Merge pull request #230 from standardhealth/dev

Many collected changes from Dev to Master

.gitignore

@@ -0,0 +1,2 @@
+/.vscode
+.DS_Store

README.md

@@ -2,11 +2,11 @@
 
 The Standard Health Record Initiative is working to create a single, high-quality health record for every individual in the United States.  For more information, see [standardhealthrecord.org](http://standardhealthrecord.org/).
 
-This GitHub repository represents an evolving computable definition of the Standard Health Record and its contents.  It represents SHR namespaces,elements, valusets, and mappings via the SIMPL format, as formally defined in [shr-grammar](https://github.com/standardhealth/shr-grammar).  The SHR definitions (and SIMPL format) are works in progress and subject to change.
+This GitHub repository represents an evolving computable definition of the Standard Health Record and its contents.  It represents SHR namespaces,elements, valusets, and mappings via the CIMPL format, as formally defined in [shr-grammar](https://github.com/standardhealth/shr-grammar).  The SHR definitions (and CIMPL format) are works in progress and subject to change.
 
 # Related Projects
 
-There are a number of projects based on the SHR, but the following projects are most closely related to the SIMPL definitional files:
+There are a number of projects based on the SHR, but the following projects are most closely related to the CIMPL definitional files:
 * [shr-grammar](https://github.com/standardhealth/shr-grammar): The formal [ANTLR4](http://www.antlr.org/) grammar definition for the SHR format
-* [shr-text-import](https://github.com/standardhealth/shr-text-import): ES6 library for importing SIMPL files into ES6 models using the ANTLR4 grammar.
-* [shr-cli](https://github.com/standardhealth/shr-cli): A [Node.js](https://nodejs.org/)-based command-line tool for importing a folder of SIMPL files and exporting into other formats.  This is particularly useful to SHR authors since it will report out any errors in the definition files.
+* [shr-text-import](https://github.com/standardhealth/shr-text-import): ES6 library for importing CIMPL files into ES6 models using the ANTLR4 grammar.
+* [shr-cli](https://github.com/standardhealth/shr-cli): A [Node.js](https://nodejs.org/)-based command-line tool for importing a folder of CIMPL files and exporting into other formats.  This is particularly useful to SHR authors since it will report out any errors in the definition files.

shr_behavior.txt → parking_lot/shr_behavior.txt

@@ -1,7 +1,7 @@
 Grammar:		DataElement 5.0
-Namespace:		shr.behavior
+Namespace:		behavior
 Description:	"The SHR Behavior domain contains data definitions related to how the person of record acts, feels, or responds to situations."
-Uses:			shr.core, shr.base, cimi.core, cimi.context, cimi.topic, cimi.statement, cimi.entity, cimi.element, cimi.encounter, shr.condition
+Uses:			shr.core
 
 
 CodeSystem:     LNC = http://loinc.org
@@ -10,243 +10,143 @@ CodeSystem:     MTH = http://ncimeta.nci.nih.gov
 CodeSystem:     UCUM = http://unitsofmeasure.org
 
 
-Element: 		BehavioralTopic
-Concept:		MTH#C0004927
-Based on:		AssertionTopic
-Description:	"Topic for observable responses, actions, or activities of the subject, independent of context. Can be used to assert or deny behaviors."
-				TopicCode should be from BehaviorFindingVS
-				Category is LNC#54511-1 "Behavior"
-
-
-EntryElement:	BehaviorAbsent
-Based on:		ClinicalStatement
-Concept:		TBD
-Description:	"A statement about a response, action, or activity not demonstrated by the subject."
-				StatementTopic is type BehaviorTopic
-				StatementContext is type AbsenceContext
-
-EntryElement: 	BehaviorPresent
-Based on:		ClinicalStatement
-Concept:		MTH#C0004927
-Description:	"A statement about observable responses, actions, or activities of the subject."
-				StatementTopic is type BehaviorTopic
-				StatementContext is type PresenceContext
-
-
-EntryElement:	SubstanceUsePresent
-Based on:		ConditionPresent   // MedicationUse
-Concept:		MTH#C024251
-Description:	"Assertion concerning the past or current use of a substance (alcohol, recreational drugs, illegal drugs, or abuse of prescription medication) that could negatively impact the subject's health."
-				TopicCode should be from SubstanceAbuseVS
-Status
-	CodeableConcept from SubstanceOfAbuseVS  	312417001
-0..1	FrequencyOfUse
-0..1	ExposureRoute
-0..1	ExposureMethod
-0..*	ExposureAmount
-
-		Element:		FrequencyOfUse
-		Based on:		EvaluationComponent
-		Concept:		MTH#C0556346
-		Description:	"A description of the frequency of substance use."
-		Value:			CodeableConcept could be from SemiquantitativeFrequencyVS	
-
-
-
-
-EntryElement:   IntravenousDrugUse
-Based on:       SubstanceUsePresent
-Concept:        MTH#C0242566
-Description:    "Records whether the subject injects recreational drugs."
-1..1            ExposureRoute is MTH#C1522726 "Intravenous route"
-1..1            ExposureMethod is MTH#C0021494 "Intravenous Injection"
-
-
-EntryElement:	NicotineUse
-Based on:		SubstanceUse
-Concept:		LNC#11367-0
-Description:	"The subject's current or past use of nicotine."
-				Value is MTH#C2363943 "Nicotine"
-//1..1            EvaluationComponent.ExposureRoute from TBD "NicotineRouteVS"  
-//1..1            EvaluationComponent.ExposureMethod from TBD "NicotineExposureMethodVS"  e.g. first hand, second hand, smoked, vaped, chewed
-
-
-// It is not clear how to handle ONC smoking status except as a simple observation. It should really be aligned with SubstanceUsed with the details recorded in attributes."
-EntryElement:	ONCSmokingStatus
-Based on:		BehaviorPresent
-Concept:		LNC#72166-2
-Description:	"Records the extent of the subject's use of tobacco."
-Value:			CodeableConcept from http://hl7.org/fhir/us/core/ValueSet/us-core-observation-ccdasmokingstatus
-				TopicCode is LNC#72166-2
-1..1			Subject // cardinality constraint
-
-// How can we indicate that a subject used to be an alcoholic, but is now sober?
-EntryElement:	AlcoholUse
-Based on:		SubstanceUse
-Concept:		MTH#C0001948
-Description:	"The subject's current or past use of alcohol."
-				Value is SCT#398624005 "alcohol"
-				EvaluationMethod from AlcoholUseScreeningToolVS
-				PanelMembers.EvaluationTopic
-includes 0..1	AlcoholBingeFrequency
-
-	Element:		AlcoholBingeFrequency
-	Based on:		QuestionAnswerRecorded
-	Concept:		MTH#C0556346
-	Description:	"How often have you had 6 or more Units if female, or 8 or more if male, on a single occasion in the last year?."
-	Value:			CodeableConcept from SemiquantitativeFrequencyVS
-
-
-EntryElement:	SubstanceAbuseTreatment
-Concept: 		TBD
-Based on:		ProcedurePerformed
-Description:	"The treatment program used to address a substance abuse problem."
-				TopicCode from SubstanceAbuseTreatmentTypeVS
-
-//--------------------------
-
-EntryElement:	ReligionInformation
-Concept:		
+EntryElement:	ReligionInformation	
 Based on:		ComponentOnlyNonLaboratoryObservation
-				ObservationTopic.EvaluationComponent
+				ObservationTopic.ObservationComponent
 includes 0..*	ReligiousAffiliation
 includes 0..1	DegreeOfReligiousObservance
 includes 0..*	ReligiousRestriction
 includes 0..1	ReligiousCongregation
 
-	Element:		ReligiousAffiliation
-	Based on:		CodedEvaluationComponent
+	EntryElement:	ReligiousAffiliation
+	Based on:		CodedObservationComponent
 	Concept:		SCT#160538000
 	Description:	"The affiliation of the person with a recognized religious group." 
 	Value:			CodeableConcept from http://hl7.org/fhir/ValueSet/v3-ReligiousAffiliation
 
 	Element:		DegreeOfReligiousObservance
-	Based on:		CodedEvaluationComponent
+	Based on:		CodedObservationComponent
 	Concept:		SCT#160553008
 	Description:	"The extent to which the religious practice is actively followed."
 	Value:			CodeableConcept from ReligiousObservanceLevelVS
 
 	Element:		ReligiousRestriction
 	Concept:		TBD
-	Based on:		CodedEvaluationComponent
+	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:		EvaluationComponent
+	Based on:		ObservationComponent
 	Description:	"A group of place of religious practice."
 	Value:			string
 
 //------------------------
 
 EntryElement:	Nutrition
 Based on:		Observation
-Concept:		
 Description:	"Quality of nutrition."
 Value:			CodeableConcept from PerformanceGradingScaleVS
-				ObservationTopic.EvaluationComponent
+				ObservationTopic.ObservationComponent
 includes 0..*	DietFollowed
 includes 0..1	HasSufficientFood
 includes 0..1	DietNutritionConcern
 
 
 EntryElement:	DietFollowed
-Concept:		TBD
-Based on:		QuestionAnswerRecorded
+Based on:		SocialHistoryObservation
 Description:	"A type of nutritional plan followed by the subject."
 Value:			CodeableConcept from DietFollowedVS if covered
 				Category is LNC#54511-1 "Behavior"
 
 EntryElement:	HasSufficientFood
-Based on:		QuestionAnswerRecorded
+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:		QuestionAnswerRecorded
+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:		Observation
+Based on:		Panel
 Concept:		LNC#28323-4
 Description:	"Quality of sleep."
-Value:			CodeableConcept from PerformanceGradingScaleVS
-				ObservationTopic.EvaluationComponent
+				DataValue from PerformanceGradingScaleVS
+				Components.ObservationComponent
 includes 0..*	SleepQualityCause
 includes 0..1	TroubleFallingAsleep
 includes 0..1	TroubleStayingAsleep
 includes 0..1	WakeFeelingRested
 includes 0..1	HoursSleepPerNight
 
