Add initial stab at Basic Composition for COVID case report #83
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| Profile: WhoCrCompositionBasic | ||
| Parent: Composition | ||
| Id: who-cr-composition-basic | ||
| Description: "WHO Case Reporting Composition - basic support for initial PoC" | ||
| Title: "WHO Case Reporting Composition - Basic" | ||
| * type = $LNC#95412-3 | ||
| * category = $LNC#55751-2 | ||
| * encounter 1..1 | ||
| * identifier 1..1 | ||
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| * section ^slicing.discriminator.type = #value | ||
| * section ^slicing.discriminator.path = "code.coding.code" | ||
| * section ^slicing.rules = #openAtEnd | ||
| * section ^slicing.ordered = true | ||
| * section ^slicing.description = "Slice of composition.section based on code" | ||
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| * section contains | ||
| patientInformation 1..1 and | ||
| clinicalStatus 1..1 and | ||
| exposureRisk 1..1 | ||
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| * section[patientInformation].title = "patient information" | ||
| * section[patientInformation].code = http://test.org/sectionCode#patientinformation | ||
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| * section[patientInformation].entry only Reference(WhoCrObservationAge or WhoCrObservationBirthSex) | ||
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| * section[clinicalStatus].title = "clinical status" | ||
| * section[clinicalStatus].code = http://test.org/sectionCode#clinicalStatus | ||
| * section[clinicalStatus].entry only Reference(WhoCrObservationLabTestDate or WhoCrObservationSymptoms or WhoCrObservationOnsetDate or WhoCrObservationComorbidities) | ||
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| * section[exposureRisk].title = "exposure risk" | ||
| * section[exposureRisk].code = http://test.org/sectionCode#exposureRisk | ||
| * section[exposureRisk].entry only Reference(WhoCrObservationHasTravelled) | ||
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| Profile: WhoCrEncounter | ||
| Parent: Encounter | ||
| Id: who-cr-encounter | ||
| Title: "WHO CR Encounter" | ||
| Description: "WHO Encounter for a case report" | ||
| * location 1..1 | ||
| * reasonCode 1..* | ||
| * reasonCode from WhoCrValueSetReasonForCovid19Testing | ||
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| Profile: WhoCrLocation | ||
| Parent: Location | ||
| Id: who-cr-location | ||
| Title: "WHO CR Location" | ||
| Description: "WHO Location for case report" | ||
| * address 1..1 | ||
| * address.country 1..1 | ||
| * address.state 1..1 | ||
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| Profile: WhoCrObservationAge | ||
| Parent: Observation | ||
| Id: who-cr-observation-age | ||
| Title: "WHO CR Observation Age" | ||
| Description: "WHO Observation of age for case report" | ||
| * code = $LNC#30525-0 | ||
| * value[x] only Quantity | ||
| * valueQuantity.value 1..1 | ||
| * valueQuantity from WhoCrValueSetAgeUnits | ||
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| Profile: WhoCrObservationBirthSex | ||
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There was a problem hiding this comment. Do we need to profile all these observations to have our patient as the subject? For observations from the QuestionnaireResponse, we should have derivedFrom pointing to the QuestionnaireResponse. However, I think a system might generate these observations directly without using the QR, so we either need two profiles or need to make having the derivedFrom as optional. |
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| Parent: Observation | ||
| Id: who-cr-observation-birth-sex | ||
| Title: "WHO CR Observation Birth Sex" | ||
| Description: "WHO Observation of birth sex for case report" | ||
| * code = $LNC#76689-9 | ||
| * value[x] only CodeableConcept | ||
| * valueCodeableConcept 1..1 | ||
| * valueCodeableConcept from WhoCrValueSetSexAtBirth | ||
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There was a problem hiding this comment. I see this isn't your work but do you know why does this linked valueset deliberately excludes There was a problem hiding this comment. I think that is because that is what the WHO form that this work is based off specifies. There was a problem hiding this comment. Yeah, it's a stupid value set. @litlfred is following up with WHO on improving it. |
