Adding output type to sequencing experiment resource.

kids-first · Sep 11, 2020 · f0ee420 · f0ee420
1 parent ec8431b
commit f0ee420
Show file tree

Hide file tree

Showing 3 changed files with 135 additions and 0 deletions.
diff --git a/site_root/input/resources/examples/Task-se-001.json b/site_root/input/resources/examples/Task-se-001.json
@@ -151,5 +151,81 @@
         ]
       }
     }
+  ],
+  "output": [
+    {
+      "type": {
+        "coding": [
+          {
+            "system": "http://fhir.kids-first.io/CodeSystem/sequencing-experiment-ouput-type",
+            "code": "genomic-file",
+            "display": "Genomic File"
+          }
+        ]
+      },
+      "valueReference": {
+        "reference": "DocumentReference/ge-001"
+      }
+    },
+    {
+      "type": {
+        "coding": [
+          {
+            "system": "http://fhir.kids-first.io/CodeSystem/sequencing-experiment-ouput-type",
+            "code": "max-insert-size",
+            "display": "Max Insert Size"
+          }
+        ]
+      },
+      "valueInteger": 999
+    },
+    {
+      "type": {
+        "coding": [
+          {
+            "system": "http://fhir.kids-first.io/CodeSystem/sequencing-experiment-ouput-type",
+            "code": "mean-depth",
+            "display": "Mean Depth"
+          }
+        ]
+      },
+      "valueInteger": 104
+    },
+    {
+      "type": {
+        "coding": [
+          {
+            "system": "http://fhir.kids-first.io/CodeSystem/sequencing-experiment-ouput-type",
+            "code": "mean-insert-size",
+            "display": "Mean Insert Size"
+          }
+        ]
+      },
+      "valueInteger": 105
+    },
+    {
+      "type": {
+        "coding": [
+          {
+            "system": "http://fhir.kids-first.io/CodeSystem/sequencing-experiment-ouput-type",
+            "code": "mean-read-length",
+            "display": "Mean Read Length"
+          }
+        ]
+      },
+      "valueInteger": 107
+    },
+    {
+      "type": {
+        "coding": [
+          {
+            "system": "http://fhir.kids-first.io/CodeSystem/sequencing-experiment-ouput-type",
+            "code": "total-reads",
+            "display": "Total Reads"
+          }
+        ]
+      },
+      "valueInteger": 99
+    }
   ]
 }
diff --git a/site_root/input/resources/terminology/CodeSystem-sequencing-experiment-output-type.json b/site_root/input/resources/terminology/CodeSystem-sequencing-experiment-output-type.json
@@ -0,0 +1,40 @@
+{
+  "resourceType": "CodeSystem",
+  "id": "sequencing-experiment-output-type",
+  "url": "http://fhir.kids-first.io/CodeSystem/sequencing-experiment-output-type",
+  "version": "0.1.0",
+  "name": "sequencing-experiment-output-type",
+  "title": "Sequencing Experiment Output Type",
+  "status": "draft",
+  "experimental": false,
+  "publisher": "Kids First DRC",
+  "description": "Output Type of the Kids First DRC Sequencing Experiment.",
+  "caseSensitive": true,
+  "content": "fragment",
+  "concept": [
+    {
+      "code": "genomic-file",
+      "display": "Genomic File"
+    },
+    {
+      "code": "max-insert-size",
+      "display": "Max Insert Size"
+    },
+    {
+      "code": "mean-depth",
+      "display": "Mean Depth"
+    },
+    {
+      "code": "mean-insert-size",
+      "display": "Mean Insert Size"
+    },
+    {
+      "code": "mean-read-length",
+      "display": "Mean Read Length" 
+    },
+    {
+      "code": "total-reads",
+      "display": "Total Reads" 
+    }
+  ]
+}
diff --git a/site_root/input/resources/terminology/ValueSet-sequencing-experiment-output-type.json b/site_root/input/resources/terminology/ValueSet-sequencing-experiment-output-type.json
@@ -0,0 +1,19 @@
+{
+    "resourceType": "ValueSet",
+    "id": "sequencing-experiment-output-type",
+    "url": "http://fhir.kids-first.io/ValueSet/sequencing-experiment-output-type",
+    "version": "0.1.0",
+    "name": "sequencing-experiment-output-type",
+    "title": "Sequencing Experiment Output Type",
+    "status": "draft",
+    "experimental": false,
+    "publisher": "Kids First DRC",
+    "description": "Output Type of the Kids First DRC Sequencing Experiment.",
+    "compose": {
+      "include": [
+        {
+          "system": "http://fhir.kids-first.io/CodeSystem/sequencing-experiment-output-type"
+        }
+      ]
+    }
+  }