 	EntryElement:	SleepQualityCause
-	Based on:		CodedEvaluationComponent
+	Based on:		CodedObservationComponent
 	Concept:		TBD
 	Description:	"Reason for poor sleep quality."
 	Value:			CodeableConcept from SleepQualityCauseVS
 
 	EntryElement:	TroubleFallingAsleep
-	Based on:		CodedEvaluationComponent
+	Based on:		CodedObservationComponent
 	Concept:		TBD
 	Description:	"How often the subject has trouble falling asleep."
 	Value:			CodeableConcept from QualitativeFrequencyVS
 
 
 	EntryElement:	TroubleStayingAsleep
-	Based on:		CodedEvaluationComponent
+	Based on:		CodedObservationComponent
 	Concept:		TBD
 	Description:	"How often the subject has trouble staying asleep."
 	Value:			CodeableConcept from QualitativeFrequencyVS
 
 	EntryElement:	WakeFeelingRested
-	Based on:		CodedEvaluationComponent
+	Based on:		CodedObservationComponent
 	Concept:		TBD
 	Description:	"How often the subject feels rested when they wake up."
 	Value:			CodeableConcept from QualitativeFrequencyVS
 
 	EntryElement:	HoursSleepPerNight
-	Based on:		EvaluationComponent
+	Based on:		ObservationComponent
 	Concept:		LNC#65968-0
 	Description:	"Typical hours spent sleeping per night."
 	Value:			Quantity with units UCUM#hr
 
 
-
-
 EntryElement:	PhysicalActivityPanel
-Based on:		Observation
+Based on:		HeadlessPanel
 Concept:		TBD
 Description:	"Questions related to physical activity."
 0..0			Value
 				Category is LNC#54511-1 "Behavior"
-				PanelMembers.EvaluationTopic
+				PanelMembers.Observation
 includes 0..1	PhysicalActivityLevel
 includes 0..1	ExerciseHoursPerWeek
 includes 0..*	PhysicalActivityLimitation
 
 
 EntryElement:	PhysicalActivityLevel
-Based on:		QuestionAnswerRecorded
+Based on:		CodedSocialHistoryObservation
 Concept:		LNC#28323-4
 Description:	"The amount of exercise or other physical activity compared to others of the same age.  See BMC Medical Research Methodology 2012 12:20 1471-2288."
-Value:			CodeableConcept from QualitativeValueScaleVS
+				DataValue from QualitativeValueScaleVS
 				Category is LNC#54511-1 "Behavior"
 
 EntryElement:	ExerciseHoursPerWeek
-Based on:		QuestionAnswerRecorded
+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:		QuestionAnswerRecorded
+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"
@@ -273,13 +173,13 @@ Value:			CodeableConcept
 
 
 	Element:		ReasonForBehavior
-	Based on:		EvaluationComponent
+	Based on:		ObservationComponent
 	Concept:		TBD
 	Description:	"Why the behavior has taken or is taking place."
 	Value:			CodeableConcept
 
 	Element:		ReadinessToChange
-	Based on:		EvaluationComponent
+	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."
 	Value:			CodeableConcept from QualitativeLikelihoodVS

shr_behavior_map.txt → parking_lot/shr_behavior_map.txt

@@ -1,11 +1,7 @@
 Grammar:	Map 5.1
-Namespace:	shr.behavior
+Namespace:	behavior
 Target:		FHIR_STU_3
 
-
-ONCSmokingStatus maps to http://hl7.org/fhir/us/core/StructureDefinition/us-core-smokingstatus:
-
-
 Religion maps to http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient:
 	Value maps to http://hl7.org/fhir/StructureDefinition/patient-religion
 

shr_behavior_vs.txt → parking_lot/shr_behavior_vs.txt

@@ -1,5 +1,5 @@
 Grammar:	ValueSet 5.0  
-Namespace:	shr.behavior
+Namespace:	behavior
 
 ValueSet:           BehaviorFindingVS
 Includes codes descending from SCT#844005 "Behavior finding (finding)"
@@ -14,27 +14,6 @@ Description:		"Includes religious restrictions that could impact care, other tha
 #no_transfusion		"Cannot receive blood products"
 #no_treatment		"Cannot receive medical treatment"
 
-ValueSet:			SubstanceOfAbuseVS
-Includes codes descending from SCT#312417001 "substance of abuse"
-
-
-ValueSet:				SubstanceAbuseTreatmentTypeVS
-#day_treatment			"Day Treatment Services"
-#inpatient				"Inpatient/Hospital"
-#inpatient_detox		"Hospital Inpatient Detoxification Services"
-#ambulatory				"Outpatient services"
-#ambulatory_detox		"Ambulatory Detoxification Services"
-#outreach				"Outreach Services"
-#intensive_outpatient	"Intensive Outpatient Services"
-#methadone_treatment	"Methadone Treatment Services"
-#residental_rehab		"Residential/Rehabilitation Services"
-#after_care				"After Care Services"
-#recovery_support		"Recovery Support Services"
-
-ValueSet:				AlcoholUseScreeningToolVS
-#audit					"AUDIT"
-#audit_c				"AUDIT-C"
-#crafft					"CRAFFT"
 
 ValueSet:				DietFollowedVS
 #vegetarian				"Vegetarian diet"