Merge branch 'main' into 340-move-the-ci-to-use-the-refactored-schema…

…tic-version
ncihtan · Feb 29, 2024 · ffb4f09 · ffb4f09
2 parents e77aa89 + d5f817a
commit ffb4f09
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Showing 2 changed files with 18 additions and 18 deletions.
diff --git a/HTAN.model.csv b/HTAN.model.csv
@@ -74,11 +74,11 @@ MERFISH Positions File,The positions file is an auxiliary MERFISH file that desc
 MERFISH Codebook File,The codebook is an auxiliary MERFISH file that describes how each grouping of bits is converted to a gene name.,,,,FALSE,Assay,,,
 Imaging Level 3 Segmentation,Object segmentations,,"Component, Filename, File Format, HTAN Parent Data File ID,  HTAN Data File ID, Imaging Segmentation Data Type, Parameter file, Software and Version, Commit SHA, Imaging Object Class, Number of Objects",,FALSE,Assay,Imaging Level 2,,
 Imaging Level 3 Image,Quality controlled imaging data,,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Parent Data File ID, HTAN Parent Channel Metadata ID, HTAN Data File ID, Imaging Assay Type, Protocol Link,Software and Version, Microscope, Objective, NominalMagnification, LensNA, WorkingDistance, Immersion, Pyramid, Zstack, Tseries, Passed QC, Comment, FOV number, FOVX, FOVY, Frame Averaging",,FALSE,Assay,"Imaging Level 3 Channels, Imaging Level 2",,
-10x Visium Spatial Transcriptomics - RNA-seq Level 1,Files contain raw RNA-seq data associated with spot/slide data.,,"Component, Filename, Run ID, File Format, HTAN Data File ID, HTAN Parent Biospecimen ID, Read Indicator, Spatial Read1, Spatial Read2, Spatial Library Construction Method, Library Preparation Days from Index, Sequencing Library Construction Days from Index, End Bias, Reverse Transcription Primer, Sequencing Platform, Capture Area, Protocol Link, Slide Version, Slide ID, Image Re-orientation, Permeabilization Time, RIN, DV200",,FALSE,Spatial Transcriptomics,Biospecimen,,
-10x Visium Spatial Transcriptomics - RNA-seq Level 2,Alignment workflows downstream of Spatial Transcriptomics RNA-seq Level 1.,,"Component, Filename, File Format, Checksum, HTAN Data File ID, HTAN Parent Data File ID, UMI Tag, Whitelist Spatial Barcode File Link, Spatial Barcode Tag, Applied Hard Trimming, Workflow Version, Workflow Link, Genomic Reference, Genomic Reference URL, Genome Annotation URL, HTAN Parent Biospecimen ID, Run ID, Capture Area",,FALSE,Spatial Transcriptomics,10x Visium Spatial Transcriptomics - RNA-seq Level 1,,
-10x Visium Spatial Transcriptomics - Auxiliary Files,"Auxiliary data associated with spot/slide analysis (aligned Images, quality control files, etc)  from Spatial Transcriptomics.",,"Component, Filename, File Format, HTAN Data File ID, HTAN Parent Biospecimen ID, HTAN Parent Data File ID, Run ID, Visium File Type, Slide ID, Capture Area, Workflow Version, Workflow Link",,FALSE,Spatial Transcriptomics,"10x Visium Spatial Transcriptomics - RNA-seq Level 1, 10x Visium Spatial Transcriptomics - RNA-seq Level 2",,
-10x Visium Spatial Transcriptomics - RNA-seq Level 3,Processed data files based on Spatial Transcriptomics RNA-seq Level 2 and Spatial Transcriptomics Auxiliary files.,,"Component, Filename, File Format, HTAN Data File ID, HTAN Parent Biospecimen ID, HTAN Parent Data File ID, Run ID, Visium File Type, Workflow Version, Workflow Link, Capture Area, Spots under tissue, Mean Reads per Spatial Spot, Median Number Genes per Spatial Spot, Sequencing Saturation, Proportion Reads Mapped, Proportion Reads Mapped to Transcriptome, Median UMI Counts per Spot",,FALSE,Spatial Transcriptomics,"10x Visium Spatial Transcriptomics - RNA-seq Level 2, 10x Visium Spatial Transcriptomics - Auxiliary Files",,
-10x Visium Spatial Transcriptomics - RNA-seq Level 4,Processed data files based on Spatial Transcriptomics RNA-seq Level 3.,,"Component, Filename, File Format, HTAN Data File ID, HTAN Parent Biospecimen ID, HTAN Parent Data File ID, Run ID, Workflow Version, Workflow Link, Visium Workflow Type, Visium Workflow Parameters Description",,FALSE,Spatial Transcriptomics,10x Visium Spatial Transcriptomics - RNA-seq Level 3,,
+10x Visium Spatial Transcriptomics - RNA-seq Level 1,Files contain raw RNA-seq data associated with spot/slide data.,,"Component, Filename, Run ID, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, Read Indicator, Spatial Read1, Spatial Read2, Spatial Library Construction Method, Library Preparation Days from Index, Sequencing Library Construction Days from Index, End Bias, Reverse Transcription Primer, Sequencing Platform, Capture Area, Protocol Link, Slide Version, Slide ID, Image Re-orientation, Permeabilization Time, RIN, DV200",,FALSE,Spatial Transcriptomics,Biospecimen,,
