Merge pull request #72 from vision-zero-oncology/feature/body-structu…

…re-r5-backport

feature/body-structure-r5-backport

input/fsh/aliases.fsh

@@ -61,3 +61,23 @@ Alias: $DiagnosesicherungCS = https://www.vision-zero-oncology.de/fhir/CodeSyste
 Alias: $RadReadProc = https://www.vision-zero-oncology.de/fhir/StructureDefinition/radiological-read-procedure
 Alias: $RadTnmReadProc = https://www.vision-zero-oncology.de/fhir/StructureDefinition/radiological-tnm-read-procedure
 Alias: $RadRecistReadProc = https://www.vision-zero-oncology.de/fhir/StructureDefinition/radiological-recist-read-procedure
+
+// HL7 Backport
+Alias: $structure = http://hl7.org/fhir/5.0/StructureDefinition/extension-BodyStructure.includedStructure.structure
+Alias: $laterality = http://hl7.org/fhir/5.0/StructureDefinition/extension-BodyStructure.includedStructure.laterality
+Alias: $landmarkDescription = http://hl7.org/fhir/5.0/StructureDefinition/extension-BodyStructure.includedStructure.bodyLandmarkOrientation.landmarkDescription
+Alias: $clockFacePosition = http://hl7.org/fhir/5.0/StructureDefinition/extension-BodyStructure.includedStructure.bodyLandmarkOrientation.clockFacePosition
+Alias: $device = http://hl7.org/fhir/5.0/StructureDefinition/extension-BodyStructure.includedStructure.bodyLandmarkOrientation.distanceFromLandmark.device
+Alias: $value = http://hl7.org/fhir/5.0/StructureDefinition/extension-BodyStructure.includedStructure.bodyLandmarkOrientation.distanceFromLandmark.value
+Alias: $surfaceOrientation = http://hl7.org/fhir/5.0/StructureDefinition/extension-BodyStructure.includedStructure.bodyLandmarkOrientation.surfaceOrientation
+Alias: $spatialReference = http://hl7.org/fhir/5.0/StructureDefinition/extension-BodyStructure.includedStructure.spatialReference
+Alias: $qualifier = http://hl7.org/fhir/5.0/StructureDefinition/extension-BodyStructure.includedStructure.qualifier
+Alias: $excludedstructure = http://hl7.org/fhir/5.0/StructureDefinition/extension-BodyStructure.excludedStructure.structure
+Alias: $excludedlaterality = http://hl7.org/fhir/5.0/StructureDefinition/extension-BodyStructure.excludedStructure.laterality
+Alias: $excludedlandmarkDescription = http://hl7.org/fhir/5.0/StructureDefinition/extension-BodyStructure.excludedStructure.bodyLandmarkOrientation.landmarkDescription
+Alias: $excludedclockFacePosition = http://hl7.org/fhir/5.0/StructureDefinition/extension-BodyStructure.excludedStructure.bodyLandmarkOrientation.clockFacePosition
+Alias: $excludeddevice = http://hl7.org/fhir/5.0/StructureDefinition/extension-BodyStructure.excludedStructure.bodyLandmarkOrientation.distanceFromLandmark.device
+Alias: $excludedvalue = http://hl7.org/fhir/5.0/StructureDefinition/extension-BodyStructure.excludedStructure.bodyLandmarkOrientation.distanceFromLandmark.value
+Alias: $excludedsurfaceOrientation = http://hl7.org/fhir/5.0/StructureDefinition/extension-BodyStructure.excludedStructure.bodyLandmarkOrientation.surfaceOrientation
+Alias: $excludedspatialReference = http://hl7.org/fhir/5.0/StructureDefinition/extension-BodyStructure.excludedStructure.spatialReference
+Alias: $excludedqualifier = http://hl7.org/fhir/5.0/StructureDefinition/extension-BodyStructure.excludedStructure.qualifier

