Merge pull request #402 from ncihtan/399-bulkrnaseq-level-2-updates-t…

…o-accommodate-salmon-files

Add sf to file format

HTAN.model.csv

@@ -6,7 +6,7 @@ Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1,
 Patient,HTAN patient,,"Component, HTAN Participant ID",,FALSE,Individual Organism,"Demographics, Family History, Exposure, Follow Up, Diagnosis, Therapy, Molecular Test",,
 File,A type of Information Content Entity specific to OS,,,,FALSE,Information Content Entity,,https://w3id.org/biolink/vocab/DataFile,
 Filename,Name of a file,,,,TRUE,,,,regex search ^.+\/\S*$
-File Format,"Format of a file (e.g. txt, csv, fastq, bam, etc.)","hdf5, bedgraph, idx, idat, bam, bai, excel, powerpoint, tif, tiff, OME-TIFF, png, doc, pdf, fasta, fastq, sam, vcf, bcf, maf, bed, chp, cel, sif, tsv, csv, txt, plink, bigwig, wiggle, gct, bgzip, zip, seg, html, mov, hyperlink, svs, md, flagstat, gtf, raw, msf, rmd, bed narrowPeak, bed broadPeak, bed gappedPeak, avi, pzfx, fig, xml, tar, R script, abf, bpm, dat, jpg, locs, Sentrix descriptor file, Python script, sav, gzip, sdf, RData, hic, ab1, 7z, gff3, json, sqlite, svg, sra, recal, tranches, mtx, tagAlign, dup, DICOM, czi, mex, cloupe, am, cell am, mpg, m, mzML,scn, dcc, rcc, pkc",,,TRUE,,,,
+File Format,"Format of a file (e.g. txt, csv, fastq, bam, etc.)","hdf5, bedgraph, idx, idat, bam, bai, excel, powerpoint, tif, tiff, OME-TIFF, png, doc, pdf, fasta, fastq, sam, vcf, bcf, maf, bed, chp, cel, sif, tsv, csv, txt, plink, bigwig, wiggle, gct, bgzip, zip, seg, html, mov, hyperlink, svs, md, flagstat, gtf, raw, msf, rmd, bed narrowPeak, bed broadPeak, bed gappedPeak, avi, pzfx, fig, xml, tar, R script, abf, bpm, dat, jpg, locs, Sentrix descriptor file, Python script, sav, gzip, sdf, RData, hic, ab1, 7z, gff3, json, sqlite, svg, sra, recal, tranches, mtx, tagAlign, dup, DICOM, czi, mex, cloupe, am, cell am, mpg, m, mzML,scn, dcc, rcc, pkc, sf",,,TRUE,,,,
 Checksum,MD5 checksum of the BAM file,,,,TRUE,Information Content Entity,,,
 HTAN Data File ID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),,,,TRUE,File,,https://docs.google.com/document/d/1podtPP8L1UNvVxx9_c_szlDcU1f8n7bige6XA_GoRVM/edit?usp=sharing,regex match ^(HTA([1-9]|1[0-6]))_((EXT)?([0-9]\d*|0000))_([0-9]\d*|0000)$ warning
 HTAN Participant ID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),,,,TRUE,Patient,,https://docs.google.com/document/d/1podtPP8L1UNvVxx9_c_szlDcU1f8n7bige6XA_GoRVM/edit?usp=sharing,regex match ^(HTA([1-9]|1[0-6]))_((EXT)?([0-9]\d*|0000))$ warning
@@ -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). 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",,,
+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",,,
@@ -161,7 +161,7 @@ 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,,
+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,,,
@@ -176,7 +176,7 @@ RPPA Level 2,Array based protemics. Each dilution curve of spot intensities is f
 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,,
+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,,,

HTAN.model.jsonld

@@ -1291,6 +1291,9 @@
                 },
                 {
                     "@id": "bts:Pkc"
+                },
+                {
+                    "@id": "bts:Sf"
                 }
             ],
             "sms:displayName": "File Format",
@@ -2836,6 +2839,23 @@
             "sms:required": "sms:false",
             "sms:validationRules": []
         },
+        {
+            "@id": "bts:Sf",
+            "@type": "rdfs:Class",
+            "rdfs:comment": "TBD",
+            "rdfs:label": "Sf",
+            "rdfs:subClassOf": [
+                {
+                    "@id": "bts:FileFormat"
+                }
+            ],
+            "schema:isPartOf": {
+                "@id": "http://schema.biothings.io"
+            },
+            "sms:displayName": "sf",
+            "sms:required": "sms:false",
+            "sms:validationRules": []
+        },
         {
             "@id": "bts:Checksum",
             "@type": "rdfs:Class",