Merge pull request #240 from standardhealth/dev

mCODE 0.7 and accompanying changes in SHR
standardhealth · Mar 13, 2019 · 3c652df · 3c652df
2 parents bae32d3 + 22460c4
commit 3c652df
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diff --git a/parking_lot/shr_immunization.txt b/parking_lot/shr_immunization.txt
@@ -33,11 +33,10 @@ Description:	"Describes the event of a patient being administered a vaccination
 
 
 EntryElement:	ImmunizationGiven
-Based on:		ProcedurePerformedStatement  
+Based on:		Procedure
 // Note: Can't inherit from MedicationUsedStatement because Status is bound to http://hl7.org/fhir/ValueSet/medication-statement-status in that class, can't be overriden to http://hl7.org/fhir/ValueSet/immunization-status
 Concept:		MTH#C0580520
 Description:	"A vaccination administered to the subject."
-//				InformationSource value is type PersonOrOrganization
 				StatementTopic is type ImmunizationTopic
 				Status from http://hl7.org/fhir/ValueSet/immunization-status
 				OccurrenceTimeOrPeriod value is type dateTime

diff --git a/parking_lot/shr_immunization_map.txt b/parking_lot/shr_immunization_map.txt
@@ -15,8 +15,8 @@ ImmunizationGiven maps to http://hl7.org/fhir/us/core/StructureDefinition/us-cor
 	constrain explanation to 0..1
 	Encounter maps to encounter
 	Reason maps to explanation.reason
-	FHIRProcedureParticipant maps to practitioner.actor
-	FHIRProcedureParticipant.ParticipationType maps to practitioner.role
+	Participant maps to practitioner.actor
+	Participant.ParticipationType maps to practitioner.role
 //	FHIRProcedureParticipant.OnBehalfOf maps to nothing
 	OccurrenceTimeOrPeriod maps to date
 	Status maps to status

diff --git a/spec/LandingPageBreastCancer.html b/spec/LandingPageBreastCancer.html
@@ -14,7 +14,7 @@ <h2>Table of Contents</h2>
 </ul>
 <h2><a name="Guidance"></a>Guidance for HL7 Voters</h2>
 <p>This section provides orientation to the ballot materials.</p>
-<h3>Where to SubjectOfInformation</h3>
+<h3>Where to Focus</h3>
 <p>There are several representations of the same content in the ballot materials. Different representations will be useful to different audiences:</p>
 <ul>
 <li><strong>Clinicians and cancer domain experts</strong> should primarily focus on the <a href="logical.html">logical models</a>. These models are the simplest representation of the content included in the ballot. <a href="valuesets.html">Value sets</a> will also be of interest.</li>

diff --git a/spec/brca.txt b/spec/brca.txt
@@ -49,15 +49,13 @@ Based on:		CancerHistologicType
 Description:	"Classification of breast cancer according to histopathologic subtypes, as determined by microscopic observation of breast tissue samples."
 				Code is LNC#44638-5 "Histologic type in Breast tumor"
 				DataValue from BreastCarcinomaHistologicTypeVS
-				SubjectOfInformation value is type ref(BreastCancerCondition)
 
