Merge pull request #253 from standardhealth/dev

Dev mCODE 0.9 to master

.travis.yml

@@ -12,7 +12,7 @@ before_install:
   - cd shr-cli/
   - yarn
 script:
-  - node . ../spec/ > run.log
+  - node . -s es6 ../spec/ > run.log
   - cat run.log
   - errors=$(grep "errors" run.log | sed $'s,\x1b\\[[0-9;]*[a-zA-Z],,g')
   - if [[ "$errors" != "0 errors" ]]; then ( echo There were errors in running shr-cli. ; exit 1 ); fi

parking_lot/CBC-Hold.txt

@@ -0,0 +1,119 @@
+
+EntryElement:   CompleteBloodCountHemogramPanelPtBldAutomatedCount  // based on long common name, could be named CompleteBloodCount-Hemogram-PanelBloodByAutomatedCount
+Based on:       DiagnosticReport
+Description:    "Complete blood count (CBC) (hemogram) panel - Blood by Automated count"
+1..1        SubjectOfRecord is type PatientSubjectOfRecord
+            Code is LNC#58410-2 "Complete blood count (hemogram) panel - Blood by Automated count"
+// ServiceCategory TBD
+            Observation
+includes    1..1  LeukocytesNCncPtBldQnAutomatedCount // based on long common name, could be named  Leukocytes_NumPerVolume_InBloodByAutomatedCount
+includes    1..1  ErythrocytesNCncPtBldQnAutomatedCount
+includes    1..1  HemoglobinMCncPtBldQn 
+includes    1..1  HematocritVFrPtBldQnAutomatedCount
+includes    1..1  ErythrocyteMeanCorpuscularVolumeEntVolPtRBCQnAutomatedCount
+includes    1..1  ErythrocyteMeanCorpuscularHemoglobinEntMassPtRBCQnAutomatedCount
+includes    1..1  ErythrocyteMeanCorpuscularHemoglobinConcentrationMCncPtRBCQnAutomatedCount
+includes    0..1  ErythrocyteDistributionWidthEntVolPtRBCQnAutomatedCount
+includes    0..1  ErythrocyteDistributionWidthRatioPtRBCQnAutomatedCount
+includes    1..1  PlateletsNCncPtBldQnAutomatedCount
+includes    0..1  PlateletDistributionWidthEntVolPtBldQnAutomatedCount
+includes    0..1  PlateletMeanVolumeEntVolPtBldQnAutomatedCount
+
+
+EntryElement:   LeukocytesNCncPtBldQnAutomatedCount
+SimpleQuantitativeLaboratoryObservation
+Description:    "Leukocytes [#/​volume] in Blood by Automated count"
+                Code is LNC#6690-2 "Leukocytes [#/​volume] in Blood by Automated count"
+                DataValue.Quantity.Units is UCUM#10*3/uL
+
+EntryElement:   ErythrocytesNCncPtBldQnAutomatedCount
+SimpleQuantitativeLaboratoryObservation
+Description:    "Erythrocytes [#/​volume] in Blood by Automated count"
+                Code is LNC#789-8 "Erythrocytes [#/​volume] in Blood by Automated count"
+                DataValue.Quantity.Units is UCUM#10*6/uL
+
+EntryElement:   HemoglobinMCncPtBldQn
+SimpleQuantitativeLaboratoryObservation
+Description:    "Hemoglobin [Mass/​volume] in Blood"
+                Code is LNC#718-7 "Hemoglobin [Mass/​volume] in Blood"
+                DataValue.Quantity.Units is UCUM#g/dL
+
+EntryElement:   HematocritVFrPtBldQnAutomatedCount
+SimpleQuantitativeLaboratoryObservation
+Description:    "Hematocrit [Volume Fraction] of Blood by Automated count"
+                Code is LNC#4544-3 "Hematocrit [Volume Fraction] of Blood by Automated count"
+                DataValue.Quantity.Units is UCUM#%
+
+EntryElement:   ErythrocyteMeanCorpuscularVolumeEntVolPtRBCQnAutomatedCount
+SimpleQuantitativeLaboratoryObservation
+Description:    "MCV [Entitic volume] by Automated count"
+                Code is LNC#787-2 "MCV [Entitic volume] by Automated count"
+                DataValue.Quantity.Units is UCUM#fL
+
+EntryElement:   ErythrocyteMeanCorpuscularHemoglobinEntMassPtRBCQnAutomatedCount
+SimpleQuantitativeLaboratoryObservation
+Description:    "MCH [Entitic mass] by Automated count"
+                Code is LNC#785-6  "MCH [Entitic mass] by Automated count"