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| Profile: WhoCrObservationLabTestDate | ||
| Parent: Observation | ||
| Id: who-cr-observation-lab-test-date | ||
| Title: "WHO CR Observation Lab Test Date" | ||
| Description: "WHO Observation for lab test date" | ||
| * code = http://test.org/obsCode#lab-test-date // TODO: code not defined in questionnaire either | ||
| * value[x] only dateTime | ||
| * valueDateTime 1..1 | ||
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| Profile: WhoCrObservationSymptoms | ||
| Parent: Observation | ||
| Id: who-cr-observation-symptoms | ||
| Title: "WHO CR Observation Symptoms" | ||
| Description: "WHO Observation if the patient has any symptoms for case report" | ||
| * code = http://test.org/obsCode#symptoms // TODO: code not defined in questionnaire either | ||
| * value[x] only CodeableConcept | ||
| * valueCodeableConcept 1..1 | ||
| * valueCodeableConcept from WhoCrValueSetYesNo | ||
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There was a problem hiding this comment. The url associated with this value set code does not appear to resolve anywhere? There was a problem hiding this comment. I also noticed that. It might be just used as an identifier rather than pointing to somewhere real but don't really know. There was a problem hiding this comment. Just odd because the url alias below it does point to a real site :| |
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| Profile: WhoCrObservationOnsetDate | ||
| Parent: Observation | ||
| Id: who-cr-observation-onset-date | ||
| Title: "WHO CR Observation Symptoms Onset Date" | ||
| Description: "WHO Observation for date of symptoms onset" | ||
| * code = $LNC#65222-2 | ||
| * value[x] only dateTime | ||
| * valueDateTime 1..1 | ||
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| Profile: WhoCrObservationComorbidities | ||
| Parent: Observation | ||
| Id: who-cr-observation-comorbidities | ||
| Title: "WHO CR Observation Co-morbidities" | ||
| Description: "WHO Observation if the patient has any co-morbidities for case report" | ||
| * code = $LNC#75618-9 | ||
| * value[x] only CodeableConcept | ||
| * valueCodeableConcept 1..1 | ||
| * valueCodeableConcept from WhoCrValueSetYesNo | ||
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| Profile: WhoCrObservationHasTravelled | ||
| Parent: Observation | ||
| Id: who-cr-observation-has-travelled | ||
| Title: "WHO CR Observation Has Travelled" | ||
| Description: "WHO Observation if the patient has travelled in the past 14 days prior to symptom onset for case report" | ||
| * code = $LNC#96542-6 | ||
| * value[x] only CodeableConcept | ||
| * valueCodeableConcept 1..1 | ||
| * valueCodeableConcept from WhoCrValueSetYesNo | ||
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| /** | ||
| * Examples | ||
| */ | ||
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| Instance: WhoCrBundleExample | ||
| InstanceOf: Bundle | ||
| Usage: #example | ||
| Title: "Who Cr Bundle Example" | ||
| Description: "Example of a clinical bundle representing a case report" | ||
| * type = #document | ||
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There was a problem hiding this comment. @de-laz the should be a #transaction - the document Bundle won't create the individual resources as we need them. If we need to get all the related documents together again in a clinical context this would be done with the composition resource which has a reference to all related resources |
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| * entry[+].fullUrl = "http://test.org/fhir/Composition/WhoCrCompositionBasicExample" | ||
| * entry[=].resource = WhoCrCompositionBasicExample | ||
| * entry[+].fullUrl = "http://test.org/fhir/Encounter/WhoCrEncounterExample" | ||
| * entry[=].resource = WhoCrEncounterExample | ||
| * entry[+].fullUrl = "http://test.org/fhir/Location/WhoCrLocationExample" | ||
| * entry[=].resource = WhoCrLocationExample | ||
| * entry[+].fullUrl = "http://test.org/fhir/Practitioner/WhoCrPractitionerExample" | ||
| * entry[=].resource = WhoCrPractitionerExample | ||
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There was a problem hiding this comment. @de-laz remove these lines - the resources shouldn't be here as they would already exist in the registry - we are only referencing them - not creating new ones |
