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Merge pull request #380 from ncihtan/data-model-updates-for-Xenium-RFC
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Data Model Updates for Xenium RFC
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@adamjtaylor
adamjtaylor authored Apr 29, 2024
2 parents ce386f5 + 028fbe6 commit 9a82965
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15 changes: 13 additions & 2 deletions HTAN.model.csv
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Expand Up @@ -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",,,
Expand Down Expand Up @@ -161,6 +161,17 @@ 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,,
Expand Down Expand Up @@ -1011,4 +1022,4 @@ Tile overlap Y,Percentage of image overlap to allow tile stitching in x directio
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,,,
Single Nucleus Capture,Nuclei isolation method,"Plates, 10x, droplet",,,FALSE,scmC-seq Level 1,,,
256 changes: 255 additions & 1 deletion HTAN.model.jsonld
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Expand Up @@ -41487,7 +41487,7 @@
{
"@id": "bts:ROIname",
"@type": "rdfs:Class",
"rdfs:comment": "ROI name (application generated)",
"rdfs:comment": "ROI name (application generated). For Xenium this is referred to as the “region name”",
"rdfs:label": "ROIname",
"rdfs:subClassOf": [
{
Expand Down Expand Up @@ -43217,6 +43217,260 @@
],
"sms:validationRules": []
},
{
"@id": "bts:10XGenomicsXeniumISSExperiment",
"@type": "rdfs:Class",
"rdfs:comment": "All data pertaining to the 10X Genomics Xenium In-Situ Hybridization experiment",
"rdfs:label": "10XGenomicsXeniumISSExperiment",
"rdfs:subClassOf": [
{
"@id": "bts:SpatialTranscriptomics"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "10X Genomics Xenium ISS Experiment",
"sms:required": "sms:false",
"sms:requiresComponent": [
{
"@id": "bts:Biospecimen"
}
],
"sms:requiresDependency": [
{
"@id": "bts:Component"
},
{
"@id": "bts:Filename"
},
{
"@id": "bts:FileFormat"
},
{
"@id": "bts:HTANParentBiospecimenID"
},
{
"@id": "bts:HTANDataFileID"
},
{
"@id": "bts:XeniumBundleContents"
},
{
"@id": "bts:SlideID"
},
{
"@id": "bts:ROIname"
},
{
"@id": "bts:PanelName"
},
{
"@id": "bts:ProtocolLink"
},
{
"@id": "bts:SoftwareandVersion"
},
{
"@id": "bts:TotalNumberofCells"
},
{
"@id": "bts:TotalNumberofTargets"
},
{
"@id": "bts:Surfacearea"
},
{
"@id": "bts:ExperimentIFChannels"
},
{
"@id": "bts:TranscriptsperCell"
},
{
"@id": "bts:PercentofTranscriptswithinCells"
},
{
"@id": "bts:DecodedTranscripts"
},
{
"@id": "bts:XeniumIFimageHTANFileID"
},
{
"@id": "bts:XeniumHEimageHTANFileID"
}
],
"sms:validationRules": []
},
{
"@id": "bts:XeniumBundleContents",
"@type": "rdfs:Class",
"rdfs:comment": "A comma separated list of filenames within the Xenium bundle zip file",
"rdfs:label": "XeniumBundleContents",
"rdfs:subClassOf": [
{
"@id": "bts:SpatialTranscriptomics"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "Xenium Bundle Contents",
"sms:required": "sms:true",
"sms:validationRules": []
},
{
"@id": "bts:PanelName",
"@type": "rdfs:Class",
"rdfs:comment": "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))",
"rdfs:label": "PanelName",
"rdfs:subClassOf": [
{
"@id": "bts:SpatialTranscriptomics"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "Panel Name",
"sms:required": "sms:true",
"sms:validationRules": []
},
{
"@id": "bts:TotalNumberofCells",
"@type": "rdfs:Class",
"rdfs:comment": "The total number of cells analyzed on the flow cell",
"rdfs:label": "TotalNumberofCells",
"rdfs:subClassOf": [
{
"@id": "bts:SpatialTranscriptomics"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "Total Number of Cells",
"sms:required": "sms:true",
"sms:validationRules": []
},
{
"@id": "bts:TotalNumberofTargets",
"@type": "rdfs:Class",
"rdfs:comment": "Refers to the target of an assay. Can be genes/transcripts or probes",
"rdfs:label": "TotalNumberofTargets",
"rdfs:subClassOf": [
{
"@id": "bts:SpatialTranscriptomics"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "Total Number of Targets",
"sms:required": "sms:true",
"sms:validationRules": []
},
{
"@id": "bts:ExperimentIFChannels",
"@type": "rdfs:Class",
"rdfs:comment": "A comma-separated list with any number of channels the user deems appropriate(Example: PanCK, CD45, CD3, DAPI)",
"rdfs:label": "ExperimentIFChannels",
"rdfs:subClassOf": [
{
"@id": "bts:SpatialTranscriptomics"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "Experiment IF Channels",
"sms:required": "sms:true",
"sms:validationRules": []
},
{
"@id": "bts:TranscriptsperCell",
"@type": "rdfs:Class",
"rdfs:comment": "Mean or Median transcript count per cell analyzed on the flow cell or slide",
"rdfs:label": "TranscriptsperCell",
"rdfs:subClassOf": [
{
"@id": "bts:SpatialTranscriptomics"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "Transcripts per Cell",
"sms:required": "sms:true",
"sms:validationRules": []
},
{
"@id": "bts:PercentofTranscriptswithinCells",
"@type": "rdfs:Class",
"rdfs:comment": "The percentage of transcripts assigned to assayed cells",
"rdfs:label": "PercentofTranscriptswithinCells",
"rdfs:subClassOf": [
{
"@id": "bts:SpatialTranscriptomics"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "Percent of Transcripts within Cells",
"sms:required": "sms:true",
"sms:validationRules": []
},
{
"@id": "bts:DecodedTranscripts",
"@type": "rdfs:Class",
"rdfs:comment": "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).",
"rdfs:label": "DecodedTranscripts",
"rdfs:subClassOf": [
{
"@id": "bts:SpatialTranscriptomics"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "Decoded Transcripts",
"sms:required": "sms:true",
"sms:validationRules": []
},
{
"@id": "bts:XeniumIFimageHTANFileID",
"@type": "rdfs:Class",
"rdfs:comment": "The HTAN Data File ID of a Imaging Level 2 file",
"rdfs:label": "XeniumIFimageHTANFileID",
"rdfs:subClassOf": [
{
"@id": "bts:SpatialTranscriptomics"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "Xenium IF image HTAN File ID",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:XeniumHEimageHTANFileID",
"@type": "rdfs:Class",
"rdfs:comment": "The HTAN Data File ID of a Imaging Level 2 file",
"rdfs:label": "XeniumHEimageHTANFileID",
"rdfs:subClassOf": [
{
"@id": "bts:SpatialTranscriptomics"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "Xenium HE image HTAN File ID",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:RPPALevel2",
"@type": "rdfs:Class",
Expand Down

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