WSG-102 Profile Authoring (#52)

* First pass at core profiles

* Profiling

* Previous work

* Fixed generation

* Unintended change removed

input/cql/HIVElements.cql

@@ -73,13 +73,17 @@ define "PREP Prescription":
   [MedicationRequest] MR
     where MR.status = 'completed'
     and MR.intent = 'order'
-    and MR.medication ~ Concepts."PrEP for HIV prevention"
+    and (MR.medication as CodeableConcept in Concepts."PrEP product prescribed Choices"
+    or MR.medication as CodeableConcept in Concepts."Current PrEP regimen Choices")
 
 define "PEP Prescription":
   [MedicationRequest] MR
       where MR.status = 'completed'
       and MR.intent = 'order'
-      and MR.medication ~ Concepts."PEP for HIV prevention"
+      and (MR.medication as CodeableConcept in Concepts."Preferred PEP backbone regimen Choices"
+      or MR.medication as CodeableConcept in Concepts."Alternative PEP backbone regimen Choices"
+      or MR.medication as CodeableConcept in Concepts."Preferred third PEP drug Choices"
+      or MR.medication as CodeableConcept in Concepts."Alternative third PEP drug Choices")
 
 define "routine viral load sample collection":
   [Procedure] P
@@ -2580,10 +2584,10 @@ define "HIV retest prior to starting ART conducted Observation":
 */
 
 define "At elevated risk for HIV acquisition B.DE225":
-  [Observation] O
-    where O.status in { 'final', 'amended', 'corrected' }
-    and exists(O.category OC where OC ~ ConceptsCustom."social-history")
-    and O.code ~ Concepts."At elevated risk for HIV acquisition - HIV.B.DE225"
+  [Condition] C
+    where C.code ~ Concepts."At elevated risk for HIV acquisition - HIV.B.DE225"
+      and C.verificationStatus.text = 'confirmed'
+
 /* End of At elevated risk for HIV acquisition B.DE225 */
 
 /*

input/cql/HIVEncounterElements.cql

@@ -1665,9 +1665,9 @@ define "HIV retest prior to starting ART conducted Observation":
 @description: Client is at elevated risk for HIV acquisition
 */
 define "At elevated risk for HIV acquisition B.DE225":
-  Elements."At elevated risk for HIV acquisition B.DE225" O
-    where O.encounter.references(EncounterId)
-      or O.effective.toInterval() starts on or before Today
+  Elements."At elevated risk for HIV acquisition B.DE225" C
+    where C.prevalenceInterval() starts on or before Today
+      or C.encounter.references(EncounterId)
 /* End of At elevated risk for HIV acquisition B.DE225 */
 
 /*
@@ -1696,6 +1696,7 @@ define "Positive B.DE251":
 define "Positive B.DE251 Condition":
   Elements."Positive B.DE251 Condition" C
     where C.prevalenceInterval() starts on or before Today
+    or C.encounter.references(EncounterId)
 define "Positive B.DE251 Observation":
   Elements."Positive B.DE251 Observation" O
     where O.encounter.references(EncounterId)

input/cql/HIVIndicatorElements.cql

@@ -1558,8 +1558,8 @@ define "Other B.DE222 Observation":
 */
 
 define "At elevated risk for HIV acquisition B.DE225":
-  exists(Elements."At elevated risk for HIV acquisition B.DE225" O 
-  where O.effective.toInterval() overlaps "Measurement Period")
+  exists(Elements."At elevated risk for HIV acquisition B.DE225" C
+    where C.prevalenceInterval() overlaps "Measurement Period")
 /* End of At elevated risk for HIV acquisition B.DE225 */
 
 /*

input/fsh/examples/HivElevatedRiskForAcquisition.fsh

@@ -0,0 +1,9 @@
+Instance: ExampleElevatedHivRiskCondition
+InstanceOf: HivElevatedRiskForAcquisition
+Title: "Example Elevated HIV Risk Condition"
+Description: "This is an example of an Elevated HIV Risk Condition resource based on the HivElevatedRiskForAcquisition profile."
+
+* verificationStatus = #confirmed
+* code = HIVConcepts#HIV.B.DE225
+* subject = Reference(Patient/example-hiv-patient) 
+* onsetDateTime = "2023-01-11T10:00:00Z" 

