Draft revision to tumor morphology profiles

input/fsh/AL_USCore.fsh

@@ -7,9 +7,10 @@ Alias:   USCorePractitioner = http://hl7.org/fhir/us/core/StructureDefinition/us
 Alias:   USCoreProcedure = http://hl7.org/fhir/us/core/StructureDefinition/us-core-procedure
 Alias:   USCoreObservationLab = http://hl7.org/fhir/us/core/StructureDefinition/us-core-observation-lab
 Alias:   USCoreOrganization = http://hl7.org/fhir/us/core/StructureDefinition/us-core-organization
-Alias:   USCoreClinicalTest = http://hl7.org/fhir/us/core/StructureDefinition/us-core-observation-clinical-test
+Alias:   USCoreClinicalResult = http://hl7.org/fhir/us/core/StructureDefinition/us-core-observation-clinical-result
 Alias:   USCoreVitalSigns = http://hl7.org/fhir/us/core/StructureDefinition/us-core-vital-signs
-Alias:   USCoreObservationImaging = http://hl7.org/fhir/us/core/StructureDefinition/us-core-observation-imaging
+Alias:   USCoreObservationSimple = http://hl7.org/fhir/us/core/StructureDefinition/us-core-simple-observation
+Alias:   USCoreSpecimen = http://hl7.org/fhir/us/core/StructureDefinition/us-core-specimen
 
 // Extensions
 Alias:   USCoreBirthSex = http://hl7.org/fhir/us/core/StructureDefinition/us-core-birthsex

input/fsh/EX_Basic.fsh

@@ -25,7 +25,7 @@ Description: "Example of Primary Cancer Condition - hematologic cancer"
 * onsetDateTime = "2020-05-12"
 * asserter = Reference(us-core-practitioner-kyle-anydoc)
 * stage.summary = NCIT#C80135 "Binet Stage B"
-* stage.assessment = Reference(binet-stage-group-B)
+//* stage.assessment = Reference(binet-stage-group-B)
 
 Instance: secondary-cancer-condition-brain-mets
 InstanceOf: SecondaryCancerCondition
@@ -62,6 +62,7 @@ Description: "Example of Cancer-Related Comorbidities"
 // absent
 * extension[comorbidConditionAbsent][0].valueCodeableConcept = SCT#414916001 "Obesity (disorder)"
 * extension[comorbidConditionAbsent][1].valueCodeableConcept = SCT#19829001 "Disorder of lung (disorder)"
+* category = ObsCat#social-history "Social History"
 
 Instance: john-anyperson-chf
 InstanceOf: USCoreCondition
@@ -196,6 +197,7 @@ Description: "Example of ECOG Performance Status"
 * performer = Reference(us-core-practitioner-kyle-anydoc)
 * valueInteger = 0
 * interpretation = LNC#LA9622-7 "Fully active, able to carry on all pre-disease performance without restriction"
+* category = ObsCat#survey "Survey"
 
 Instance: karnofsky-performance-status-normal-activity
 InstanceOf: KarnofskyPerformanceStatus
@@ -208,7 +210,7 @@ Description: "Example of Karnofsky Performance Status"
 * performer = Reference(us-core-practitioner-kyle-anydoc)
 * valueInteger = 90
 * interpretation = LNC#LA29176-7 "Able to carry on normal activity; minor signs or symptoms of disease"
-
+* category = ObsCat#survey "Survey"
 
 Instance: cancer-related-surgical-procedure-lobectomy
 InstanceOf: CancerRelatedSurgicalProcedure
@@ -248,6 +250,7 @@ Description: "Example of TNM Clinical Stage Group"
 * hasMember[0] = Reference(tnm-clinical-primary-tumor-category-cT3)
 * hasMember[1] = Reference(tnm-clinical-regional-nodes-category-cN3)
 * hasMember[2] = Reference(tnm-clinical-distant-metastases-category-cM0)
+* category = ObsCat#imaging "Imaging"
 