+                DataValue.Quantity.Units is UCUM#pg
+
+EntryElement:   ErythrocyteMeanCorpuscularHemoglobinConcentrationMCncPtRBCQnAutomatedCount
+SimpleQuantitativeLaboratoryObservation
+Description:    "MCHC [Mass/​volume] by Automated count"
+                Code is LNC#786-4 "MCHC [Mass/​volume] by Automated count"
+                DataValue.Quantity.Units is UCUM#g/dL
+
+EntryElement:   ErythrocyteDistributionWidthEntVolPtRBCQnAutomatedCount
+SimpleQuantitativeLaboratoryObservation
+Description:    "Erythrocyte distribution width [Entitic volume] by Automated count"
+                Code is LNC#21000-5 "Erythrocyte distribution width [Entitic volume] by Automated count"
+                DataValue.Quantity.Units is UCUM#fL
+
+EntryElement:   ErythrocyteDistributionWidthRatioPtRBCQnAutomatedCount
+SimpleQuantitativeLaboratoryObservation
+Description:    "Erythrocyte distribution width [Ratio] by Automated count"
+                Code is LNC#788-0  "Erythrocyte distribution width [Ratio] by Automated count"
+                DataValue.Quantity.Units is UCUM#%
+
+EntryElement:   PlateletsNCncPtBldQnAutomatedCount
+SimpleQuantitativeLaboratoryObservation
+Description:    "Platelets [#/​volume] in Blood by Automated count"
+                Code is LNC#777-3 "Platelets [#/​volume] in Blood by Automated count"
+                DataValue.Quantity.Units is UCUM#10*3/uL
+
+EntryElement:   PlateletDistributionWidthEntVolPtBldQnAutomatedCount
+SimpleQuantitativeLaboratoryObservation
+Description:    "Platelet distribution width [Entitic volume] in Blood by Automated count"
+                Code is LNC#32207-3 "Platelet distribution width [Entitic volume] in Blood by Automated count"
+                DataValue.Quantity.Units is UCUM#fL
+
+EntryElement:   PlateletMeanVolumeEntVolPtBldQnAutomatedCount
+SimpleQuantitativeLaboratoryObservation
+Description:    "Platelet mean volume [Entitic volume] in Blood by Automated count"
+                Code is LNC#32623-1 "Platelet mean volume [Entitic volume] in Blood by Automated count"
+                DataValue.Quantity.Units is UCUM#fL
+
+
+EntryElement:   UrinalysisDipstickPanelPtUrineTestStripAutomated
+Based on:       Panel
+Description:    "Urinalysis dipstick panel - Urine by Automated test strip"
+1..1            SubjectOfRecord is type PatientSubjectOfRecord
+                Code is LNC#50556-0 "Urinalysis dipstick panel - Urine by Automated test strip"
+                PanelMembers.Observation
+includes        0..*  UrinalysisDipstickPanelMember  
+
+        EntryElement:   UrinalysisDipstickPanelMember
+        Based on:       LaboratoryObservation
+        Description:    "Members of Urinalysis dipstick panel LNC#50556-0"
+                        Code from UrinalysisDipstickPanelMembersVS
+
+EntryElement:   HepaticFunction2000Panel-SerumOrPlasma  
+Based on:       Panel
+Description:    "24325-3 Hepatic function 2000 panel - Serum or Plasma"
+                Code is LNC#24325-3 "Hepatic function 2000 panel - Serum or Plasma"
+                PanelMembers.Observation
+includes        0..* HepaticFunction2000PanelMember
+
+        EntryElement:   HepaticFunction2000PanelMember
+        Based on:       LaboratoryObservation
+        Description:    "Members of Hepatic Function 2000 panel LNC#24325-3"
+                        Code from HepaticFunctionPanelMembersVS 

parking_lot/shr_behavior.txt

@@ -1,5 +1,5 @@
 Grammar:		DataElement 5.0
-Namespace:		behavior
+Namespace:		shr.sdh
 Description:	"The SHR Behavior domain contains data definitions related to how the person of record acts, feels, or responds to situations."
 Uses:			shr.core
 