input/fsh/examples/HivKeyPopulation.fsh

@@ -0,0 +1,11 @@
+Instance: ExampleHivKeyPopulation
+InstanceOf: HivKeyPopulation
+Title: "Example HIV Key Population Observation"
+Description: "This is an example of an HIV Key Population Observation resource based on the HivKeyPopulation profile."
+
+* status = #final
+* category = http://terminology.hl7.org/CodeSystem/observation-category#social-history
+* code = HIVConcepts#HIV.B.DE50 "Key Population Status"
+* subject = Reference(Patient/HivPatient) 
+* effectiveDateTime = "2023-01-12T14:00:00Z" 
+* valueCodeableConcept = HIVConcepts#HIV.B.DE52 "Men who have sex with men"

input/fsh/examples/HivOnArt.fsh

@@ -0,0 +1,10 @@
+Instance: ExampleHivOnArt
+InstanceOf: HivOnArt
+Title: "Example HIV On ART Medication Statement"
+Description: "This is an example of an On ART Medication Statement resource based on the HivOnArtMedicationStatement profile."
+
+* status = #active
+* medicationCodeableConcept = HIVConcepts#HIV.D.DE91
+* subject = Reference(Patient/example-hiv-patient) 
+* effectiveDateTime = "2022-01-17T12:00:00Z" 
+* reasonCode = HIVConcepts#HIV.D.DE38

input/fsh/examples/HivPatient.fsh

@@ -0,0 +1,4 @@
+Instance: ExampleHivPatient
+InstanceOf: HivPatient
+
+* id = "example-hiv-patient"

input/fsh/examples/HivPepPrescriptions.fsh

@@ -0,0 +1,45 @@
+Instance: ExamplePreferredPepBackbonePrescription
+InstanceOf: HivPreferredPepBackbonePrescription
+Title: "Example Preferred PEP Backbone Prescription"
+Description: "This is an example of a preferred PEP backbone prescription resource based on the PreferredPepBackbonePrescription profile."
+
+* status = #completed
+* intent = #order
+* medicationCodeableConcept = HIVConcepts#HIV.C.DE92 "TDF + 3TC"
+* subject = Reference(Patient/example-hiv-patient)
+* authoredOn = "2023-01-12T14:00:00Z" 
+
+Instance: ExampleAltPepBackbonePrescription
+InstanceOf: HivAltPepBackbonePrescription
+Title: "Example Alternative PEP Backbone Prescription"
+Description: "This is an example of an alternative PEP backbone prescription resource based on the AltPepBackbonePrescription profile."
+
+* status = #completed
+* intent = #order
+* medicationCodeableConcept = HIVConcepts#HIV.C.DE96 "ABC + 3TC"
+* subject = Reference(Patient/example-hiv-patient)
+* authoredOn = "2023-01-11T14:00:00Z" 
+
+Instance: ExamplePreferredThirdPepPrescription
+InstanceOf: HivPreferredThirdPepPrescription
+Title: "Example Preferred Third PEP Prescription"
+Description: "This is an example of a preferred third PEP prescription resource based on the PreferredThirdPepPrescription profile."
+
+* status = #completed
+* intent = #order
+* medicationCodeableConcept = HIVConcepts#HIV.C.DE100 "DTG"
+* subject = Reference(Patient/example-hiv-patient)
+* authoredOn = "2023-01-14T14:00:00Z" 
+
+Instance: ExampleAltThirdPepPrescription
+InstanceOf: HivAltThirdPepPrescription
+Title: "Example Alternative Third PEP Prescription"
+Description: "This is an example of an alternative Third PEP prescription resource based on the AltThirdPepPrescription profile."
+
+* status = #completed
+* intent = #order
+* medicationCodeableConcept = HIVConcepts#HIV.C.DE103 "DRV/r"
+* subject = Reference(Patient/example-hiv-patient)
+* authoredOn = "2023-01-10T14:00:00Z" 
+
+

input/fsh/examples/HivPrepPrescriptions.fsh

@@ -0,0 +1,21 @@
+Instance: ExamplePrepProductPrescription
+InstanceOf: HivPrepProductPrescription
+Title: "Example PrEP Product Prescription"
+Description: "This is an example of a PREP Product Prescription resource based on the PrepProductPrescription profile."
+
+* status = #completed
+* intent = #order
+* medicationCodeableConcept = HIVConcepts#HIV.C.DE81
+* subject = Reference(Patient/example-hiv-patient) 
+* authoredOn = "2023-01-05T10:00:00Z" 
+
+Instance: ExampleCurrentPrepRegimenPrescription
+InstanceOf: HivCurrentPrepRegimenPrescription
+Title: "Example Current PrEP Regimen Prescription"
+Description: "This is an example of a current PrEP regimen prescription resource based on the CurrentPrepRegimen profile."
+
+* status = #completed
+* intent = #order
+* medicationCodeableConcept = HIVConcepts#HIV.C.DE19 "TDF"
+* subject = Reference(Patient/example-hiv-patient) 
+* authoredOn = "2023-01-06T10:00:00Z" 