input/fsh/bodystructure.fsh

@@ -11,13 +11,66 @@ Description: "Profile for the base definition of all body structures."
     bodyStructureIdentifier 1..1 
 * identifier[bodyStructureIdentifier].use = #usual
 * identifier[bodyStructureIdentifier].type = http://hl7.org/fhir/resource-types#BodyStructure
-* identifier[bodyStructureIdentifier].type.coding.system 1..
-* identifier[bodyStructureIdentifier].type.coding.code 1..
-* identifier[bodyStructureIdentifier].value 1..
-// * location 0..0
-// * locationQualifier 0..0
-* extension 0..*
-* extension contains Diagnosis named diagnosis 0..* MS
+* identifier[bodyStructureIdentifier].type.coding 1..*
+* identifier[bodyStructureIdentifier].value 1..1
+* location 0..0
+* locationQualifier 0..0
+* extension contains Diagnosis named diagnosis 0..* MS and
+    IncludedStructure named included-structure 1..* MS and
+    ExcludedStructure named excluded-structure 0..* MS
+
+
+Extension: IncludedStructure
+Id: included-structure
+Title: "Included Structure"
+Description: "Description of the included Structure of the Body Structure"
+* ^url = "http://hl7.org/fhir/5.0/StructureDefinition/extension-BodyStructure.includedStructure"
+* extension contains 
+    $structure 1..* MS 
+    and $laterality 0..* MS
+    and $landmarkDescription 0..* MS 
+    and $clockFacePosition 0..* MS 
+    and $device 0..* MS 
+    and $value 0..* MS 
+    and $surfaceOrientation 0..* MS 
+    and $spatialReference 0..* MS 
+    and $qualifier 0..* MS 
+* extension[$structure].value[x] only CodeableConcept
+* extension[$laterality].value[x] only CodeableConcept
+* extension[$landmarkDescription].value[x] only CodeableConcept
+* extension[$clockFacePosition].value[x] only CodeableConcept
+* extension[$device].value[x] only Reference or CodeableConcept
+* extension[$value].value[x] only Quantity
+* extension[$surfaceOrientation].value[x] only CodeableConcept
+* extension[$spatialReference].value[x] only Reference or CodeableConcept
+* extension[$qualifier].value[x] only CodeableConcept
+
+
+
+Extension: ExcludedStructure
+Id: excluded-structure
+Title: "Excluded Structure"
+Description: "Description of the excluded Structure of the Body Structure"
+* ^url = "http://hl7.org/fhir/5.0/StructureDefinition/extension-BodyStructure.excludedStructure"
+* extension contains
+    $excludedstructure 1..* MS and
+    $excludedlaterality 0..* MS and
+    $excludedlandmarkDescription 0..* MS and
+    $excludedclockFacePosition 0..* MS and
+    $excludeddevice 0..* MS and
+    $excludedvalue 0..* MS and
+    $excludedsurfaceOrientation 0..* MS and
+    $excludedspatialReference 0..* MS and
+    $excludedqualifier 0..* MS
+* extension[$excludedstructure].value[x] only CodeableConcept
+* extension[$excludedlaterality].value[x] only CodeableConcept
+* extension[$excludedlandmarkDescription].value[x] only CodeableConcept
+* extension[$excludedclockFacePosition].value[x] only CodeableConcept
+* extension[$excludeddevice].value[x] only Reference or CodeableConcept
+* extension[$excludedvalue].value[x] only Quantity
+* extension[$excludedsurfaceOrientation].value[x] only CodeableConcept
+* extension[$excludedspatialReference].value[x] only Reference or CodeableConcept
+* extension[$excludedqualifier].value[x] only CodeableConcept
 
 
 Extension: Diagnosis
@@ -31,12 +84,15 @@ Description: "Enables to reference a diagnosis <Condition> the body stucture ref
 
 
 Instance: example-body-structure
-InstanceOf: BodyStructure
+InstanceOf: Body_Structure_Base
 Usage: #example
 * identifier.use = #usual
 * identifier.type = http://hl7.org/fhir/resource-types#BodyStructure
 * identifier.system = "http://radiology.hospital.example.org"
 * identifier.value = "Tumor 1234"
 * patient = Reference(ExamplePatient)
-* extension.url = "https://www.vision-zero-oncology.de/fhir/StructureDefinition/diagnosis"
-* extension.valueReference = Reference(ExampleCondition)
+* extension[diagnosis].url = "https://www.vision-zero-oncology.de/fhir/StructureDefinition/diagnosis"
+* extension[diagnosis].valueReference = Reference(ExampleCondition)
+* extension[included-structure].extension[$structure].valueCodeableConcept.coding = $SCT#14975008 "Forearm"
+* extension[included-structure].extension[$laterality].valueCodeableConcept.coding = $SCT#419161000 "Unilateral left"
+* extension[included-structure].extension[$qualifier].valueCodeableConcept.coding = $SCT#263929005 "Volar"

input/fsh/tumor.fsh

@@ -14,8 +14,7 @@ Id: tumor
 Title: "Profile Tumor"
 Description: "Profile of a tumor"
 * insert Metadata
-* morphology 1.. MS
-* location 1.. MS
+* morphology 1..1 MS
 * patient MS
 
 Extension: PartOf
@@ -28,7 +27,7 @@ Description: "Enables to reference a Tumor <BodyStructure> from its respective S
 * ^context[=].expression = "Specimen"
 
 // Examples
-Instance: CerebellarSarcoma
+Instance: SplenicStructure
 InstanceOf: Tumor
 Usage: #example
 Title: "Tumor Example - Cerebellar Sarcoma"
@@ -37,14 +36,14 @@ Description: "Example for the Tumor profile"
 * identifier[bodyStructureIdentifier].type = http://hl7.org/fhir/resource-types#BodyStructure
 * identifier[bodyStructureIdentifier].system = "http://radiology.hospital.example.org"
 * identifier[bodyStructureIdentifier].value = "Tumor 1234"
-* morphology = $SCT#17302008 "Cerebellar sarcoma (morphologic abnormality)"
-* location = $SCT#1010600003 "Structure of left cerebellar hemisphere (body structure)"
+* morphology = $SCT#4147007 "Mass (morphologic abnormality)"
+* extension[included-structure].extension[$structure].valueCodeableConcept.coding = $SCT#78961009 "Splenic structure (body structure)"
 * patient = Reference(ExamplePatient)
 
 Instance: blood-specimen
 InstanceOf: TumorSpecimen
 Usage: #example
-* extension[partOf].valueReference = Reference(CerebellarSarcoma)
+* extension[partOf].valueReference = Reference(SplenicStructure)
 * status = #available
 * type = $SCT#16210851000119107 "Cerebellar neoplasm specimen (specimen)"
 * subject = Reference(ExamplePatient)

sushi-config.yaml

@@ -28,6 +28,8 @@ dependencies:
   de.gematik.isik-basismodul: 2.0.0
   de.medizininformatikinitiative.kerndatensatz.biobank: 1.0.3
   hl7.fhir.uv.ips: 1.0.0
+  hl7.fhir.extensions.r5: 4.0.1 
+
 
 pages:
   index.md: