Merge pull request #385 from ncihtan/scRNAseq-updates-374

374-Library-Construction-Updates
ncihtan · Apr 19, 2024 · a970f6e · a970f6e
2 parents 62cc25d + 8988535
commit a970f6e
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Showing 2 changed files with 82 additions and 2 deletions.
diff --git a/HTAN.model.csv b/HTAN.model.csv
@@ -287,7 +287,7 @@ Median UMIs per Cell Number,Number,,,,TRUE,scRNA-seq Level 1,,,
 Cell Median Number Reads,Median number of reads per cell. Number,,,,TRUE,scRNA-seq Level 3,,,
 Cell Median Number Genes,Median number of genes detected per cell. Number,,,,TRUE,scRNA-seq Level 3,,,
 Cell Total,Number of sequenced  cells. Applies to raw counts matrix only.,,,,TRUE,scRNA-seq Level 3,,,
-Library Construction Method,Process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors [OBI_0000711],"Smart-seq2, Smart-SeqV4, 10xV1.0, 10xV1.1, 10xV2, 10xV3,10xV3.1, CEL-seq2, Drop-seq, inDropsV2, inDropsV3, TruDrop, sci-ATAC-seq, Nextera XT",,,TRUE,Sequencing,,http://purl.obolibrary.org/obo/OBI_0000711,
+Library Construction Method,Process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors [OBI_0000711],"Smart-seq2, Smart-SeqV4, 10xV1.0, 10xV1.1, 10xV2, 10xV3,10xV3.1, CEL-seq2, Drop-seq, inDropsV2, inDropsV3, TruDrop, sci-ATAC-seq, Nextera XT, 10x Multiome, 10x FLEX, 10x GEM 3', 10x GEM 5'",,,TRUE,Sequencing,,http://purl.obolibrary.org/obo/OBI_0000711,
 Input Cells and Nuclei,"Number of cells and number of nuclei input; entry format: number, number",,,,TRUE,scRNA-seq Level 1,,,
 CEL-seq2,Highly-multiplexed plate-based single-cell RNA-Seq assay,,"Empty Well Barcode, Well Index",,FALSE,scRNA-seq Level 1,,,
 Empty Well Barcode,Unique cell barcode assigned to empty cells used as controls in CEL-seq2 assays.,,,,TRUE,scRNA-seq Level 1,,,
@@ -1011,4 +1011,4 @@ 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,,,
diff --git a/HTAN.model.jsonld b/HTAN.model.jsonld
@@ -30198,6 +30198,18 @@
                 },
                 {
                     "@id": "bts:NexteraXT"
+                },
+                {
+                    "@id": "bts:10xMultiome"
+                },
+                {
+                    "@id": "bts:10xFLEX"
+                },
+                {
+                    "@id": "bts:10xGEM3'"
+                },
+                {
+                    "@id": "bts:10xGEM5'"
                 }
             ],
             "sms:displayName": "Library Construction Method",
@@ -49346,6 +49358,74 @@
             "sms:required": "sms:false",
             "sms:validationRules": []
         },
+        {
+            "@id": "bts:10xMultiome",
+            "@type": "rdfs:Class",
+            "rdfs:comment": "TBD",
+            "rdfs:label": "10xMultiome",
+            "rdfs:subClassOf": [
+                {
+                    "@id": "bts:LibraryConstructionMethod"
+                }
+            ],
+            "schema:isPartOf": {
+                "@id": "http://schema.biothings.io"
+            },
+            "sms:displayName": "10x Multiome",
+            "sms:required": "sms:false",
+            "sms:validationRules": []
+        },
+        {
+            "@id": "bts:10xFLEX",
+            "@type": "rdfs:Class",
+            "rdfs:comment": "TBD",
+            "rdfs:label": "10xFLEX",
+            "rdfs:subClassOf": [
+                {
+                    "@id": "bts:LibraryConstructionMethod"
+                }
+            ],
+            "schema:isPartOf": {
+                "@id": "http://schema.biothings.io"
+            },
+            "sms:displayName": "10x FLEX",
+            "sms:required": "sms:false",
+            "sms:validationRules": []
+        },
+        {
+            "@id": "bts:10xGEM3'",
+            "@type": "rdfs:Class",
+            "rdfs:comment": "TBD",
+            "rdfs:label": "10xGEM3'",
+            "rdfs:subClassOf": [
+                {
+                    "@id": "bts:LibraryConstructionMethod"
+                }
+            ],
+            "schema:isPartOf": {
+                "@id": "http://schema.biothings.io"
+            },
+            "sms:displayName": "10x GEM 3'",
+            "sms:required": "sms:false",
+            "sms:validationRules": []
+        },
+        {
+            "@id": "bts:10xGEM5'",
+            "@type": "rdfs:Class",
+            "rdfs:comment": "TBD",
+            "rdfs:label": "10xGEM5'",
+            "rdfs:subClassOf": [
+                {
+                    "@id": "bts:LibraryConstructionMethod"
+                }
+            ],
+            "schema:isPartOf": {
+                "@id": "http://schema.biothings.io"
+            },
+            "sms:displayName": "10x GEM 5'",
+            "sms:required": "sms:false",
+            "sms:validationRules": []
+        },
         {
             "@id": "bts:EmptyWellBarcode",
             "@type": "rdfs:Class",