Merge branch 'main' into data-model-updates-for-Xenium-RFC

ncihtan · Apr 29, 2024 · 2e22eb3 · 2e22eb3
2 parents f731914 + ce386f5
commit 2e22eb3
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Showing 2 changed files with 45 additions and 5 deletions.
diff --git a/HTAN.model.csv b/HTAN.model.csv
@@ -315,7 +315,7 @@ Feature Reference Id,"Unique ID for this feature. Must not contain whitespace, q
 Spike In,A set of known synthetic RNA molecules with known sequence that are added to the cell lysis mix,"ERCC, Other Spike In, No Spike In, PhiX",,,TRUE,scRNA-seq Level 1,,,
 ERCC,The External RNA Controls Consortium (ERCC) spike in set is commonly used in single-cell experiments for normalization,,Spike In Concentration,,FALSE,Spike In,,,
 Spike In Concentration,The final concentration or dilution (for commercial sets) of the spike in mix [PMID:21816910],,,,TRUE,ERCC,,https://www.ncbi.nlm.nih.gov/pubmed/21816910,
-Sequencing Platform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,"Illumina Next Seq 500, Illumina Next Seq 550, Illumina Next Seq 2500, Illumina NovaSeq 6000,  Illumina MiSeq, 454 GS FLX Titanium, AB SOLiD 4, AB SOLiD 2, AB SOLiD 3, Complete Genomics, Illumina HiSeq X Ten, Illumina HiSeq X Five, Illumina Genome Analyzer II, Illumina Genome Analyzer IIx, Illumina HiSeq 2000, Illumina HiSeq 2500, Illumina HiSeq 4000, Illumina MiSeq, Illumina NextSeq, Ion Torrent PGM, Ion Torrent Proton, Ion Torrent S5, PacBio RS, NovaSeq 6000, NovaSeqS4, Ultima Genomics UG100, Oxford Nanopore minION, GridION, PromethION, PacBio Sequel2, Revio, Other, unknown, Not Reported",,,TRUE,Device,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group,
+Sequencing Platform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,"Illumina Next Seq 500, Illumina Next Seq 550, Illumina Next Seq 2500, Illumina NovaSeq 6000,  Illumina MiSeq, 454 GS FLX Titanium, AB SOLiD 4, AB SOLiD 2, AB SOLiD 3, Complete Genomics, Illumina HiSeq X Ten, Illumina HiSeq X Five, Illumina Genome Analyzer II, Illumina Genome Analyzer IIx, Illumina HiSeq 2000, Illumina HiSeq 2500, Illumina HiSeq 4000, Illumina MiSeq, Illumina NextSeq, Ion Torrent PGM, Ion Torrent Proton, Ion Torrent S5, PacBio RS, NovaSeq 6000, NovaSeqS4, Ultima Genomics UG100, Oxford Nanopore minION, GridION, PromethION, PacBio Sequel2, Revio, Illumina NextSeq 1000,  Illumina NextSeq 2000, Other, unknown, Not Reported",,,TRUE,Device,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group,
 Technical Replicate Group,A common term for all files belonging to the same cell or library. Provide a numbering of each library prep batch (can differ from encapsulation and sequencing batch),,,,FALSE,Sequencing,,,
 Total Number of Input Cells,Number of cells loaded/placed on plates,,,,TRUE,Sequencing,,,
 Sequencing Batch ID,Links samples to a specific local sequencer run. Can be string or 'null',,,,TRUE,Sequencing,,,

diff --git a/HTAN.model.jsonld b/HTAN.model.jsonld
@@ -30514,6 +30514,12 @@
                 {
                     "@id": "bts:Revio"
                 },
+                {
+                    "@id": "bts:IlluminaNextSeq1000"
+                },
+                {
+                    "@id": "bts:IlluminaNextSeq2000"
+                },
                 {
                     "@id": "bts:Other"
                 },
@@ -50489,6 +50495,40 @@
             "sms:required": "sms:false",
             "sms:validationRules": []
         },
+        {
+            "@id": "bts:IlluminaNextSeq1000",
+            "@type": "rdfs:Class",
+            "rdfs:comment": "TBD",
+            "rdfs:label": "IlluminaNextSeq1000",
+            "rdfs:subClassOf": [
+                {
+                    "@id": "bts:SequencingPlatform"
+                }
+            ],
+            "schema:isPartOf": {
+                "@id": "http://schema.biothings.io"
+            },
+            "sms:displayName": "Illumina NextSeq 1000",
+            "sms:required": "sms:false",
+            "sms:validationRules": []
+        },
+        {
+            "@id": "bts:IlluminaNextSeq2000",
+            "@type": "rdfs:Class",
+            "rdfs:comment": "TBD",
+            "rdfs:label": "IlluminaNextSeq2000",
+            "rdfs:subClassOf": [
+                {
+                    "@id": "bts:SequencingPlatform"
+                }
+            ],
+            "schema:isPartOf": {
+                "@id": "http://schema.biothings.io"
+            },
+            "sms:displayName": "Illumina NextSeq 2000",
+            "sms:required": "sms:false",
+            "sms:validationRules": []
+        },
         {
             "@id": "bts:Unknown",
             "@type": "rdfs:Class",
@@ -51159,10 +51199,10 @@
                     "@id": "bts:AJCCPathologicStage"
                 },
                 {
-                    "@id": "bts:SequencingPlatform"
+                    "@id": "bts:MetastasisatDiagnosisSite"
                 },
                 {
-                    "@id": "bts:MetastasisatDiagnosisSite"
+                    "@id": "bts:SequencingPlatform"
                 },
                 {
                     "@id": "bts:TypeofSmokeExposure"
@@ -51716,10 +51756,10 @@
                     "@id": "bts:AJCCPathologicStage"
                 },
                 {
-                    "@id": "bts:SequencingPlatform"
+                    "@id": "bts:MetastasisatDiagnosisSite"
                 },
                 {
-                    "@id": "bts:MetastasisatDiagnosisSite"
+                    "@id": "bts:SequencingPlatform"
                 },
                 {
                     "@id": "bts:AJCCClinicalT"