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| * entry[+].fullUrl = "http://test.org/fhir/Observation/WhoCrObservationAgeExample" | ||
| * entry[=].resource = WhoCrObservationAgeExample | ||
| * entry[+].fullUrl = "http://test.org/fhir/Observation/WhoCrObservationBirthSexExample" | ||
| * entry[=].resource = WhoCrObservationBirthSexExample | ||
| * entry[+].fullUrl = "http://test.org/fhir/Observation/WhoCrObservationLabTestDateExample" | ||
| * entry[=].resource = WhoCrObservationLabTestDateExample | ||
| * entry[+].fullUrl = "http://test.org/fhir/Observation/WhoCrObservationSymptomsExample" | ||
| * entry[=].resource = WhoCrObservationSymptomsExample | ||
| * entry[+].fullUrl = "http://test.org/fhir/Observation/WhoCRObservationOnsetDateExample" | ||
| * entry[=].resource = WhoCRObservationOnsetDateExample | ||
| * entry[+].fullUrl = "http://test.org/fhir/Observation/WhoCrObservationComorbiditiesExample" | ||
| * entry[=].resource = WhoCrObservationComorbiditiesExample | ||
| * entry[+].fullUrl = "http://test.org/fhir/Observation/WhoCrObservationHasTravelledExample" | ||
| * entry[=].resource = WhoCrObservationHasTravelledExample | ||
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| Instance: WhoCrCompositionBasicExample | ||
| InstanceOf: WhoCrCompositionBasic | ||
| Usage: #example | ||
| Title: "Who Cr Composition Basic Example" | ||
| Description: "Basic Composition example" | ||
| * status = #final | ||
| * identifier.system = "http://test.org/identifier/who-covid-19-case-report" | ||
| * identifier.value = "1111" | ||
| * encounter = Reference(WhoCrEncounterExample) | ||
| * date = "2021-01-18" | ||
| * author = Reference(WhoCrPractitionerExample) | ||
| * title = "WHO COVID-19 Case Report" | ||
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| * section[+].title = "patient information" | ||
| * section[=].code = http://test.org/sectionCode#patientinformation | ||
| * section[=].entry[+] = Reference(WhoCrObservationAgeExample) | ||
| * section[=].entry[+] = Reference(WhoCrObservationBirthSexExample) | ||
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| * section[+].title = "clinical status" | ||
| * section[=].code = http://test.org/sectionCode#clinicalStatus | ||
| * section[=].entry[+] = Reference(WhoCrObservationLabTestDateExample) | ||
| * section[=].entry[+] = Reference(WhoCrObservationSymptomsExample) | ||
| * section[=].entry[+] = Reference(WhoCRObservationOnsetDateExample) | ||
| * section[=].entry[+] = Reference(WhoCrObservationComorbiditiesExample) | ||
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| * section[+].title = "exposure risk" | ||
| * section[=].code = http://test.org/sectionCode#exposureRisk | ||
| * section[=].entry[+] = Reference(WhoCrObservationHasTravelledExample) | ||
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| Instance: WhoCrEncounterExample | ||
| InstanceOf: Encounter | ||
| Usage: #example | ||
| Title: "WHO CR Encounter Example" | ||
| Description: "Encounter example" | ||
| * location.location = Reference(WhoCrLocationExample) | ||
| * status = #finished | ||
| * class = http://terminology.hl7.org/CodeSystem/v3-ActCode#ACUTE | ||
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| Instance: WhoCrLocationExample | ||
| InstanceOf: Location | ||
| Usage: #example | ||
| Title: "Who Cr Location Example" | ||
| Description: "Location example" | ||
| * address.country = "ZA" | ||
| * address.state = "KZN" | ||
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| Instance: WhoCrPractitionerExample | ||
| InstanceOf: Practitioner | ||
| Usage: #example | ||
| Title: "Who Cr Practitioner Example" | ||
| Description: "Practitioner example" | ||
| * name[0].given[0] = "Homer" | ||
| * name[1].family = "Simpson" | ||
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| Instance: WhoCrObservationAgeExample | ||
| InstanceOf: WhoCrObservationAge | ||
| Usage: #example | ||
| Title: "Who Cr Observation Age Example" | ||
| Description: "Observation Age Example" | ||
| * status = #final | ||
| * valueQuantity.value = 35 | ||
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| Instance: WhoCrObservationBirthSexExample | ||
| InstanceOf: WhoCrObservationBirthSex | ||
| Usage: #example | ||
| Title: "Who Cr Observation Birth Sex Example" | ||
| Description: "Observation Birth Sex Example" | ||
| * status = #final | ||
