Metadata, NanoString GeoMx DSP ROI DCC Segment Annotation Metadata",,,
@@ -134,7 +134,7 @@ Scan Offset X,Offset X of the scan for GeoMx Analysis,,,,TRUE,NanoString GeoMx D
 Scan Offset Y,Offset Y of the scan for GeoMx Analysis,,,,TRUE,NanoString GeoMx DSP ROI RCC Segment Annotation Metadata,,,
 Binding Density,The binding density as reported by the application,,,,FALSE,NanoString GeoMx DSP ROI RCC Segment Annotation Metadata,,,
 Positive norm factor,The Positive Control Normalization factor calculated using pos-hyb controls,,,,FALSE,NanoString GeoMx DSP ROI RCC Segment Annotation Metadata,,,
-Surface area,Surface area of the ROI in square microns (µm2),,,,TRUE,"NanoString GeoMx DSP ROI RCC Segment Annotation Metadata, NanoString GeoMx DSP ROI DCC Segment Annotation Metadata",,,
+Surface area,"Surface area of the ROI in square microns (µm^2). In CosMx, this is referred to as the Scan Area. In Xenium, this is referred to as the Region Area",,,,TRUE,"NanoString GeoMx DSP ROI RCC Segment Annotation Metadata, NanoString GeoMx DSP ROI DCC Segment Annotation Metadata",,,
 Nuclei count,Number of nuclei detected in the segment (if applicable),,,,TRUE,"NanoString GeoMx DSP ROI RCC Segment Annotation Metadata, NanoString GeoMx DSP ROI DCC Segment Annotation Metadata",,,
 Tissue Stain,e.g. CD45 or PanCK (if masking was performed),,,,FALSE,NanoString GeoMx DSP ROI RCC Segment Annotation Metadata,,,
 NanoString GeoMx DSP ROI DCC Segment Annotation Metadata,GeoMx ROI and Segment Metadata Attributes. The assayed biospecimen should be reported one per row with the associated ROI coordinates. ,,"HTAN Parent Biospecimen ID, Scan name, Slide name, ROI name, Segment name, ROI X Coordinate,ROI Y Coordinate, Tags, Scan Height, Scan Width, Scan Offset X, Scan Offset Y, Surface area, Nuclei count, Sequencing Saturation, MapQ30, Raw reads, Stitched reads, Aligned reads, Deduplicated reads, In Situ Negative median, Biological probe median",,FALSE,Assay,,,
@@ -161,10 +161,34 @@ Stripe Window,"Binning size used for calling significant architectural stripes.
 Loop Calling,Tool used for identifying loop interactions,,,,TRUE,Sequencing,,,
 Imaging Level 4,Derived imaging data: Object-by-feature array,,"Component, Filename, File Format, HTAN Parent Data File ID, HTAN Parent Channel Metadata ID, HTAN Data File ID, Parameter file, Software and Version, Commit SHA,Number of Objects, Number of Features,Imaging Object Class, Imaging Summary Statistic",,FALSE,Assay,Imaging Level 3 Channels,,
 SRRS Imaging Level 2,SRRS-specific HTAN raw and pre-processed image data,,"Component, Filename, File Format, HTAN Participant ID, HTAN Parent Biospecimen ID,  HTAN Data File ID, Channel Metadata Filename, Imaging Assay Type, Protocol Link, Software and Version, Microscope, Objective, NominalMagnification, Pyramid, Zstack, Tseries, Passed QC, Frame Averaging, Image ID, DimensionOrder, PhysicalSizeX, PhysicalSizeXUnit, PhysicalSizeY, PhysicalSizeYUnit, Pixels BigEndian, PlaneCount, SizeC, SizeT, SizeX, SizeY, SizeZ, PixelType",,FALSE,Assay,Biospecimen,,
+10X Genomics Xenium ISS Experiment,"All data pertaining to the 10X Genomics Xenium In-Situ Hybridization experiment",,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, Xenium Bundle Contents, Slide ID, ROI name, Panel Name, Protocol Link, Software and Version,Total Number of Cells, Total Number of Targets, Surface area, Experiment IF Channels, Transcripts per Cell, Percent of Transcripts within Cells, Decoded Transcripts, Xenium IF image HTAN File ID, Xenium HE image HTAN File ID",,FALSE,Spatial Transcriptomics,Biospecimen,,