 Instance: tnm-clinical-distant-metastases-category-cM0
 InstanceOf: TNMDistantMetastasesCategory
@@ -260,6 +263,7 @@ Description: "Example of TNM Clinical Distant Metastases Category"
 * performer = Reference(us-core-practitioner-kyle-anydoc)
 * effectiveDateTime = "2019-04-01"
 * valueCodeableConcept = SCT#1229901006 "American Joint Committee on Cancer cM0 (qualifier value)"
+* category = ObsCat#imaging "Imaging"
 
 Instance: tnm-clinical-primary-tumor-category-cT3
 InstanceOf: TNMPrimaryTumorCategory
@@ -272,6 +276,7 @@ Description: "Example of TNM Clinical Primary Tumor Category"
 * subject = Reference(cancer-patient-john-anyperson)
 * performer = Reference(us-core-practitioner-kyle-anydoc)
 * effectiveDateTime = "2019-04-01"
+* category = ObsCat#imaging "Imaging"
 
 Instance: tnm-clinical-regional-nodes-category-cN3
 InstanceOf: TNMRegionalNodesCategory
@@ -284,6 +289,7 @@ Description: "Example of TNM Clinical Regional Nodes Category"
 * subject = Reference(cancer-patient-john-anyperson)
 * performer = Reference(us-core-practitioner-kyle-anydoc)
 * effectiveDateTime = "2019-04-01"
+* category = ObsCat#imaging "Imaging"
 
 Instance: cancer-related-medication-request-gefitinib
 InstanceOf: CancerRelatedMedicationRequest
@@ -351,6 +357,7 @@ Description: "Hemoglobin lab result to support TNMStageGroup example"
 * effectiveDateTime = "2020-03-06"
 * performer = Reference(us-core-practitioner-owen-oncologist)
 * valueQuantity = 13.5 'g/dl' "g/dl"
+* category = ObsCat#laboratory "laboratory"
 
 Instance: history-of-cancer-metastatic-to-liver
 InstanceOf: HistoryOfMetastaticCancer
@@ -360,6 +367,7 @@ Description: "Example showing history of metastatic cancer in liver."
 * subject = Reference(cancer-patient-adam-everyman)
 * effectiveDateTime = "2018-11-16"
 * performer = Reference(us-core-practitioner-owen-oncologist)
+* category = ObsCat#social-history "Social History"
 
 Instance: no-history-of-metastatic-cancer 
 InstanceOf: HistoryOfMetastaticCancer
@@ -370,6 +378,7 @@ Description: "Example showing no history of metastatic cancer"
 * effectiveDateTime = "2018-11-16"
 * performer = Reference(us-core-practitioner-owen-oncologist)
 * valueBoolean = false
+* category = ObsCat#social-history "Social History"
 
 Instance: histologic-behavior-and-type-non-small-cell
 InstanceOf: HistologicBehaviorAndType
@@ -394,19 +403,19 @@ Description: "Example of intermediate histologic grade."
 * status = #final "final"
 * performer = Reference(us-core-practitioner-kyle-anydoc)
 