| * valueCodeableConcept = $cs-gender#male | ||
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| Instance: WhoCrObservationLabTestDateExample | ||
| InstanceOf: WhoCrObservationLabTestDate | ||
| Usage: #example | ||
| Title: "Who Cr Observation Lab Test Date Example" | ||
| Description: "Lab Test Date Example" | ||
| * status = #final | ||
| * valueDateTime = "2021-01-18" | ||
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| Instance: WhoCrObservationSymptomsExample | ||
| InstanceOf: WhoCrObservationSymptoms | ||
| Usage: #example | ||
| Title: "Who Cr Observation Symptoms Example" | ||
| Description: "Observation Symptoms Example" | ||
| * status = #final | ||
| * valueCodeableConcept = $cs-v2-0136#Y | ||
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| Instance: WhoCRObservationOnsetDateExample | ||
| InstanceOf: WhoCrObservationOnsetDate | ||
| Usage: #example | ||
| Title: "Who CR Observation Onset DateExample" | ||
| Description: "Observation Onset DateExample" | ||
| * status = #final | ||
| * valueDateTime = "2021-01-15" | ||
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| Instance: WhoCrObservationComorbiditiesExample | ||
| InstanceOf: WhoCrObservationComorbidities | ||
| Usage: #example | ||
| Title: "Who Cr Observation ComorbiditiesExample" | ||
| Description: "Observation ComorbiditiesExample" | ||
| * status = #final | ||
| * valueCodeableConcept = $cs-v2-0136#Y | ||
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| Instance: WhoCrObservationHasTravelledExample | ||
| InstanceOf: WhoCrObservationHasTravelled | ||
| Usage: #example | ||
| Title: "Who Cr Observation Has Travelled Example" | ||
| Description: "Observation Has Travelled Example" | ||
| * status = #final | ||
| * valueCodeableConcept = $cs-v2-0136#N | ||
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| Original file line number | Diff line number | Diff line change |
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| Instance: WhoCrQuestionnaireResponseBasic | ||
| InstanceOf: QuestionnaireResponse | ||
| Usage: #example | ||
| Title: "Who Cr Questionnaire Response Basic" | ||
| Description: "Questionnaire response example" | ||
| * identifier.system = "http://test.org/response-id" | ||
| * identifier.value = "1111" | ||
| * questionnaire = Canonical(WhoCrQuestionnaireCovid19Surveillance) | ||
| * status = #completed | ||
| * authored = "2021-01-20T11:29:52+02:00" | ||
| * author = Reference(WhoCrPractitionerExample) | ||
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| * item[+].linkId = "report_country" | ||
| * item[=].text = "Reporting country:" | ||
| * item[=].definition = "http://openhie.github.io/covid-19/StructureDefinition/WhoCrSurveillanceDataDictionary#WhoCrSurveillanceDataDictionary.report.country" | ||
| * item[=].answer[+].valueCoding = $vs-iso3166-1-2#ZA | ||
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| * item[+].linkId = "report_test_reason" | ||
| * item[=].text = "Why tested for COVID-19:" | ||
| * item[=].definition = "http://openhie.github.io/covid-19/StructureDefinition/WhoCrSurveillanceDataDictionary#WhoCrSurveillanceDataDictionary.report.testReason" | ||
| * item[=].answer[+].valueCoding = WhoCrCodeSystemReasonForTesting#CASE_CONTACT | ||
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| * item[+].linkId = "section_patient_info" | ||
| * item[=].text = "Patient information" | ||
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| * item[=].item[+].linkId = "patinfo_ID" | ||
| * item[=].item[=].text = "Unique Case Identifier (used in country):" | ||
| * item[=].item[=].definition = "http://openhie.github.io/covid-19/StructureDefinition/WhoCrSurveillanceDataDictionary#WhoCrSurveillanceDataDictionary.patientInfo.caseId" | ||
| * item[=].item[=].answer[+].valueString = "123456789" | ||
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| * item[=].item[+].linkId = "patinfo_ageonset" | ||
| * item[=].item[=].text = "Age (use days if <1 month, months if <1 year):" | ||
| * item[=].item[=].definition = "http://openhie.github.io/covid-19/StructureDefinition/WhoCrSurveillanceDataDictionary#WhoCrSurveillanceDataDictionary.patientInfo.onsetAge" | ||
| * item[=].item[=].answer[+].valueQuantity = 34 'a' | ||
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| * item[=].item[+].linkId = "patinfo_sex" | ||
| * item[=].item[=].text = "Sex at birth:" | ||