input/fsh/examples/HivStatusCondition.fsh

@@ -0,0 +1,10 @@
+Instance: ExampleHivPositiveCondition
+InstanceOf: HivStatusCondition
+Title: "Example HIV Positive Status Condition"
+Description: "This is an example of an HIV Positive Status Condition resource based on the HivStatusCondition profile."
+
+* clinicalStatus = #active
+* category = http://terminology.hl7.org/CodeSystem/condition-category#encounter-diagnosis
+* code = HIVConcepts#HIV.B.DE116
+* subject = Reference(Patient/example-hiv-patient)
+* onsetDateTime = "2023-01-15T08:30:00Z" 

input/fsh/examples/HivStatusObservation.fsh

@@ -0,0 +1,10 @@
+Instance: ExampleHivStatusPositiveObservation
+InstanceOf: HivStatusObservation
+Title: "Example HIV Positive Status Observation"
+Description: "This is an example of an HIV Positive Status Observation resource based on the HivStatusObservation profile."
+
+* status = #final
+* code = HIVConcepts#HIV.B.DE115
+* subject = Reference(Patient/HivExamplePatient) // Reference to a Patient resource
+* effectiveDateTime = "2023-01-10T09:00:00Z" // Example effective dateTime
+* valueCodeableConcept = HIVConcepts#HIV.B.DE116 "HIV-positive"

input/fsh/examples/HivTest.fsh

@@ -0,0 +1,12 @@
+Instance: HivTest
+InstanceOf: HivTest
+Title: "Example HIV Test Observation for Positive Result"
+Description: "This is an example of an HIV Test Observation resource based on the HivTest profile for a positive test result."
+
+* status = #final
+* category = http://terminology.hl7.org/CodeSystem/observation-category#laboratory
+* code = HIVConcepts#HIV.B.DE81 "HIV Test"
+* subject = Reference(Patient/example-hiv-patient) 
+* effectiveDateTime = "2023-01-01T14:30:00Z" 
+* issued = "2023-01-03T15:00:00Z" // Example issued time
+* valueCodeableConcept = HIVConcepts#HIV.B.DE112 "HIV-positive"

input/fsh/profiles/HivAltPepBackbonePrescription.fsh

@@ -0,0 +1,11 @@
+Profile: HivAltPepBackbonePrescription
+Parent: MedicationRequest
+Description: "A profile for MedicationRequest representing an alternative PEP backbone prescription."
+* ^meta.profile[+] = "http://hl7.org/fhir/uv/crmi/StructureDefinition/crmi-shareablestructuredefinition"
+* ^meta.profile[+] = "http://hl7.org/fhir/uv/crmi/StructureDefinition/crmi-publishablestructuredefinition"
+* ^experimental = true
+* ^title = "Alternative PEP Backbone Prescription"
+* intent = #order
+* medication[x] only CodeableConcept
+* medicationCodeableConcept from HIV.C.DE95 (required)
+

input/fsh/profiles/HivAltThirdPepPrescription.fsh

@@ -0,0 +1,11 @@
+Profile: HivAltThirdPepPrescription
+Parent: MedicationRequest
+Description: "A profile for MedicationRequest representing an alternative Third PEP drug choice prescription."
+* ^meta.profile[+] = "http://hl7.org/fhir/uv/crmi/StructureDefinition/crmi-shareablestructuredefinition"
+* ^meta.profile[+] = "http://hl7.org/fhir/uv/crmi/StructureDefinition/crmi-publishablestructuredefinition"
+* ^experimental = true
+* ^title = "Alternative Third PEP Prescription"
+* intent = #order
+* medication[x] only CodeableConcept
+* medicationCodeableConcept from HIV.C.DE101 (required)
+

input/fsh/profiles/HivCurrentPrepRegimenPrescription.fsh

@@ -0,0 +1,10 @@
+Profile: HivCurrentPrepRegimenPrescription
+Parent: MedicationRequest
+Description: "A profile for MedicationRequest representing a prescription of a current PrEP regimen."
+* ^meta.profile[+] = "http://hl7.org/fhir/uv/crmi/StructureDefinition/crmi-shareablestructuredefinition"
+* ^meta.profile[+] = "http://hl7.org/fhir/uv/crmi/StructureDefinition/crmi-publishablestructuredefinition"
+* ^experimental = true
+* ^title = "Current PrEP Regimen Prescription"
+* intent = #order
+* medication[x] only CodeableConcept
+* medicationCodeableConcept from HIV.C.DE17 (required)