@@ -31,13 +31,11 @@ includes 0..1	ReligiousCongregation
 	Value:			CodeableConcept from ReligiousObservanceLevelVS
 
 	Element:		ReligiousRestriction
-	Concept:		TBD
 	Based on:		CodedObservationComponent
 	Description:	"Any restriction on that derives from religion and may impact medical treatment, other than dietary (handled elsewhere)."
 	Value:			CodeableConcept from ReligiousRestrictionVS
 
 	Element:		ReligiousCongregation
-	Concept:		TBD
 	Based on:		ObservationComponent
 	Description:	"A group of place of religious practice."
 	Value:			string
@@ -62,20 +60,18 @@ Value:			CodeableConcept from DietFollowedVS if covered
 
 EntryElement:	HasSufficientFood
 Based on:		SocialHistoryObservation
-Concept:		TBD
 Description:	"Frequency that the person of record unable to obtain food to stay hunger."
 Value:			CodeableConcept from QualitativeFrequencyVS
 				Category is LNC#54511-1 "Behavior"
 
 EntryElement:	DietNutritionConcern
 Based on:		SocialHistoryObservation
-Concept:		TBD
 Description:	"An anxiety or worry about the diet or nutritional intake of the subject."
 Value:			CodeableConcept from DietNutritionConcernVS
 				Category is LNC#54511-1 "Behavior"
 
 EntryElement:	SleepQuality
-Based on:		Panel
+Based on:		ComponentOnlyObservation
 Concept:		LNC#28323-4
 Description:	"Quality of sleep."
 				DataValue from PerformanceGradingScaleVS
@@ -88,27 +84,23 @@ includes 0..1	HoursSleepPerNight
 
 	EntryElement:	SleepQualityCause
 	Based on:		CodedObservationComponent
-	Concept:		TBD
 	Description:	"Reason for poor sleep quality."
 	Value:			CodeableConcept from SleepQualityCauseVS
 
 	EntryElement:	TroubleFallingAsleep
 	Based on:		CodedObservationComponent
-	Concept:		TBD
 	Description:	"How often the subject has trouble falling asleep."
 	Value:			CodeableConcept from QualitativeFrequencyVS
 
 
 	EntryElement:	TroubleStayingAsleep
 	Based on:		CodedObservationComponent
-	Concept:		TBD
 	Description:	"How often the subject has trouble staying asleep."
 	Value:			CodeableConcept from QualitativeFrequencyVS
 
 	EntryElement:	WakeFeelingRested
 	Based on:		CodedObservationComponent
-	Concept:		TBD
-	Description:	"How often the subject feels rested when they wake up."
+		Description:	"How often the subject feels rested when they wake up."
 	Value:			CodeableConcept from QualitativeFrequencyVS
 
 	EntryElement:	HoursSleepPerNight
@@ -120,7 +112,6 @@ includes 0..1	HoursSleepPerNight
 
 EntryElement:	PhysicalActivityPanel
 Based on:		HeadlessPanel
-Concept:		TBD
 Description:	"Questions related to physical activity."
 0..0			Value
 				Category is LNC#54511-1 "Behavior"
@@ -139,49 +130,42 @@ Description:	"The amount of exercise or other physical activity compared to othe
 
 EntryElement:	ExerciseHoursPerWeek
 Based on:		SocialHistoryObservation
-Concept:		TBD
 Description:	"Hours of moderate or vigorous activity per week."
 Value:			IntegerQuantity  // TODO: potentially change to ratio with Units hours per one week
 				Category is LNC#54511-1 "Behavior"
 
