Resolving Feedback Issues

KazeemHamzat · KazeemHamzat · commit f02911a0bac6 · 2025-01-21T19:31:09.000Z
Added recommended components to OBS + update Task &amp; DR Resources
diff --git a/DiagnosticReport/DiagnosticReport-GenomicReport-VariantAssessment.json b/DiagnosticReport/DiagnosticReport-GenomicReport-VariantAssessment.json
@@ -102,6 +102,11 @@
           "system": "http://loinc.org",
           "code": "LA6576-8",
           "display": "Positive"
+        },
+        {
+          "system": "http://snomed.info/sct",
+          "code": "699866005",
+          "display": "Brown-Vialetto-Van Laere syndrome"
         }
       ]
     }
diff --git a/Observation/Observation-GenomicsVariantSLC52A2-Example.json b/Observation/Observation-GenomicsVariantSLC52A2-Example.json
@@ -1,6 +1,6 @@
 {
   "resourceType": "Observation",
-  "id": "Observation-GenomicsVariant-SLC52A2",
+  "id": "Observation-GenomicsVariantSLC52A2",
   "meta": {
     "profile": [
       "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
@@ -35,11 +35,6 @@
       {
         "system": "http://loinc.org",
         "code": "69548-6"
-      },
-      {
-        "system": "http://snomed.info/sct",
-        "code": "699866005",
-        "display": "Brown-Vialetto-Van Laere syndrome"
       }
     ]
   },
@@ -82,17 +77,16 @@
         "coding": [
           {
             "system": "http://loinc.org",
-            "code": "48018-6"
+            "code": "48004-6"
           }
-        ],
-        "text": "SLC52A2"
+        ]
       },
       "valueCodeableConcept": {
         "coding": [
           {
-            "system": "http://www.genenames.org/",
-            "code": "HGNC:30224",
-            "display": "SLC52A2"
+            "system": "https://hgvs-nomenclature.org/stable/",
+            "code": "NM_024531.4:c.9163>A p.(Gly306Arg)",
+            "display": "NM_024531.4:c.9163>A p.(Gly306Arg)"
           }
         ]
       }
@@ -102,16 +96,35 @@
         "coding": [
           {
             "system": "http://loinc.org",
-            "code": "53034-5"
+            "code": "81290-9"
           }
         ]
       },
       "valueCodeableConcept": {
+        "coding": [
+          {
+            "system": "https://hgvs-nomenclature.org/stable/",
+            "code": "Chr8:g.1455840683>A",
+            "display": "Chr8:g.1455840683>A"
+          }
+        ]
+      }
+    },
+    {
+      "code": {
         "coding": [
           {
             "system": "http://loinc.org",
-            "code": "LA6705-3",
-            "display": "homozygous"
+            "code": "81252-9"
+          }
+        ]
+      },
+      "valueCodeableConcept": {
+        "coding": [
+          {
+            "system": "http://www.sequenceontology.org",
+            "code": "SO:0001583",
+            "display": "missense_variant"
           }
         ]
       }
@@ -121,16 +134,35 @@
         "coding": [
           {
             "system": "http://loinc.org",
-            "code": "94186-4"
+            "code": "48018-6"
+          }
+        ]
+      },
+      "valueCodeableConcept": {
+        "coding": [
+          {
+            "system": "http://www.genenames.org/",
+            "code": "HGNC:30224",
+            "display": "SLC52A2"
+          }
+        ]
+      }
+    },
+    {
+      "code": {
+        "coding": [
+          {
+            "system": "http://loinc.org",
+            "code": "53034-5"
           }
         ]
       },
       "valueCodeableConcept": {
         "coding": [
           {
             "system": "http://loinc.org",
-            "code": "LA4489-6",
-            "display": "Unknown"
+            "code": "LA6705-3",
+            "display": "homozygous"
           }
         ]
       }