 
 EntryElement:	BreastTNMClinicalPrognosticStagePanel
 Based on:		TNMClinicalPrognosticStagePanel
 // Concept inherited from parent class, was not breast-specific in BrCa ballot either, was MTH#C2216702 "Malignant Neoplasm of Breast Staging"
 Description:	"A panel of breast cancer staging information that is performed prior to surgery, based on evidence such as physical examination, imaging, and/or biopsy. The panel should not include both a DCISNuclearGrade and a BreastCancerHistologicGrade, since the latter implies an invasive cancer."
 				Code is TBD#TBD // was MTH#C2216702 "Malignant Neoplasm of Breast Staging" //Not LNC#21908-9 since that is AJCC-specific and also not breast cancer specific. We do however, give the LOINC list of stage values as the preferred codes.
-				SubjectOfInformation value is type ref(BreastCancerCondition)
 //				PanelMembers.Observation.TNMClinicalPrimaryTumorClassification is type BreastTNMClinicalPrimaryTumorClassification
 //				PanelMembers.Observation.TNMClinicalRegionalNodesClassification is type BreastTNMClinicalRegionalNodesClassification
 //				PanelMembers.Observation.TNMClinicalDistantMetastasesClassification is type BreastTNMClinicalDistantMetastasesClassification
@@ -73,7 +71,6 @@ EntryElement: 	BreastTNMClinicalPrimaryTumorClassification
 Based on:		TNMClinicalPrimaryTumorClassification
 // Concept inherited from parent class, was not breast-specific in BrCa ballot either.
 Description:	"Classification based on the size and extent of the primary breast tumor, assessed prior to surgery, based on evidence such as physical examination, imaging, and/or biopsy."
-				SubjectOfInformation value is type ref(BreastCancerCondition)
 				PanelMembers.Observation
 					includes 0..1 TumorDimensions //TODO: need to distinguish tumor dimensions between clinical and pathologic, specify method?
 
@@ -82,7 +79,6 @@ EntryElement:	BreastTNMClinicalRegionalNodesClassification
 Based on:		TNMClinicalRegionalNodesClassification
 // Concept inherited from parent class, was not breast-specific in BrCa ballot either.
 Description:	"Classification of the presence or absence of metastases in regional lymph nodes for breast cancer, assessed using tests that are done before surgery."
-				SubjectOfInformation value is type ref(BreastCancerCondition)
 				PanelMembers.Observation
 					includes 0..*	BreastClinicalLymphNodeInvolvement
 
@@ -91,6 +87,7 @@ EntryElement:	BreastClinicalLymphNodeInvolvement
 Based on:		ComponentOnlyNonLaboratoryObservation
 Concept:		MTH#C0806692 "Lymph Node Involvement"
 Description:	"Clinical assessment of lymph nodes for presence of cancer cells in staging the N category in breast cancer."
+0..1			RelatedCancerCondition
 				BodySite is type BreastLymphNodeBodySite
 				Method from LymphNodeClinicalMethodVS if covered
 				Components.ObservationComponent
@@ -123,14 +120,12 @@ EntryElement:	BreastTNMClinicalDistantMetastasesClassification
 Based on:		TNMClinicalDistantMetastasesClassification
 // Concept inherited from parent class, was not breast-specific in BrCa ballot either.
 Description:	"Classification of the presence or absense of metastases in remote anatomical locations relative to the breast, assessed using tests that are done before surgery."
-				SubjectOfInformation value is type ref(BreastCancerCondition)
 
 
 EntryElement:	BreastTNMPathologicPrognosticStagePanel
 Based on:		TNMPathologicPrognosticStagePanel
 // Concept inherited from parent class, was not breast-specific in BrCa ballot either, was MTH#C2216702 "Malignant Neoplasm of Breast Staging"
 Description:	"A panel of breast cancer staging information that is performed prior to surgery, based on evidence such as physical examination, imaging, and/or biopsy. The panel includes biomarkers and histologic grade scales used specifically for breast cancer. The panel should not include both a DCISNuclearGrade and a BreastCancerHistologicGrade, since the latter implies an invasive cancer."
-				SubjectOfInformation value is type ref(BreastCancerCondition)
 //				PanelMembers.Observation.TNMPathologicPrimaryTumorClassification is type BreastTNMPathologicPrimaryTumorClassification
 //				PanelMembers.Observation.TNMPathologicRegionalNodesClassification is type BreastTNMPathologicRegionalNodesClassification
 //				PanelMembers.Observation.TNMPathologicDistantMetastasesClassification is type BreastTNMPathologicDistantMetastasesClassification
@@ -146,15 +141,13 @@ EntryElement:	BreastTNMPathologicPrimaryTumorClassification
 Based on:		TNMPathologicPrimaryTumorClassification
 // Concept inherited from parent class, was not breast-specific in BrCa ballot.
 Description:	"Classification of the primary breast tumor, based on its size and extent, assessed through pathologic analysis of a tumor specimen."
-				SubjectOfInformation value is type ref(BreastCancerCondition)
 				PanelMembers.Observation
 					includes 0..1 TumorDimensions //TODO: need to distinguish tumor dimensions between clinical and pathologic, specify method?
 
 EntryElement:	BreastTNMPathologicRegionalNodesClassification
 Based on:		TNMPathologicRegionalNodesClassification
 // Concept inherited from parent class, was not breast-specific in BrCa ballot.
 Description:	"Classification of the presence or absence of metastases in regional lymph nodes for breast cancer, assessed through pathologic analysis of a specimen."
-				SubjectOfInformation value is type ref(BreastCancerCondition)
 				PanelMembers.Observation
 					includes 0..*	BreastPathologicalLymphNodeInvolvement
 
@@ -240,7 +233,7 @@ EntryElement:	BreastTNMPathologicDistantMetastasesClassification
 Based on:		TNMPathologicDistantMetastasesClassification
 // Concept inherited from parent class, was not breast-specific in BrCa ballot.
 Description:	"Classification of the presence or absense of metastases in remote anatomical locations relative to the breast, assessed through pathologic analysis of a specimen."
-				SubjectOfInformation value is type ref(BreastCancerCondition)
+
 
 EntryElement:	HER2ReceptorStatus
 Based on:		TumorMarkerObservation
@@ -451,6 +444,7 @@ The is currently no LOINC code for Mammaprint test."
 				Interpretation from RecurrenceRiskScoreInterpretationVS
 				Specimen is type BreastSpecimen
 0..0			Device
+
 
 /************* LEGACY BEGIN ************		 
 
@@ -562,7 +556,7 @@ Based on:		Observation
 Concept:		MTH#C0678941
 Description:	"Whether a subject carries a mutation in a particular gene."
 Value:			CodeableConcept from PositiveNegativeVS
-//				SubjectOfInformation.CodeableConcept from GeneIdentifierVS
+//				GeneName from GeneIdentifierVS
 0..0			ReferenceRange
 //0..0			DeltaFlag
 0..0			BodySite
@@ -590,15 +584,15 @@ includes 1..1	BRCA2Variant
 	Based on:		GeneticVariant
 	Description:	"Whether the patient has a mutation in the BRCA1 gene."
 	Value:			CodeableConcept from PositiveNegativeVS
-//					SubjectOfInformation.CodeableConcept is HGNC#BRCA1Gene
+//					GeneName is HGNC#BRCA1Gene
 
 
 	Element:		BRCA2Variant
 	Concept:		TBD
 	Based on:		GeneticVariant
 	Description:	"Whether the patient has a mutation in the BRCA2 gene."
 	Value:			CodeableConcept from PositiveNegativeVS
-//					SubjectOfInformation.CodeableConcept is HGNC#BRCA2Gene
+//					GeneName is HGNC#BRCA2Gene
 
 
 FHIR Genomics:

diff --git a/spec/brca_vs.txt b/spec/brca_vs.txt
@@ -335,15 +335,6 @@ Description:	"Antibodies relevant to Ki-67 Text."
 #30-9 			"30-9 - CAP#32160" 
 #IR/IS62 		"IR / IS626 - CAP#32168"
 
-ValueSet:		TumorMarginDescriptionVS
-SCT#129738007	"Lesion with circumscribed margin"
-SCT#129741003	"Lesion with indistinct margin"					
-SCT#129739004	"Lesion with microlobulated margin"
-SCT#129740002	"Lesion with obscured margin"
-SCT#129742005	"Lesion with spiculated margin"
-// TODO: Add codes for additional tumor margin descriptions (from Penrad)
-// Angular margin, Smooth margin, Intraductal extension, Irregular margin, Lobulated margin, Macrolobulated margin, Non circumscribed margin
-
 