-
-Instance: tumor-morphology-report-non-small-cell-intermediate-grade
-InstanceOf: TumorMorphology
-Description: "Example of a tumor morphology report showing non-small cell cancer with an intermediate histologic grade."
-* extension[relatedCondition].valueReference = Reference(primary-cancer-condition-nsclc)
-* subject = Reference(cancer-patient-john-anyperson)
-* effectiveDateTime = "2019-04-01"
-* specimen = Reference(human-specimen-lung)
-* result[0] = Reference(histologic-grade-intermediate)
-* result[1] = Reference(histologic-behavior-and-type-non-small-cell)
-* status = #final "final"
-* issued = "2019-04-15T13:28:17.239+02:00"
-
+//Instance: tumor-morphology-report-non-small-cell-intermediate-grade
+//InstanceOf: TumorMorphology
+//Description: "Example of a tumor morphology report showing non-small cell cancer with an intermediate histologic grade."
+//* extension[relatedCondition].valueReference = Reference(primary-cancer-condition-nsclc)
+//* subject = Reference(cancer-patient-john-anyperson)
+//* effectiveDateTime = "2019-04-01"
+//* specimen = Reference(human-specimen-lung)
+//* result[0] = Reference(histologic-grade-intermediate)
+//* result[1] = Reference(histologic-behavior-and-type-non-small-cell)
+//* status = #final "final"
+//* issued = "2019-04-15T13:28:17.239+02:00"
+
+/*
 Instance: rhabdomyosarcoma-risk-assessment-low
 InstanceOf: RhabdomyosarcomaRiskAssessment
 Description: "Example of rhabdomyosarcoma with a low risk assessment."
@@ -417,7 +426,6 @@ Description: "Example of rhabdomyosarcoma with a low risk assessment."
 * effectiveDateTime = "2021-04-01"
 * performer = Reference(us-core-practitioner-kyle-anydoc)
 
-
 Instance: all-risk-assessment-high
 InstanceOf: ALLRiskAssessment
 Description: "Example of leukemia with a standard risk assessment."
@@ -427,6 +435,7 @@ Description: "Example of leukemia with a standard risk assessment."
 * focus = Reference(primary-cancer-condition-nonspecific)
 * effectiveDateTime = "2021-04-01"
 * performer = Reference(us-core-practitioner-kyle-anydoc)
+*/
 
 Instance: john-anyperson-hd
 InstanceOf: USCoreCondition
@@ -463,6 +472,7 @@ Description: "Example of Patient"
 * extension[USCoreEthnicity].extension[text].valueString = "Not Hispanic or Latino"
 * extension[USCoreBirthSex].valueCode = #F
 
+/*
 Instance: lansky-play-performance-status-twenty
 InstanceOf: LanskyPlayPerformanceStatus
 Description: "Example of Lansky Play Performance Status."
@@ -484,6 +494,7 @@ Description: "Example of Deauville Scale."
 * interpretation = NCIT#C99750 "London Deauville Criteria Point Scale 5"
 * status = #final "final"
 * effectiveDateTime = "2019-04-01"
+*/
 
 Instance: body-surface-area-example
 InstanceOf: BodySurfaceArea

input/fsh/EX_ExtendedExample.fsh

@@ -160,6 +160,7 @@ Description: "mCODE Example for Cancer-Related Comorbidities"
 // absent -- These could also be references, but having a resource representing a non-condition would be unusual
 * extension[comorbidConditionAbsent][0].valueCodeableConcept = SCT#414916001 "Obesity (disorder)"
 * extension[comorbidConditionAbsent][1].valueCodeableConcept = SCT#19829001 "Disorder of lung (disorder)"
+* category = ObsCat#social-history "Social History"
 
 /* Not used -- model of comorbidities as Questionnaire
 Instance: cancer-related-comorbidity-response-jenny-m
@@ -195,6 +196,7 @@ Description: "Extended example: example showing ECOG performance status"
 * valueInteger = 0
 * interpretation = LNC#LA9622-7 "Fully active, able to carry on all pre-disease performance without restriction"
 * method = SCT#5880005 "Physical examination procedure (procedure)"
+* category = ObsCat#survey "Survey"
 
 // body weight and height added to calculate BSA needed to convert chemotherapy relative dose orders to absolute doses for CancerRelatedMedicationAdministration
 
@@ -248,6 +250,7 @@ Description: "Extended example: example showing TNM staging (stage group)"
 * hasMember[1] = Reference(tnm-pathologic-regional-nodes-category-jenny-m)
 * hasMember[2] = Reference(tnm-pathologic-distant-metastases-category-jenny-m)
 * performer = Reference(us-core-practitioner-owen-oncologist)
+* category = ObsCat#imaging "Imaging"
 