@@ -140,12 +172,18 @@
         "coding": [
           {
             "system": "http://loinc.org",
-            "code": "48001-2"
+            "code": "94186-4"
           }
         ]
       },
       "valueCodeableConcept": {
-        "text": "Biallelic Pathogenic:SLC52A2 missense variant"
+        "coding": [
+          {
+            "system": "http://loinc.org",
+            "code": "LA4489-6",
+            "display": "Unknown"
+          }
+        ]
       }
     },
     {
@@ -164,8 +202,7 @@
             "code": "LA6683-2",
             "display": "Germline"
           }
-        ],
-        "text": "Pathogenic"
+        ]
       }
     }
   ]
diff --git a/Task/Task-GenomicReport-FollowupRecommendation.json b/Task/Task-GenomicReport-FollowupRecommendation.json
@@ -1,27 +1,57 @@
 {
-  "resourceType" : "Task",
-  "id" : "Task-GenomicReport-FollowupRecommendation",
-  "meta" : {
-    "profile" : [
+  "resourceType": "Task",
+  "id": "Task-GenomicReport-FollowupRecommendation",
+  "meta": {
+    "profile": [
       "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/followup-recommendation"
     ]
   },
-  "status" : "requested",
-  "intent" : "proposal",
-  "code" : {
-    "coding" : [
+  "status": "requested",
+  "intent": "proposal",
+  "code": {
+    "coding": [
       {
-        "system" : "http://loinc.org",
-        "code" : "LA14021-2",
-        "display" : "Confirmatory testing recommended"
+        "system": "http://loinc.org",
+        "code": "LA14021-2",
+        "display": "Confirmatory testing recommended"
       }
     ]
   },
-  "description" : "Testing of Pheobe's parents is recommended (via referral to the clinical genetics service) in order to confirm that both are heterozygous carriers of the missense variant.",
-  "for" : {
-    "reference" : "Patient/Patient-PheobeSmitham-Example"
+  "description": "Testing of Pheobe's parents is recommended (via referral to the clinical genetics service) in order to confirm that both are heterozygous carriers of the missense variant.",
+  "for": {
+    "reference": "Patient/Patient-PheobeSmitham-Example"
   },
-  "reasonReference" : {
-    "reference" : "Observation/Observation-GenomicImplication-Therapeutic"
-  }
+  "reasonReference": {
+    "reference": "Observation/Observation-GenomicImplication-Therapeutic"
+  },
+  "input": [
+    {
+      "type": {
+        "coding": [
+          {
+            "system": "http://terminology.hl7.org/CodeSystem/v3-RoleCode",
+            "code": "NFTH",
+            "display": "natural father"
+          }
+        ]
+      },
+      "valueReference": {
+        "reference": "Patient/Patient-PheobeSmithamFather-Example"
+      }
+    },
+    {
+      "type": {
+        "coding": [
+          {
+            "system": "http://terminology.hl7.org/CodeSystem/v3-RoleCode",
+            "code": "NMTH",
+            "display": "natural mother"
+          }
+        ]
+      },
+      "valueReference": {
+        "reference": "Patient/Patient-PheobeSmithamMother-Example"
+      }
+    }
+  ]
 }

Original file line number	Diff line number	Diff line change
`@@ -102,6 +102,11 @@`
`102`	`102`	`"system": "http://loinc.org",`
`103`	`103`	`"code": "LA6576-8",`
`104`	`104`	`"display": "Positive"`
	`105`	`+ },`
	`106`	`+ {`
	`107`	`+ "system": "http://snomed.info/sct",`
	`108`	`+ "code": "699866005",`
	`109`	`+ "display": "Brown-Vialetto-Van Laere syndrome"`
`105`	`110`	`}`
`106`	`111`	`]`
`107`	`112`	`}`
Original file line number	Diff line number	Diff line change
`@@ -1,6 +1,6 @@`
`1`	`1`	`{`
`2`	`2`	`"resourceType": "Observation",`
`3`		`- "id": "Observation-GenomicsVariant-SLC52A2",`
	`3`	`+ "id": "Observation-GenomicsVariantSLC52A2",`
`4`	`4`	`"meta": {`