 ValueSet:		ReceptorVS
 Includes codes descending from SCT#116647005 "Receptor (substance)"

diff --git a/spec/ig-mcode-config.json b/spec/ig-mcode-config.json
@@ -0,0 +1,63 @@
+{
+    "projectName": "HL7 FHIR Implementation Guide: minimal Common Oncology Data Elements (mCODE), Release 0.7 - US Realm (Draft for Comment 1)",
+    "projectShorthand": "oncocore",
+    "projectURL": "http://hl7.org/fhir/us/projectURL/",
+    "fhirURL": "http://hl7.org/fhir/us/shr/",
+    "entryTypeURL": "http://hl7.org/fhir/us/entryTypeURL/spec/",
+    "fhirTarget": "FHIR_DSTU_2",
+    "filterStrategy":
+	{
+        "filter": true,
+		"strategy": "element",
+        "target": ["shr.base.Entry", "shr.core.Patient", "shr.core.Condition", "shr.core.MedicationStatement", "shr.core.SurgicalProcedure", "shr.core.RadiationProcedure", "shr.core.ECOGPerformanceStatus", "shr.core.KarnofskyPerformanceStatus", "oncocore.CancerCondition", "oncocore.CancerHistologicType", "oncocore.CancerHistologicGrade", "oncocore.CancerDiseaseStatus", "oncocore.DistantMetastases", "oncocore.TNMClinicalPrognosticStagePanel",
+        "oncocore.TNMClinicalStageGroup",
+        "oncocore.TNMClinicalPrimaryTumorClassification",
+        "oncocore.TNMClinicalRegionalNodesClassification",
+        "oncocore.TNMClinicalDistantMetastasesClassification",
+        "oncocore.TNMPathologicPrognosticStagePanel",
+        "oncocore.TNMPathologicStageGroup",
+        "oncocore.TNMPathologicPrimaryTumorClassification",
+        "oncocore.TNMPathologicRegionalNodesClassification",
+        "oncocore.TNMPathologicDistantMetastasesClassification",
+        "oncocore.CancerGeneticMarkerAnalysisResult",
+        "oncocore.TumorMarkerObservation"
+        ]
+	},
+    "implementationGuide":
+	{
+        "npmName": "oncocore",
+        "version": "0.7.0",
+		"includeLogicalModels": false,
+		"includeModelDoc": true,
+        "indexContent": "IndexFolder_Oncocore",
+		"primarySelectionStrategy":
+		{
+            "strategy": "entry",
+			"primary": ["shr.core.Patient", "shr.core.Condition", "shr.core.MedicationStatement", "shr.core.SurgicalProcedure", "shr.core.RadiationProcedure", "shr.core.ECOGPerformanceStatus", "shr.core.KarnofskyPerformanceStatus", "oncocore.CancerCondition", "oncocore.CancerHistologicType", "oncocore.CancerHistologicGrade", "oncocore.CancerDiseaseStatus", "oncocore.DistantMetastases", "oncocore.TNMClinicalPrognosticStagePanel",
+            "oncocore.TNMClinicalStageGroup",
+            "oncocore.TNMClinicalPrimaryTumorClassification",
+            "oncocore.TNMClinicalRegionalNodesClassification",
+            "oncocore.TNMClinicalDistantMetastasesClassification",
+            "oncocore.TNMPathologicPrognosticStagePanel",
+            "oncocore.TNMPathologicStageGroup",
+            "oncocore.TNMPathologicPrimaryTumorClassification",
+            "oncocore.TNMPathologicRegionalNodesClassification",
+            "oncocore.TNMPathologicDistantMetastasesClassification",
+            "oncocore.CancerGeneticMarkerAnalysisResult",
+            "oncocore.TumorMarkerObservation"
+            ],
+            "hideSupporting": true
+		}
+	},
+    "publisher": "The MITRE Corporation",
+    "contact": [
+        {
+            "telecom": [
+                {
+                    "system": "url",
+                    "value": "http://www.hl7.org/Special/committees/cic/index.cfm"
+                }
+            ]
+        }
+    ]
+}
diff --git a/spec/odh_occupation.txt b/spec/odh_occupation.txt
@@ -34,7 +34,6 @@ Outside of ODH, the employment arrangement between an employer and a person (one
 				Code is LNC#74165-2 "HistoryOfEmploymentStatus"
 				DataValue from https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.7129
 0..0			Components
-0..0			SubjectOfInformation
 