input/fsh/profiles/HivElevatedRiskForAcquisition.fsh

@@ -0,0 +1,9 @@
+Profile: HivElevatedRiskForAcquisition
+Parent: Condition
+Description: "A condition identifying patients at elevated risk for HIV acquisition."
+* ^meta.profile[+] = "http://hl7.org/fhir/uv/crmi/StructureDefinition/crmi-shareablestructuredefinition"
+* ^meta.profile[+] = "http://hl7.org/fhir/uv/crmi/StructureDefinition/crmi-publishablestructuredefinition"
+* ^experimental = true
+* ^title = "Elevated HIV Risk Acquisition Condition"
+* verificationStatus from http://hl7.org/fhir/ValueSet/condition-ver-status (required)
+* code = HIVConcepts#HIV.B.DE225

input/fsh/profiles/HivKeyPopulation.fsh

@@ -0,0 +1,11 @@
+Profile: HivKeyPopulation
+Parent: Observation
+Description: "An observation describing Patient's key population status"
+* ^meta.profile[+] = "http://hl7.org/fhir/uv/crmi/StructureDefinition/crmi-shareablestructuredefinition"
+* ^meta.profile[+] = "http://hl7.org/fhir/uv/crmi/StructureDefinition/crmi-publishablestructuredefinition"
+* ^experimental = true
+* ^title = "Patient Key Population Status"
+* value[x] only CodeableConcept
+* category = http://terminology.hl7.org/CodeSystem/observation-category#social-history
+* valueCodeableConcept from HIV.B.DE50 (required)
+* code = HIVConcepts#HIV.B.DE50

input/fsh/profiles/HivOnArt.fsh

@@ -0,0 +1,11 @@
+Profile: HivOnArt
+Parent: MedicationStatement
+Description: "A medication statement describing a Patient's ART program"
+* ^meta.profile[+] = "http://hl7.org/fhir/uv/crmi/StructureDefinition/crmi-shareablestructuredefinition"
+* ^meta.profile[+] = "http://hl7.org/fhir/uv/crmi/StructureDefinition/crmi-publishablestructuredefinition"
+* ^experimental = true
+* ^title = "On ART Medication Statement"
+* medication[x] only CodeableConcept
+* medicationCodeableConcept from HIV.D.DE90 (required)
+* reasonCode = HIVConcepts#HIV.D.DE38
+

input/fsh/profiles/HivPatient.fsh

@@ -0,0 +1,10 @@
+Profile: HivPatient
+Parent: Patient
+
+
+// Gender
+// Geographic Region
+// Date of Birth
+
+
+

input/fsh/profiles/HivPreferredPepBackbonePrescription.fsh

@@ -0,0 +1,11 @@
+
+Profile: HivPreferredPepBackbonePrescription
+Parent: MedicationRequest
+Description: "A profile for MedicationRequest representing a preferred PEP backbone prescription."
+* ^meta.profile[+] = "http://hl7.org/fhir/uv/crmi/StructureDefinition/crmi-shareablestructuredefinition"
+* ^meta.profile[+] = "http://hl7.org/fhir/uv/crmi/StructureDefinition/crmi-publishablestructuredefinition"
+* ^experimental = true
+* ^title = "Preferred PEP Backbone Prescription"
+* intent = #order
+* medication[x] only CodeableConcept
+* medicationCodeableConcept from HIV.C.DE91 (required)

input/fsh/profiles/HivPreferredThirdPepPrescription.fsh

@@ -0,0 +1,11 @@
+Profile: HivPreferredThirdPepPrescription
+Parent: MedicationRequest
+Description: "A profile for MedicationRequest representing the preferred third PEP drug choice prescription."
+* ^meta.profile[+] = "http://hl7.org/fhir/uv/crmi/StructureDefinition/crmi-shareablestructuredefinition"
+* ^meta.profile[+] = "http://hl7.org/fhir/uv/crmi/StructureDefinition/crmi-publishablestructuredefinition"
+* ^experimental = true
+* ^title = "Preferred Third PEP Prescription"
+* intent = #order
+* medication[x] only CodeableConcept
+* medicationCodeableConcept from HIV.C.DE99 (required)
+