| * item[=].item[=].definition = "http://openhie.github.io/covid-19/StructureDefinition/WhoCrSurveillanceDataDictionary#WhoCrSurveillanceDataDictionary.patientInfo.birthSex" | ||
| * item[=].item[=].answer[+].valueCoding = $cs-gender#male | ||
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| * item[=].item[+].linkId = "patinfo_placediagnosed" | ||
| * item[=].item[=].text = "Place where the case was diagnosed:" | ||
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| * item[=].item[=].item[+].linkId = "patinfo_idadmin0" | ||
| * item[=].item[=].item[=].text = "Country:" | ||
| * item[=].item[=].item[=].definition = "http://openhie.github.io/covid-19/StructureDefinition/WhoCrSurveillanceDataDictionary#WhoCrSurveillanceDataDictionary.patientInfo.identified.country" | ||
| * item[=].item[=].item[=].answer[+].valueCoding = $vs-iso3166-1-2#ZA | ||
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| * item[=].item[=].item[=].item[+].linkId = "patinfo_idadmin1" | ||
| * item[=].item[=].item[=].item[=].text = "Admin Level 1 (province):" | ||
| * item[=].item[=].item[=].item[=].definition = "http://openhie.github.io/covid-19/StructureDefinition/WhoCrSurveillanceDataDictionary#WhoCrSurveillanceDataDictionary.patientInfo.identified.subnational" | ||
| * item[=].item[=].item[=].item[=].answer[+].valueCoding = $cs-iso3166-2#ZA-KZN | ||
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| * item[+].linkId = "section_clinical_status" | ||
| * item[=].text = "Clinical Status" | ||
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| * item[=].item[+].linkId = "Lab_date1" | ||
| * item[=].item[=].text = "Date of first laboratory confirmation test:" | ||
| * item[=].item[=].definition = "http://openhie.github.io/covid-19/StructureDefinition/WhoCrSurveillanceDataDictionary#WhoCrSurveillanceDataDictionary.clinicalStatus.lab.confirmedDate" | ||
| * item[=].item[=].answer[+].valueDate = "2021-01-20" | ||
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| * item[=].item[+].linkId = "patcourse_asymp" //TODO: variable name/short label is opposite to meaning of question | ||
| * item[=].item[=].text = "Any symptoms or signs at time of specimen collection that resulted in first laboratory confirmation?" | ||
| * item[=].item[=].definition = "http://openhie.github.io/covid-19/StructureDefinition/WhoCrSurveillanceDataDictionary#WhoCrSurveillanceDataDictionary.clinicalStatus.patientCourse.asymptomatic" | ||
| * item[=].item[=].answer[+].valueCoding = $cs-v2-0136#Y | ||
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| * item[=].item[=].item[+].linkId = "patcourse_dateonset" | ||
| * item[=].item[=].item[=].text = "Date of onset of symptoms:" | ||
| * item[=].item[=].item[=].definition = "http://openhie.github.io/covid-19/StructureDefinition/WhoCrSurveillanceDataDictionary#WhoCrSurveillanceDataDictionary.clinicalStatus.patientCourse.onsetDate" | ||
| * item[=].item[=].item[=].answer[+].valueDate = "2021-01-15" | ||
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| * item[=].item[+].linkId = "section_comorbidity" | ||
| * item[=].item[=].text = "Underlying conditions and comorbidity:" | ||
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| * item[=].item[=].item[+].linkId = "Comcond_any" | ||
| * item[=].item[=].item[=].text = "Any underlying conditions?" | ||
| * item[=].item[=].item[=].definition = "http://openhie.github.io/covid-19/StructureDefinition/WhoCrSurveillanceDataDictionary#WhoCrSurveillanceDataDictionary.clinicalStatus.comorbidities.any" | ||
| * item[=].item[=].item[=].answer[+].valueCoding = $cs-v2-0136#N | ||
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| * item[+].linkId = "section_exposure_risk" | ||
| * item[=].text = "Exposure risk in the 14 days prior to symptom onset (prior to testing if asymptomatic)" | ||
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| * item[=].item[+].linkId = "expo_travel" | ||
| * item[=].item[=].text = "Has the case travelled in the 14 days prior to symptom onset?" | ||
| * item[=].item[=].definition = "http://openhie.github.io/covid-19/StructureDefinition/WhoCrSurveillanceDataDictionary#WhoCrSurveillanceDataDictionary.exposure.travel.hasTravelled" | ||
| * item[=].item[=].answer[+].valueCoding = $cs-v2-0136#N |
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This appears like it would cause deploy even when PRs are made to master. This doesn't seem correct so I removed it.