 Instance: tnm-clinical-primary-tumor-category-jenny-m
 InstanceOf: TNMPrimaryTumorCategory
@@ -260,6 +263,8 @@ Description: "Extended example: example showing TNM staging (T)"
 * valueCodeableConcept = SCT#1228938002 "American Joint Committee on Cancer cT3 (qualifier value)"
 * method = SCT#897275008 "American Joint Commission on Cancer, Cancer Staging Manual, 8th edition neoplasm staging system (tumor staging)"
 * performer = Reference(us-core-practitioner-owen-oncologist)
+* category = ObsCat#imaging "Imaging"
+
 
 Instance: tnm-clinical-regional-nodes-category-jenny-m
 InstanceOf: TNMRegionalNodesCategory
@@ -272,6 +277,7 @@ Description: "Extended example: example showing TNM staging (N)"
 * valueCodeableConcept = SCT#1229967007 "American Joint Committee on Cancer cN0 (qualifier value)"
 * method = SCT#897275008 "American Joint Commission on Cancer, Cancer Staging Manual, 8th edition neoplasm staging system (tumor staging)"
 * performer = Reference(us-core-practitioner-owen-oncologist)
+* category = ObsCat#imaging "Imaging"
 
 Instance: tnm-clinical-distant-metastases-category-jenny-m
 InstanceOf: TNMDistantMetastasesCategory
@@ -284,6 +290,7 @@ Description: "Extended example: example showing TNM staging (M)"
 * valueCodeableConcept = SCT#1229901006 "American Joint Committee on Cancer cM0 (qualifier value)"
 * method = SCT#897275008 "American Joint Commission on Cancer, Cancer Staging Manual, 8th edition neoplasm staging system (tumor staging)"
 * performer = Reference(us-core-practitioner-owen-oncologist)
+* category = ObsCat#imaging "Imaging"
 
 // Tumor marker test results 3-16-2018
 
@@ -503,6 +510,7 @@ Description: "Extended example: example showing TNM staging (stage group)"
 * hasMember[1] = Reference(tnm-pathologic-regional-nodes-category-jenny-m)
 * hasMember[2] = Reference(tnm-pathologic-distant-metastases-category-jenny-m)
 * performer = Reference(us-core-practitioner-owen-oncologist)
+* category = ObsCat#imaging "Imaging"
 
 Instance: tnm-pathologic-primary-tumor-category-jenny-m
 InstanceOf: TNMPrimaryTumorCategory
@@ -515,6 +523,7 @@ Description: "Extended example: example showing TNM staging (T)"
 * valueCodeableConcept = SCT#1229859000 "American Joint Committee on Cancer pT3 (qualifier value)"
 * method = SCT#897275008 "American Joint Commission on Cancer, Cancer Staging Manual, 8th edition neoplasm staging system (tumor staging)"
 * performer = Reference(us-core-practitioner-owen-oncologist)
+* category = ObsCat#imaging "Imaging"
 
 Instance: tnm-pathologic-regional-nodes-category-jenny-m
 InstanceOf: TNMRegionalNodesCategory
@@ -527,6 +536,7 @@ Description: "Extended example: example showing TNM staging (N)"
 * valueCodeableConcept = SCT#1229947003 "American Joint Committee on Cancer pN0 (qualifier value)"
 * method = SCT#897275008 "American Joint Commission on Cancer, Cancer Staging Manual, 8th edition neoplasm staging system (tumor staging)"
 * performer = Reference(us-core-practitioner-owen-oncologist)
+* category = ObsCat#imaging "Imaging"
 
 Instance: tnm-pathologic-distant-metastases-category-jenny-m
 InstanceOf: TNMDistantMetastasesCategory
@@ -539,6 +549,7 @@ Description: "Extended example: example showing TNM staging (M)"
 * valueCodeableConcept = AbsentReason#not-applicable "Not Applicable"   // cancer is not metastatic, pM0 is not valid
 * method = SCT#897275008 "American Joint Commission on Cancer, Cancer Staging Manual, 8th edition neoplasm staging system (tumor staging)"
 * performer = Reference(us-core-practitioner-owen-oncologist)
+* category = ObsCat#imaging "Imaging"
 