input/fsh/profiles/HivPrepActive.fsh

@@ -0,0 +1,11 @@
+Profile: HivPrepActive
+Parent: MedicationStatement
+Description: "A medication statement describing a patient on active PrEP"
+* ^meta.profile[+] = "http://hl7.org/fhir/uv/crmi/StructureDefinition/crmi-shareablestructuredefinition"
+* ^meta.profile[+] = "http://hl7.org/fhir/uv/crmi/StructureDefinition/crmi-publishablestructuredefinition"
+* ^experimental = true
+* ^title = "HIV Prep Active"
+* reasonCode = HIVConcepts#HIV.C.DE76
+* medicationCodeableConcept from HIV.C.DE80 (required)
+
+

input/fsh/profiles/HivPrepProductPrescription.fsh

@@ -0,0 +1,10 @@
+Profile: HivPrepProductPrescription
+Parent: MedicationRequest
+Description: "A profile for MedicationRequest representing a prescription of a PrEP product."
+* ^meta.profile[+] = "http://hl7.org/fhir/uv/crmi/StructureDefinition/crmi-shareablestructuredefinition"
+* ^meta.profile[+] = "http://hl7.org/fhir/uv/crmi/StructureDefinition/crmi-publishablestructuredefinition"
+* ^experimental = true
+* ^title = "PrEP Product Prescription"
+* intent = #order
+* medication[x] only CodeableConcept
+* medicationCodeableConcept from HIV.C.DE80 (required)

input/fsh/profiles/HivStatusCondition.fsh

@@ -0,0 +1,10 @@
+Profile: HivStatusCondition
+Parent: Condition
+Description: "A condition representing a patient's HIV status."
+* ^meta.profile[+] = "http://hl7.org/fhir/uv/crmi/StructureDefinition/crmi-shareablestructuredefinition"
+* ^meta.profile[+] = "http://hl7.org/fhir/uv/crmi/StructureDefinition/crmi-publishablestructuredefinition"
+* ^experimental = true
+* ^title = "HIV Status Condition"
+* clinicalStatus from http://hl7.org/fhir/ValueSet/condition-clinical (required) 
+* category = http://terminology.hl7.org/CodeSystem/condition-category#encounter-diagnosis
+* code from http://smart.who.int/hiv/ValueSet/HIV.B.DE115 (required)

input/fsh/profiles/HivStatusObservation.fsh

@@ -0,0 +1,10 @@
+Profile: HivStatusObservation
+Parent: Observation
+Description: "An observation representing a patient's HIV status."
+* ^meta.profile[+] = "http://hl7.org/fhir/uv/crmi/StructureDefinition/crmi-shareablestructuredefinition"
+* ^meta.profile[+] = "http://hl7.org/fhir/uv/crmi/StructureDefinition/crmi-publishablestructuredefinition"
+* ^experimental = true
+* ^title = "HIV Status Observation"
+* code = HIVConcepts#HIV.B.DE115
+* value[x] only CodeableConcept
+* valueCodeableConcept from http://smart.who.int/hiv/ValueSet/HIV.B.DE115 (required)

input/fsh/profiles/HivTest.fsh

@@ -0,0 +1,17 @@
+Profile: HivTest
+Parent: Observation
+Description: "An DAK-specific HIV test observation with possible results"
+* ^meta.profile[+] = "http://hl7.org/fhir/uv/crmi/StructureDefinition/crmi-shareablestructuredefinition"
+* ^meta.profile[+] = "http://hl7.org/fhir/uv/crmi/StructureDefinition/crmi-publishablestructuredefinition"
+* ^experimental = true
+* ^title = "HIV Test"
+* code = HIVConcepts#HIV.B.DE81
+* category = http://terminology.hl7.org/CodeSystem/observation-category#laboratory
+* value[x] only CodeableConcept
+* valueCodeableConcept from HIV.B.DE111 (required)
+* effective[x] ^short = "Time at which test performed"
+* effective[x] only dateTime or instant
+* effective[x] ^definition = "The point in time at which the test was performed"
+* issued ^short = "Time at which test results returned"
+* issued ^definition = "The point in time at which the test results were returned to the patient or provider"
+

input/fsh/profiles/template.fsh.tmpl

@@ -0,0 +1,8 @@
+Profile: 
+Parent: 
+Description: ""
+* ^meta.profile[+] = "http://hl7.org/fhir/uv/crmi/StructureDefinition/crmi-shareablestructuredefinition"
+* ^meta.profile[+] = "http://hl7.org/fhir/uv/crmi/StructureDefinition/crmi-publishablestructuredefinition"
+* ^experimental = true
+* ^title = ""
+