Add Oxford Nanopore (#411)

* Add Oxford Nanopore * Rebuild NF.jsonld, json * Add prep kit * Rebuild NF.jsonld, json --------- Co-authored-by: nf-osi[bot] <nf-osi@sagebionetworks.org>
nf-osi · Mar 20, 2024 · 8a7e811 · 8a7e811
1 parent b27fad3
commit 8a7e811
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diff --git a/NF.jsonld b/NF.jsonld
@@ -4945,6 +4945,8 @@
       "@id" : "bts:TruSeq"
     }, {
       "@id" : "bts:TruSeqstandardtotalRNAlibrarykit"
+    }, {
+      "@id" : "bts:OxfordNanoporeDirectRNASequencingKit"
     }, {
       "@id" : "bts:unknown"
     } ],
@@ -9623,6 +9625,10 @@
       "@id" : "bts:VarioskanLUX"
     }, {
       "@id" : "bts:Panorama1.0T"
+    }, {
+      "@id" : "bts:OxfordNanopore"
+    }, {
+      "@id" : "bts:OtherPlatform"
     }, {
       "@id" : "bts:NotApplicable"
     } ],
@@ -9685,6 +9691,17 @@
     },
     "sms:displayName" : "sNF94.3",
     "sms:required" : "sms:false"
+  }, {
+    "@id" : "bts:OtherPlatform",
+    "@type" : "rdfs:Class",
+    "rdfs:comment" : "TBD",
+    "rdfs:label" : "OtherPlatform",
+    "rdfs:subClassOf" : [ ],
+    "schema:isPartOf" : {
+      "@id" : "http://schema.biothings.io/"
+    },
+    "sms:displayName" : "Other Platform",
+    "sms:required" : "sms:false"
   }, {
     "@id" : "bts:unilateral",
     "@type" : "rdfs:Class",
@@ -18507,6 +18524,17 @@
     },
     "sms:displayName" : "University of South Dakota",
     "sms:required" : "sms:false"
+  }, {
+    "@id" : "bts:OxfordNanopore",
+    "@type" : "rdfs:Class",
+    "rdfs:comment" : "TBD",
+    "rdfs:label" : "OxfordNanopore",
+    "rdfs:subClassOf" : [ ],
+    "schema:isPartOf" : {
+      "@id" : "http://schema.biothings.io/"
+    },
+    "sms:displayName" : "Oxford Nanopore",
+    "sms:required" : "sms:false"
   }, {
     "@id" : "bts:EnVision2103MultiplateReader",
     "@type" : "rdfs:Class",
@@ -22808,6 +22836,17 @@
     },
     "sms:displayName" : "jpg",
     "sms:required" : "sms:false"
+  }, {
+    "@id" : "bts:OxfordNanoporeDirectRNASequencingKit",
+    "@type" : "rdfs:Class",
+    "rdfs:comment" : "TBD",
+    "rdfs:label" : "OxfordNanoporeDirectRNASequencingKit",
+    "rdfs:subClassOf" : [ ],
+    "schema:isPartOf" : {
+      "@id" : "http://schema.biothings.io/"
+    },
+    "sms:displayName" : "Oxford Nanopore Direct RNA Sequencing Kit",
+    "sms:required" : "sms:false"
   }, {
     "@id" : "bts:GermlineVariants",
     "@type" : "rdfs:Class",

diff --git a/modules/Assay/Parameter.yaml b/modules/Assay/Parameter.yaml
@@ -108,6 +108,9 @@ enums:
       TruSeq standard total RNA library kit:
         description: ''
         source: https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/truseq-stranded-total-rna.html
+      Oxford Nanopore Direct RNA Sequencing Kit:
+        description: Vendor catalog SQK-RNA004.
+        source: https://store.nanoporetech.com/us/sequencing-kits.html 
       unknown: 
         description: information not provided
   MRISequenceEnum:

diff --git a/modules/Assay/Platform.yaml b/modules/Assay/Platform.yaml
@@ -216,5 +216,9 @@ enums:
         source: https://www.thermofisher.com/us/en/home/life-science/lab-equipment/microplate-instruments/plate-readers/models/varioskan.html
       Panorama 1.0T:
         description: A conventional MRI scanner from Philips.
+      Oxford Nanopore:
+        description: Nanopore sequencing allows a much larger read length range, with easy prep from native or amplified DNA and RNA.
+        source: https://nanoporetech.com/platform
+      Other Platform:
       Not Applicable:
         description: ''