 // 21-Gene Assay
 

input/fsh/EX_ExtendedExample_Pediatric.fsh

@@ -168,6 +168,7 @@ Description: "Extended pediatric example: example showing Lansky performance sta
 * valueInteger = 80
 * interpretation = NCIT#C69424 "Lansky Performance Status 80"
 * method = SCT#5880005 "Physical examination procedure (procedure)"
+* category = ObsCat#survy "Survey"
 
 Instance: cancer-related-medication-request-cyclophosphamide-brian-l
 InstanceOf: CancerRelatedMedicationRequest
@@ -373,6 +374,7 @@ Description: "Extended pediatric example: body surface area"
 * performer = Reference(us-core-practitioner-owen-oncologist)
 * valueQuantity = 0.59 'm2' "square meter"
 
+/*
 Instance: all-risk-assessment-standard-brian-l
 InstanceOf: ALLRiskAssessment
 Description: "Extended pediatric example: ALL risk assessment standard"
@@ -382,6 +384,6 @@ Description: "Extended pediatric example: ALL risk assessment standard"
 * focus = Reference(primary-cancer-condition-brian-l)
 * effectiveDateTime = "2021-02-08"
 * performer = Reference(us-core-practitioner-owen-oncologist)
-
+*/
 
 

input/fsh/EX_Staging_Other.fsh

@@ -18,6 +18,7 @@ RuleSet: StagingInstanceRuleSet
 
 //-------------------------------------------------
 
+/*
 Instance: binet-stage-group-B
 InstanceOf: CLLBinetStage
 Description: "Example of Binet staging for CLL."
@@ -116,3 +117,5 @@ InstanceOf: RhabdomyosarcomaClinicalGroupStage
 Description: "Example of Rhabdomyosarcoma Clinical Group Stage for rhabdomyosarcoma staging."
 * insert StagingInstanceRuleSet
 * valueCodeableConcept = SCT#405957007 "Intergroup rhabdomyosarcoma study post-surgical clinical group IA: localized tumor, confined to site of origin, completely resected (finding)"
+
+*/

input/fsh/SD_ComorbidCondition.fsh

@@ -1,5 +1,5 @@
 Profile: Comorbidities
-Parent: Observation
+Parent: USCoreObservationSimple
 Id: mcode-comorbidities
 Title: "Comorbidities Profile"
 Description: "General structure for capturing comorbid conditions with respect to a primary ('index') condition. The user can use this profile in three ways: (1) free-form, listing any conditions they wish to highlight as significant comorbidities, (2) following a formal paradigm such as the Charlson Comorbidity Index or the NCI Comorbidity Index, or (3) use disease categories defined for registry reporting purposes, such as those defined by Center for International Blood and Marrow Transplant Research (CIBMTR)."

input/fsh/SD_Extensions.fsh

@@ -113,7 +113,7 @@ Description: "The purpose of a treatment, medication, or procedure."
 Extension: NormalizationBasis
 Id: mcode-normalization-basis
 Title:  "Normalization Basis Extension"
-Description: "How the drug dosage was normalized."
+Description: "The method (e.g., body weight, body surface area, flat dose, age) used to normalize the medication dosage."
 * insert ExtensionContext(DomainResource)
 * insert ExtensionContext(Extension)
 * insert ExtensionContext(MedicationRequest)

input/fsh/SD_Genomics.fsh

@@ -81,7 +81,7 @@ Description: "The result of a tumor marker test. Tumor marker tests are generall
 * extension[relatedCondition] ^definition = "Associates the tumor marker test with a condition, if one exists. Condition can be given by a reference or a code. In the case of a screening test such as prostate-specific antigen (PSA), there may be no existing condition to reference."
 