 EntryElement:	RetirementDate
 Based on:		SocialHistoryObservation
@@ -45,13 +44,11 @@ Outside of ODH, a characterization of the employment arrangement between an empl
 				Code is LNC#87510-4 "Date of Retirement"
 0..0			Components
 0..0			RelevantTime // The result value contains the date of retirement, so having a relevant time would be redundant.
-0..0			SubjectOfInformation
 
 EntryElement:	CombatZonePeriod
 Based on:		SocialHistoryObservation
 0..0			Components
 0..0			RelevantTime // Since the result data value contains the time period of combat zone activity, the relevant time is redundant
-0..0			SubjectOfInformation
 
 EntryElement:	UsualWork
 Based on:		CodedSocialHistoryObservation
@@ -61,14 +58,18 @@ Example: a person has worked for a total of 30 years as a building carpenter (Oc
 Usual Work does not include work that was unpaid or voluntary."
 				DataValue from https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.7186
 				Code is LNC#21843-8	"History of Usual occupation"
-				SubjectOfInformation value is type CodeableConcept
-				SubjectOfInformation from https://vsac.nlm.nih.gov/valueset/2.16.840.1.113883.1.11.19579/expansion // family member value set
+0..1			SubjectOfInformationCode from https://vsac.nlm.nih.gov/valueset/2.16.840.1.113883.1.11.19579/expansion // family member value set
 				Components.ObservationComponent
 includes 1..1 	UsualIndustry 
 includes 0..1	UsualOccupationDuration 
 1..1			RelevantTime 
 				RelevantTime value is type TimePeriod
 
+	Element:		SubjectOfInformationCode
+	Description:	"The person referred the information in this resource relates to, if different than the person of record."
+		//The entity this condition or observation relates to, for example, a person related to the SubjectOfRecord. The SubjectOfInformation is only required if the person or thing observed is different than the SubjectOfRecord. SubjectOfInformation should not be an anatomical location.  Examples: The focus for cancer progression would be the cancer condition; for wound length, an instance of a wound (a condition). In the case where the SubjectOfInformation is a related person, the value may be a RelatedPerson resource or a concept code with the relationship to the SubjectOfRecord (e.g., wife)
+	Value:			CodeableConcept
+
 	Element:		UsualIndustry
 	Based on:		CodedObservationComponent
 	Description:	"The industry (type of business) in which the subject has worked for the longest duration while in the usual occupation.
@@ -93,8 +94,7 @@ A person's job can be a social determinant of their health and information about
 At a minimum, it is important to have a record of a person's current job(s); i.e., the job(s) in which a person is engaged at the time that he or she presents to a health care provider, regardless of duration, and to retain that information over time. In the event a person recently stopped working (e.g. retired without another job, became unemployed or disabled and unable to work), the most recent job(s) is used instead of the current job(s)."
 0..0			DataValue
 0..0			DataAbsentReason
-				SubjectOfInformation value is type CodeableConcept
-				SubjectOfInformation from https://vsac.nlm.nih.gov/valueset/2.16.840.1.113883.1.11.19579/expansion 
+0..1			SubjectOfInformationCode from https://vsac.nlm.nih.gov/valueset/2.16.840.1.113883.1.11.19579/expansion 
 				Code is LNC#11341-5 "History of Occupation"
 0..1			Employer // must be extension; cannot be a result value or an evaluation component because the value is a reference to Person or Organization
 				Components.ObservationComponent