 EntryElement:	PhysicalActivityLimitation
-Concept:		TBD
 Based on:		SocialHistoryObservation
 Description:	"Anything that limits physical activity, including health factors, logistical, monetary, or social restrictions."
 Value:			CodeableConcept from PhysicalActivityLimitationVS
 				Category is LNC#54511-1 "Behavior"
 
 
 EntryElement:	ViolentRiskToOthers
-Concept:		TBD
 Based on:		BehaviorPresent
 Description:	"Risk or danger posed by the focal subject to others."
 Value:			CodeableConcept from QualitativeValueScaleVS
 
 EntryElement:	ViolentRiskToSelf
-Concept:		TBD
 Based on:		BehaviorPresent
 Description:	"Risk or danger posed by the focal subject to his or herself."
 Value:			CodeableConcept from QualitativeValueScaleVS
 
 /*
 EntryElement:	Mood
-Concept:		TBD
 Description:	""
 Value:			CodeableConcept
 
 
 
 	Element:		ReasonForBehavior
 	Based on:		ObservationComponent
-	Concept:		TBD
-	Description:	"Why the behavior has taken or is taking place."
+		Description:	"Why the behavior has taken or is taking place."
 	Value:			CodeableConcept
 
 	Element:		ReadinessToChange
 	Based on:		ObservationComponent
-	Concept:		TBD
-	Description:	"How motivated the subject is to change the behavior, if the behavior is ongoing, and change would be beneficial."
+		Description:	"How motivated the subject is to change the behavior, if the behavior is ongoing, and change would be beneficial."
 	Value:			CodeableConcept from QualitativeLikelihoodVS
 
 

parking_lot/shr_behavior_map.txt

@@ -1,5 +1,5 @@
 Grammar:	Map 5.1
-Namespace:	behavior
+Namespace:	shr.sdh
 Target:		FHIR_STU_3
 
 Religion maps to http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient:

parking_lot/shr_behavior_vs.txt

@@ -1,5 +1,5 @@
 Grammar:	ValueSet 5.0  
-Namespace:	behavior
+Namespace:	shr.sdh
 
 ValueSet:           BehaviorFindingVS
 Includes codes descending from SCT#844005 "Behavior finding (finding)"

parking_lot/shr_careplan.txt

@@ -1,19 +1,17 @@
 Grammar:	DataElement 5.0
 Namespace:	careplan
 
-Uses:			shr.core
+Uses:		shr.core
 
 EntryElement:	CareTeam
 Based on:	Entity  // very similar to organization (could be info item)
-Concept:	TBD
 Description: "Planned participants in the coordination and delivery of care for a patient or group."
 0..*		Participant
 //0..*		Participant.ParticipationType from HealthcareRoleVS /* or CodeableConcept from http://hl7.org/fhir/ValueSet/c80-practice-codes
 
 
-EntryElement:	Goal  // Target (Future) Health State
+EntryElement:	        Goal  // Target (Future) Health State
 Based on:		Entity
-Concept:		MTH#C0018017
 Description:	"A broad statement about what should be accomplished for or by a patient or other subject. It represents the intended long-term outcome toward which an individual or a group aspires, and toward which, effort is directed, in the form of activities."
 1..1			Patient
 0..1			Title
@@ -29,19 +27,16 @@ Description:	"A broad statement about what should be accomplished for or by a pa
 0..*			Goal   // subgoals, which may be objectives
 
 Element:		PlannedActivities	
-Concept:		TBD
 Description:	"Activites planned for this goal"
 Value:			ref(ActionTopic)  // restict to Actions with planned context
 
 Element:		ActualActivities	
-Concept:		TBD
 Description:	"Activites carried out for this goal"
 Value:			ref(ActionTopic)  // restict to Actions with performed context
 
 
 Element:		Objective
 Based on:		Goal
-Concept:		TBD
 Description:	"Describes the  of an expected or desired achievement that is well-defined, specific, measurable, and derived from one or more goals. 
 The context is inherited from the context of the parent goal, i.e., if the goal is #proposed, then the objective is also #proposed"
 0..*			Category from http://hl7.org/fhir/ValueSet/observation-category if covered 
@@ -50,13 +45,11 @@ The context is inherited from the context of the parent goal, i.e., if the goal
 0..*			RelatedFinding
 