+Xenium Bundle Contents,A comma separated list of filenames within the Xenium bundle zip file,,,,TRUE,Spatial Transcriptomics,,,
+Panel Name,"The human-readable panel name. This could be the Gene Panel name or Protein Panel name. In Xenium, this refers to the string entered as the name in panel specification (e.g. Xenium Human Immuno-Oncology Add-on B Gene Expression). In CosMx, this refers to the panel name as it appears in the CosMx catalog (e.g. CosMx Human Universal Cell Characterization Panel (1000-plex))",,,,TRUE,Spatial Transcriptomics,,,
+Total Number of Cells,The total number of cells analyzed on the flow cell,,,,TRUE,Spatial Transcriptomics,,,
+Total Number of Targets,Refers to the target of an assay. Can be genes/transcripts or probes,,,,TRUE,Spatial Transcriptomics,,,
+Experiment IF Channels,"A comma-separated list with any number of channels the user deems appropriate(Example: PanCK, CD45, CD3, DAPI)",,,,TRUE,Spatial Transcriptomics,,,
+Transcripts per Cell,Mean or Median transcript count per cell analyzed on the flow cell or slide,,,,TRUE,Spatial Transcriptomics,,,
+Percent of Transcripts within Cells,The percentage of transcripts assigned to assayed cells,,,,TRUE,Spatial Transcriptomics,,,
+Decoded Transcripts,"In Xenium, this is the number of high-quality, decoded-to-gene nuclear transcripts divided by the total segmented nuclear area to get a transcript density (units are reported in 100um^2).",,,,TRUE,Spatial Transcriptomics,,,
+Xenium IF image HTAN File ID,The HTAN Data File ID of a Imaging Level 2 file,,,,FALSE,Spatial Transcriptomics,,,
+Xenium HE image HTAN File ID,The HTAN Data File ID of a Imaging Level 2 file,,,,FALSE,Spatial Transcriptomics,,,
 RPPA Level 2,Array based protemics. Each dilution curve of spot intensities is fitted using the monotone increasing B-spline model in the SuperCurve R package. This fits a single curve using all the samples on a slide with the signal intensity as the response variable and the dilution steps as independent variables. The fitted curve is plotted with the signal intensities on the y-axis and the log2-concentration of proteins on the x-axis for diagnostic purposes.,,"Component, Filename, File Format, HTAN Participant ID, HTAN Parent Biospecimen ID,  HTAN Parent Data File ID, HTAN Data File ID, HTAN RPPA Antibody Table, Assay Type, Protocol Link, Software and Version",,FALSE,Assay,Biospecimen,,
 HTAN RPPA Antibody Table,A table containing antibody level metadata for RPPA,,"HTAN RPPA Antibody Table ID, Filename, File Format, Ab Name Reported on Dataset, GENCODE Gene Symbol Target, UNIPROT Protein ID Target, Phosphoprotein Flag, Vendor, Catalog Number, Internal Ab ID, Species, RPPA Dilution, Phospho Site, RPPA Validation Status, Clone, Clonality, Antibody Notes",,TRUE,RPPA Level 2,,,
 RPPA Level 3,Level 3 Reverse Phase Protein Array (RPPA) data contains intra-batch normalized intensities.,,"Component, Filename, File Format, HTAN Participant ID, HTAN Parent Biospecimen ID,  HTAN Parent Data File ID, HTAN Data File ID, Assay Type, Software and Version, Normalization Method",,FALSE,Assay,Biospecimen,,
 RPPA Level 4,Level 4 Reverse Phase Protein Array (RPPA) data contains intra-batch corrected intensities.,,"Component, Filename, File Format, HTAN Participant ID, HTAN Parent Biospecimen ID, HTAN Parent Data File ID, HTAN Data File ID, Assay Type, Batch Correction Method",,FALSE,Assay,RPPA Level 2,,