`5`	`5`	`"profile": [`
`6`	`6`	`"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"`
`@@ -35,11 +35,6 @@`
`35`	`35`	`{`
`36`	`36`	`"system": "http://loinc.org",`
`37`	`37`	`"code": "69548-6"`
`38`		`- },`
`39`		`- {`
`40`		`- "system": "http://snomed.info/sct",`
`41`		`- "code": "699866005",`
`42`		`- "display": "Brown-Vialetto-Van Laere syndrome"`
`43`	`38`	`}`
`44`	`39`	`]`
`45`	`40`	`},`
`@@ -82,17 +77,16 @@`
`82`	`77`	`"coding": [`
`83`	`78`	`{`
`84`	`79`	`"system": "http://loinc.org",`
`85`		`- "code": "48018-6"`
	`80`	`+ "code": "48004-6"`
`86`	`81`	`}`
`87`		`- ],`
`88`		`- "text": "SLC52A2"`
	`82`	`+ ]`
`89`	`83`	`},`
`90`	`84`	`"valueCodeableConcept": {`
`91`	`85`	`"coding": [`
`92`	`86`	`{`
`93`		`- "system": "http://www.genenames.org/",`
`94`		`- "code": "HGNC:30224",`
`95`		`- "display": "SLC52A2"`
	`87`	`+ "system": "https://hgvs-nomenclature.org/stable/",`
	`88`	`+ "code": "NM_024531.4:c.9163>A p.(Gly306Arg)",`
	`89`	`+ "display": "NM_024531.4:c.9163>A p.(Gly306Arg)"`
`96`	`90`	`}`
`97`	`91`	`]`
`98`	`92`	`}`
`@@ -102,16 +96,35 @@`
`102`	`96`	`"coding": [`
`103`	`97`	`{`
`104`	`98`	`"system": "http://loinc.org",`
`105`		`- "code": "53034-5"`
	`99`	`+ "code": "81290-9"`
`106`	`100`	`}`
`107`	`101`	`]`
`108`	`102`	`},`
`109`	`103`	`"valueCodeableConcept": {`
	`104`	`+ "coding": [`
	`105`	`+ {`
	`106`	`+ "system": "https://hgvs-nomenclature.org/stable/",`
	`107`	`+ "code": "Chr8:g.1455840683>A",`
	`108`	`+ "display": "Chr8:g.1455840683>A"`
	`109`	`+ }`
	`110`	`+ ]`
	`111`	`+ }`
	`112`	`+ },`
	`113`	`+ {`
	`114`	`+ "code": {`
`110`	`115`	`"coding": [`
`111`	`116`	`{`
`112`	`117`	`"system": "http://loinc.org",`
`113`		`- "code": "LA6705-3",`
`114`		`- "display": "homozygous"`
	`118`	`+ "code": "81252-9"`
	`119`	`+ }`
	`120`	`+ ]`
	`121`	`+ },`
	`122`	`+ "valueCodeableConcept": {`
	`123`	`+ "coding": [`
	`124`	`+ {`
	`125`	`+ "system": "http://www.sequenceontology.org",`
	`126`	`+ "code": "SO:0001583",`
	`127`	`+ "display": "missense_variant"`
`115`	`128`	`}`
`116`	`129`	`]`
`117`	`130`	`}`
`@@ -121,16 +134,35 @@`
`121`	`134`	`"coding": [`
`122`	`135`	`{`
`123`	`136`	`"system": "http://loinc.org",`
`124`		`- "code": "94186-4"`
	`137`	`+ "code": "48018-6"`
	`138`	`+ }`
	`139`	`+ ]`
	`140`	`+ },`
	`141`	`+ "valueCodeableConcept": {`
	`142`	`+ "coding": [`
	`143`	`+ {`
	`144`	`+ "system": "http://www.genenames.org/",`
	`145`	`+ "code": "HGNC:30224",`
	`146`	`+ "display": "SLC52A2"`
	`147`	`+ }`
	`148`	`+ ]`
	`149`	`+ }`
	`150`	`+ },`
	`151`	`+ {`
	`152`	`+ "code": {`
	`153`	`+ "coding": [`
	`154`	`+ {`
	`155`	`+ "system": "http://loinc.org",`
	`156`	`+ "code": "53034-5"`
`125`	`157`	`}`
`126`	`158`	`]`
`127`	`159`	`},`
`128`	`160`	`"valueCodeableConcept": {`
`129`	`161`	`"coding": [`
`130`	`162`	`{`
`131`	`163`	`"system": "http://loinc.org",`
`132`		`- "code": "LA4489-6",`
`133`		`- "display": "Unknown"`
	`164`	`+ "code": "LA6705-3",`
	`165`	`+ "display": "homozygous"`
`134`	`166`	`}`
`135`	`167`	`]`
`136`	`168`	`}`
`@@ -140,12 +172,18 @@`
`140`	`172`	`"coding": [`
`141`	`173`	`{`
`142`	`174`	`"system": "http://loinc.org",`
`143`		`- "code": "48001-2"`
	`175`	`+ "code": "94186-4"`
`144`	`176`	`}`
`145`	`177`	`]`
`146`	`178`	`},`
`147`	`179`	`"valueCodeableConcept": {`
`148`		`- "text": "Biallelic Pathogenic:SLC52A2 missense variant"`
	`180`	`+ "coding": [`
	`181`	`+ {`
	`182`	`+ "system": "http://loinc.org",`
	`183`	`+ "code": "LA4489-6",`
	`184`	`+ "display": "Unknown"`
	`185`	`+ }`
	`186`	`+ ]`
`149`	`187`	`}`
`150`	`188`	`},`
`151`	`189`	`{`
`@@ -164,8 +202,7 @@`
`164`	`202`	`"code": "LA6683-2",`
`165`	`203`	`"display": "Germline"`
`166`	`204`	`}`
`167`		`- ],`
`168`		`- "text": "Pathogenic"`
	`205`	`+ ]`
`169`	`206`	`}`
`170`	`207`	`}`
`171`	`208`	`]`