+10x Visium Spatial Transcriptomics - RNA-seq Level 2,Alignment workflows downstream of Spatial Transcriptomics RNA-seq Level 1.,,"Component, Filename, File Format, Checksum,HTAN Parent Data File ID, HTAN Data File ID, UMI Tag, Whitelist Spatial Barcode File Link, Spatial Barcode Tag, Applied Hard Trimming, Workflow Version, Workflow Link, Genomic Reference, Genomic Reference URL, Genome Annotation URL, HTAN Parent Biospecimen ID, Run ID, Capture Area",,FALSE,Spatial Transcriptomics,10x Visium Spatial Transcriptomics - RNA-seq Level 1,,
+10x Visium Spatial Transcriptomics - Auxiliary Files,"Auxiliary data associated with spot/slide analysis (aligned Images, quality control files, etc)  from Spatial Transcriptomics.",,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Parent Data File ID, HTAN Data File ID, Run ID, Visium File Type, Slide ID, Capture Area, Workflow Version, Workflow Link",,FALSE,Spatial Transcriptomics,"10x Visium Spatial Transcriptomics - RNA-seq Level 1, 10x Visium Spatial Transcriptomics - RNA-seq Level 2",,
+10x Visium Spatial Transcriptomics - RNA-seq Level 3,Processed data files based on Spatial Transcriptomics RNA-seq Level 2 and Spatial Transcriptomics Auxiliary files.,,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Parent Data File ID, HTAN Data File ID, Run ID, Visium File Type, Workflow Version, Workflow Link, Capture Area, Spots under tissue, Mean Reads per Spatial Spot, Median Number Genes per Spatial Spot, Sequencing Saturation, Proportion Reads Mapped, Proportion Reads Mapped to Transcriptome, Median UMI Counts per Spot",,FALSE,Spatial Transcriptomics,"10x Visium Spatial Transcriptomics - RNA-seq Level 2, 10x Visium Spatial Transcriptomics - Auxiliary Files",,
+10x Visium Spatial Transcriptomics - RNA-seq Level 4,Processed data files based on Spatial Transcriptomics RNA-seq Level 3.,,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Parent Data File ID, HTAN Data File ID, Run ID, Workflow Version, Workflow Link, Visium Workflow Type, Visium Workflow Parameters Description",,FALSE,Spatial Transcriptomics,10x Visium Spatial Transcriptomics - RNA-seq Level 3,,
 Visium File Type,The file type generated for the visium experiment.,"reference png, reference jpg, json scale factors, probe dataset csv, qc result html, filtered mex, unfiltered mex, tissue_positions, barcodes, features, fiducial image png, fiducial image jpg, detected image png, detected jpg, high res image, low res image, json scale factors, probe dataset csv",,,TRUE,Spatial Transcriptomics,,,
 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,,,

diff --git a/HTAN.model.jsonld b/HTAN.model.jsonld
@@ -39236,10 +39236,10 @@
                     "@id": "bts:FileFormat"
                 },
                 {
-                    "@id": "bts:HTANDataFileID"
+                    "@id": "bts:HTANParentBiospecimenID"
                 },
                 {
-                    "@id": "bts:HTANParentBiospecimenID"
+                    "@id": "bts:HTANDataFileID"
                 },
                 {
                     "@id": "bts:ReadIndicator"
@@ -39462,10 +39462,10 @@
                     "@id": "bts:Checksum"
                 },
                 {
-                    "@id": "bts:HTANDataFileID"
+                    "@id": "bts:HTANParentDataFileID"
                 },
                 {
-                    "@id": "bts:HTANParentDataFileID"
+                    "@id": "bts:HTANDataFileID"
                 },
                 {
                     "@id": "bts:UMITag"
@@ -39556,15 +39556,15 @@
                 {
                     "@id": "bts:FileFormat"
                 },
-                {
-                    "@id": "bts:HTANDataFileID"
-                },
                 {
                     "@id": "bts:HTANParentBiospecimenID"
                 },
                 {
                     "@id": "bts:HTANParentDataFileID"
                 },
+                {
+                    "@id": "bts:HTANDataFileID"
+                },
                 {
                     "@id": "bts:RunID"
                 },
@@ -39686,15 +39686,15 @@
                 {
                     "@id": "bts:FileFormat"
                 },
-                {
-                    "@id": "bts:HTANDataFileID"
-                },
                 {
                     "@id": "bts:HTANParentBiospecimenID"
                 },
                 {
                     "@id": "bts:HTANParentDataFileID"
                 },
+                {
+                    "@id": "bts:HTANDataFileID"
+                },
                 {
                     "@id": "bts:RunID"
                 },
@@ -39836,15 +39836,15 @@
                 {
                     "@id": "bts:FileFormat"
                 },
-                {
-                    "@id": "bts:HTANDataFileID"
-                },
                 {
                     "@id": "bts:HTANParentBiospecimenID"
                 },
                 {
                     "@id": "bts:HTANParentDataFileID"
                 },
+                {
+                    "@id": "bts:HTANDataFileID"
+                },
                 {
                     "@id": "bts:RunID"
                 },