+Nanostring CosMx SMI Experiment,"RNA and Protein Panel assays applied as part of Nanostring CosMx Spatial Molecular Imager (SMI)",,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, CosMx Bundle Contents, Slide ID, CosMx Assay Type, Panel Name, Protocol Link, Software and Version, Total Number of Cells, Total Number of Targets, Number of FOVs, Surface area, Experiment IF Channels, Transcripts per Cell, Percent of Transcripts within Cells, Mean Total Transcripts per Area, Unique Genes, Total Negative Probe Counts",,FALSE,Spatial Transcriptomics,Biospecimen,,
+CosMx Bundle Contents,A comma separated list of filenames within the CosMx bundle zip file,,,,TRUE,Spatial Transcriptomics,,,
+CosMx Assay Type,The specification for barcodes on each image. Either RNA probe or protein antibody according to the assay,"RNA, Protein",,,TRUE,Spatial Transcriptomics,,,
+Panel Name,"The human-readable panel name. This could be the Gene Panel name or Protein Panel name. In Xenium, this refers to the string entered as the name in panel specification (e.g. Xenium Human Immuno-Oncology Add-on B Gene Expression). In CosMx, this refers to the panel name as it appears in the CosMx catalog (e.g. CosMx Human Universal Cell Characterization Panel (1000-plex))",,,,TRUE,Spatial Transcriptomics,,,
+Total Number of Cells,The total number of cells analyzed on the flow cell,,,,TRUE,Spatial Transcriptomics,,,
+Total Number of Targets,Refers to the target of an assay. Can be genes/transcripts or probes,,,,TRUE,Spatial Transcriptomics,,,
+Number of FOVs,The total number of FOVs recorded for the sample on a single flow cell,,,,TRUE,Spatial Transcriptomics,,,
+Experiment IF Channels,"A comma-separated list with any number of channels the user deems appropriate(Example: PanCK, CD45, CD3, DAPI)",,,,TRUE,Spatial Transcriptomics,,,
+Transcripts per Cell,Mean or Median transcript count per cell analyzed on the flow cell or slide,,,,TRUE,Spatial Transcriptomics,,,
+Percent of Transcripts within Cells,The percentage of transcripts assigned to assayed cells,,,,TRUE,Spatial Transcriptomics,,,
+Mean Total Transcripts per Area,The mean total transcripts per um3,,,,TRUE,Spatial Transcriptomics,,,
+Unique Genes,The total unique genes detected above background,,,,FALSE,Spatial Transcriptomics,,,
+Total Negative Probe Counts,Mean Total Negative probe counts/cell,,,,TRUE,Spatial Transcriptomics,,,
 Mass Spectrometry Level 1,"Mass Spectrometry derived data that includes proteomics, metabolomics, and lipidomics, level 1",,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, MS Batch ID, MS-based Assay Type, Analyte Type, MS-based Targeted, MS Instrument Vendor and Model, MS Source, Polarity, Mass Range Low Value, Mass Range High Value, Data Collection Mode, MS Scan Mode, MS Labeling, Protocol Link, LC Instrument Vendor and Model, LC Column Vendor and Model, LC Resin, LC Length Value, LC Temp Value, LC ID Value, LC Flow Rate, LC Gradient, LC Mobile Phase A, LC Mobile Phase B, Software and Version, MS Instrument Metadata File",,FALSE,Assay,Biospecimen,,
 Mass Spectrometry Level 2,"Mass Spectrometry derived data that includes proteomics, metabolomics, and lipidomics, level 2",,"Component, Filename, File Format, HTAN Data File ID, HTAN Parent Biospecimen ID, HTAN Parent Data File ID, MS Assay Category, Software and Version, Mass Spectrometry Auxiliary File",,FALSE,Assay,Mass Spectrometry Level 1,,
 Mass Spectrometry Level 3,"Mass Spectrometry derived data that includes proteomics, metabolomics, and lipidomics, level 3",,"Component, Filename, File Format, HTAN Data File ID, HTAN Parent Biospecimen ID, HTAN Parent Data File ID, MS Assay Category, Software and Version, Mass Spectrometry Auxiliary File",,FALSE,Assay,Mass Spectrometry Level 2,,