 Profile: HumanSpecimen
-Parent: Specimen
+Parent: USCoreSpecimen
 Id: mcode-human-specimen
 Title:  "Human Specimen Profile"
 Description:  "A specimen taken from a Patient for the purpose of oncology-related testing. The profile includes extensions to specify a more precise body site and an identifier of source body structure at that site (for example, a tumor identifier)."

input/fsh/SD_Histology.fsh

@@ -1,11 +1,11 @@
 Profile: TumorMorphology
-Parent: USCoreDiagnosticReportProfileLaboratoryReporting
+Parent: USCoreObservationSimple
 Id: mcode-tumor-morphology
 Title: "Tumor Morphology Report"
-Description: "ICD-O-3 morphology determined from examination of tumor sample, composed of three parts: histologic type, the malignant potential of the tumor (behavior) and the tumor grade (degree of differentiation)."
+Description: "Tumor morphology can include information on the type of cell (type), the malignant potential of the tumor (behavior), and the degree of differentiation (grade). For some cancers, the type and behavior are described in the ICD-O-3 code."
 * ^extension[FMM].valueInteger = 4
 * specimen only Reference(HumanSpecimen)
-* specimen 0..1 MS
+* specimen MS
 * code = LNC#77753-2  // Tumor morphology panel Cancer
 * subject only Reference(CancerPatient)
 * subject ^definition = "Patient whose test result is recorded."
@@ -14,14 +14,8 @@ Description: "ICD-O-3 morphology determined from examination of tumor sample, co
 * extension contains RelatedCondition named relatedCondition 0..* MS 
 * extension[relatedCondition] ^short = "Condition associated with this test."
 * extension[relatedCondition] ^definition = "Associates the tumor marker test with a condition, if one exists. Condition can be given by a reference or a code. In the case of a screening test such as prostate-specific antigen (PSA), there may be no existing condition to reference."
-* insert SliceReferenceOnProfile(result)
-* result contains histologyBehaviorAndType 0..1 and grade 0..1
-* result[histologyBehaviorAndType] only Reference(HistologicBehaviorAndType)
-* result[histologyBehaviorAndType] ^short = "Histology Behavior Type being reported using ICD-O-3"
-* result[histologyBehaviorAndType] ^definition = "The ICD-O-3 4-digit histology code for the tumor, with the 5th digit behavior code for the tumor"
-* result[grade] only Reference(HistologicGrade)
-* result[grade] ^short = "Tumor grade code being reported using SNOMED"
-* result[grade] ^definition = "The histologic grade of the tumor"
+* hasMember only Reference(HistologicBehaviorAndType or HistologicGrade)
+
 
 Profile: HistologicBehaviorAndType
 Parent: USCoreObservationLab
@@ -48,11 +42,11 @@ Profile: HistologicGrade
 Parent: USCoreObservationLab
 Id: mcode-histologic-grade
 Title: "Histologic Grade"
-Description: "Histologic grade determined from examination of tumor sample."
+Description: "Histologic grade determined from examination of tumor sample. The grade system should be captured using the method data element."
 * ^extension[FMM].valueInteger = 4
 * specimen only Reference(HumanSpecimen)
 * specimen 0..1 MS  // is not MS in US Core 4.0.0 and 5.0.1 
-* code = LNC#33732-9 // Histology grade [Identifier] in Cancer specimen  (could be 21858-6 Grade Cancer)
+* code = NCIT#C18000 // Histologic Grade
 * value[x] 1..1
 * value[x] only CodeableConcept
 * value[x] from HistologicGradeVS (extensible)
@@ -70,3 +64,4 @@ Description: "Histologic grade determined from examination of tumor sample."
 // RelatedCondition added 11/14/2022, see https://chat.fhir.org/#narrow/stream/229074-CodeX/topic/Reference.20between.20tumor.20characteristics.20and.20cancer.20diagnosis
 
 
+