Merge pull request #303 from ncihtan/302-sequencing-saturation-mapq30…

…-not-defined-as-an-attribute
ncihtan · Sep 28, 2023 · 977b782 · 977b782
2 parents da1b30e + 39ea488
commit 977b782
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Showing 2 changed files with 5 additions and 19 deletions.
diff --git a/HTAN.model.csv b/HTAN.model.csv
@@ -135,7 +135,7 @@ Positive norm factor,The Positive Control Normalization factor calculated using
 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",,,
 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,,,
+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,,,
 Slide name,"Similar to a Run ID, the slide name indicates the slide a given ROI is linked to (as reported in Segment Summary).",,,,FALSE,NanoString GeoMx DSP ROI DCC Segment Annotation Metadata,,,
 Raw reads,Reads not yet analyzed in any way to be used for data analysis. The number of reads that pass filter from the flow cell represented in the FASTQ file. ,,,,FALSE,NanoString GeoMx DSP ROI DCC Segment Annotation Metadata,,,
 Stitched reads,"Represents consensus from the overlapping sequence of read 1 and 2. This is a % of the aligned reads that were overlapped and consensus confirmed, usually upward of 80% but less in terms of number of reads than aligned reads",,,,FALSE,NanoString GeoMx DSP ROI DCC Segment Annotation Metadata,,,

diff --git a/HTAN.model.jsonld b/HTAN.model.jsonld
@@ -9650,7 +9650,10 @@
                     "@id": "bts:Nucleicount"
                 },
                 {
-                    "@id": "bts:SequencingSaturationMapQ30"
+                    "@id": "bts:SequencingSaturation"
+                },
+                {
+                    "@id": "bts:MapQ30"
                 },
                 {
                     "@id": "bts:Rawreads"
@@ -52747,23 +52750,6 @@
             "sms:required": "sms:false",
             "sms:validationRules": []
         },
-        {
-            "@id": "bts:SequencingSaturationMapQ30",
-            "@type": "rdfs:Class",
-            "rdfs:comment": "TBD",
-            "rdfs:label": "SequencingSaturationMapQ30",
-            "rdfs:subClassOf": [
-                {
-                    "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata"
-                }
-            ],
-            "schema:isPartOf": {
-                "@id": "http://schema.biothings.io"
-            },
-            "sms:displayName": "Sequencing Saturation MapQ30",
-            "sms:required": "sms:false",
-            "sms:validationRules": []
-        },
         {
             "@id": "bts:Yes",
             "@type": "rdfs:Class",