 		Element:		ResultTargeted
-		Concept:		TBD
-		Description:	"The desired value or status to be achieved."
+				Description:	"The desired value or status to be achieved."
 		Value:			CodeableConcept or Range or Quantity
 
 		Element:		ResultAchieved
-		Concept:		TBD
-		Description:	"The actual value or status achieved."
+				Description:	"The actual value or status achieved."
 		Value:			CodeableConcept or Range or Quantity
 
 
@@ -80,7 +73,7 @@ Description:    "A series of coordinated treatment actions taken with a certain
         0..*    MedicationAdministration  // mlt: to cover clinician-administered meds in a clinical setting.
         0..*    SurgicalProcedure
         0..*    RadiationProcedure
-        0..*	BodySite  // anatomical location is given in the individual actions
+        0..*      // anatomical location is given in the individual actions
         0..0    Device
         0..0    Method
 

parking_lot/shr_immunization.txt

@@ -18,14 +18,13 @@ Description:	"A specific type or manufactured instance of a vaccine, a prophylac
 
 Element: 		ImmunizationTopic
 Based on:		MedicationUseTopic
-Concept:		TBD
 Description:	"Describes the event of a patient being administered a vaccination or a record of a vaccination as reported by a patient, a clinician or another party and may include vaccine reaction information and what vaccination protocol was followed."
 				Medication is type Vaccine // in the case of immunization not given, the vaccine will have a Type, but not a lot or manufacturer. 
 0..1			AnatomicalLocation
 0..1			Dosage
 0..1			DoseSequenceNumber
 0..*			Outcome
-//0..*			ref(AdverseReactionPresenceStatement)
+//0..*			ref(AdverseReaction)
 
 	Element:		DoseSequenceNumber
 	Description:	"Dose number within series."
@@ -43,22 +42,19 @@ Description:	"A vaccination administered to the subject."
 /*
 EntryElement:	ImmunizationNotGiven
 Based on:		ProcedureNotPerformedStatement
-Concept:		TBD
 Description:	"An immunization that was not given to the subject."
 				ImmunizationActionTopic
 //				NonOccurrenceTimeOrPeriod value is type date
 				Reason from http://hl7.org/fhir/ValueSet/no-immunization-reason
 
 EntryElement:	ImmunizationRequested
 Based on:		ProcedureRequestedStatement
-Concept:		TBD
 Description:	"An immunization that is proposed or planned for the subject."
 				StatementTopic is type ImmunizationActionTopic
 				// Need reason value set for Reason
 
 EntryElement:	ImmunizationRequestedAgainst
 Based on:		ProcedureRequestedAgainstStatement
-Concept:		TBD
 Description:	"An immunization that is specifically not recommended, perhaps contraindicated for the individual."
 				StatementTopic is type ImmunizationActionTopic
 				Reason from ...  // TODO: Need value set for RequestedAgainst reasons
@@ -67,7 +63,6 @@ Description:	"An immunization that is specifically not recommended, perhaps cont
 /* Example of detailed profile - Comment out for now
 
 EntryElement:	ZostavaxImmunizationAdministered
-Concept:		TBD
 Based on:		ImmunizationGiven
 				Vaccine is CVX#36 "VZIG"
 1..1			AgeOfSubjectAtTimeOfEvent // extension particular to this vaccination - should be >60 to qualify for reimbursement

parking_lot/shr_immunization_map.txt

@@ -7,7 +7,7 @@ ImmunizationGiven maps to http://hl7.org/fhir/us/core/StructureDefinition/us-cor
 	ImmunizationTopic.Vaccine.LotNumber maps to lotNumber
 	ImmunizationTopic.Vaccine.Manufacturer maps to manufacturer
 	ImmunizationTopic.Vaccine.ExpirationDate maps to expirationDate
-	ImmunizationTopic.Dosage.AdministrationBodySite maps to site
+	ImmunizationTopic.Dosage.AdministrationBodyLocation maps to site
 	ImmunizationTopic.Dosage.RouteIntoBody maps to route
 	ImmunizationTopic.Dosage.DoseAmount maps to doseQuantity
 	constrain vaccinationProtocol to 1..1