Valuesets mz

input/fsh/examples/1-NeisseriaGonorrhoeae-Broker/1bSpec-NeisseriaGonorrhoeae.fsh

@@ -3,7 +3,7 @@ InstanceOf: ChElmSpecimen
 Usage: #example
 Title: "1bSpec - Neisseria Gonorrhoeae"
 Description: "Example for a CH ELM Specimen: Laboratory"
-* type.text = "Material declared by LOINC system axis"
+* type.text = "Material declared by Observation.code or non-mandatory"
 * subject = Reference(1Pat-DM)
 * collection.collectedDateTime = "2023-07-10T14:10:00+02:00"
 

input/fsh/examples/1-NeisseriaGonorrhoeae/1Spec-NeisseriaGonorrhoeae.fsh

@@ -3,7 +3,7 @@ InstanceOf: ChElmSpecimen
 Usage: #example
 Title: "1Spec - Neisseria Gonorrhoeae"
 Description: "Example for a CH ELM Specimen: Laboratory"
-* type.text = "Material declared by LOINC system axis"
+* type.text = "Material declared by Observation.code or non-mandatory"
 * subject = Reference(1Pat-DM)
 * collection.collectedDateTime = "2023-07-01"
 

input/fsh/examples/3Doc-CPE.fsh

@@ -0,0 +1,151 @@
+Instance: 3Doc-CPE
+InstanceOf: ChElmDocument
+Usage: #example
+Title: "3Doc - Carbapenemase-producing Enterobacteriaceae (CPE)"
+Description: "Example for a CH ELM Document: Laboratory Report (organism in addition to the leading LOINC code)"
+* meta.profile[0] = "http://hl7.eu/fhir/laboratory/StructureDefinition/Bundle-eu-lab"
+* identifier.system = "urn:ietf:rfc:3986"
+* identifier.value = "urn:uuid:1301332d-6012-443f-9690-72913db2e3cc"
+* type = #document
+* timestamp = "2023-08-05T11:30:00+02:00"
+* entry[0].fullUrl = "http://test.fhir.ch/r4/Composition/3Comp-CPE"
+* entry[=].resource = 3Comp-CPE
+* entry[+].fullUrl = "http://test.fhir.ch/r4/DiagnosticReport/3DR-CPE"
+* entry[=].resource = 3DR-CPE
+* entry[+].fullUrl = "http://test.fhir.ch/r4/Patient/3Pat-HF"
+* entry[=].resource = 3Pat-HF
+* entry[+].fullUrl = "http://test.fhir.ch/r4/Observation/3Obs-CPE"
+* entry[=].resource = 3Obs-CPE
+* entry[+].fullUrl = "http://test.fhir.ch/r4/Specimen/3Spec-Specimen"
+* entry[=].resource = 3Spec-Specimen
+* entry[+].fullUrl = "http://test.fhir.ch/r4/ServiceRequest/3SR-Order"
+* entry[=].resource = 3SR-Order
+* entry[+].fullUrl = "http://test.fhir.ch/r4/Organization/3Org-Labor"
+* entry[=].resource = 3Org-Labor
+* entry[+].fullUrl = "http://test.fhir.ch/r4/PractitionerRole/3PR-KsAbc"
+* entry[=].resource = 3PR-KsAbc
+* entry[+].fullUrl = "http://test.fhir.ch/r4/Practitioner/3Pract-KsAbc"
+* entry[=].resource = 3Pract-KsAbc
+* entry[+].fullUrl = "http://test.fhir.ch/r4/Organization/3Org-KsAbc"
+* entry[=].resource = 3Org-KsAbc
+
+Instance: 3Comp-CPE
+InstanceOf: Composition
+Usage: #inline
+* language = #de-CH
+* identifier.system = "urn:ietf:rfc:3986"
+* identifier.value = "urn:uuid:1301332d-6012-443f-9690-72913db2e3cc"
+* status = #final
+* type.coding[0].version = "http://snomed.info/sct/2011000195101"
+* type.coding[=] = $sct#4241000179101 "Laborbericht"
+* type.coding[+] = $loinc#11502-2 "Laboratory report"
+* subject = Reference(3Pat-HF)
+* date = "2023-08-05T11:30:00+02:00"
+* author = Reference(3Org-Labor)
+* title = "Laborbericht vom 05.08.2023"
+* section.title = "Analyseergebnisse der mikrobiologischen Untersuchung"
+* section.code = $loinc#18725-2 "Microbiology studies (set)"
+* section.entry = Reference(3Obs-CPE)
+
+Instance: 3DR-CPE
+InstanceOf: DiagnosticReport
+Usage: #inline
+* extension.url = "http://hl7.org/fhir/5.0/StructureDefinition/extension-DiagnosticReport.composition"
+* extension.valueReference = Reference(3Comp-CPE)
+* identifier.system = "urn:ietf:rfc:3986"
+* identifier.value = "urn:uuid:1301332d-6012-443f-9690-72913db2e3cc"
+* basedOn = Reference(3SR-Order)
+* status = #final
+* code = $loinc#11502-2 "Laboratory report"
+* subject = Reference(3Pat-HF)
+* performer = Reference(3Org-Labor)
+* specimen = Reference(3Spec-Specimen)
+* result = Reference(3Obs-CPE)
+
+Instance: 3Pat-HF
+InstanceOf: Patient
+Usage: #inline
+* identifier.system = "urn:oid:2.16.756.5.32"
+* identifier.value = "7561234567897"
+* name.family = "F"
+* name.given = "H"
+* gender = #female
+* birthDate = "1985-10-17"
+* address.use = #home
+* address.city = "Derendingen"
+* address.state = "SO"
+* address.postalCode = "4552"
+* address.country = "CH"
+* address.country.extension.url = "http://hl7.org/fhir/StructureDefinition/iso21090-SC-coding"
+* address.country.extension.valueCoding = urn:iso:std:iso:3166#CH
+
+
+Instance: 3Obs-CPE
+InstanceOf: Observation
+Usage: #inline
+* status = #final
+* category = $observation-category#laboratory "Laboratory"
+* code = $loinc#85827-4 "Carbapenem resistance bla OXA-48-like gene [Presence] by Molecular method"
+* subject = Reference(3Pat-HF)
+* effectiveDateTime = "2023-08-04T08:25:00+02:00"
+* performer = Reference(3Org-Labor)
+* valueCodeableConcept = $sct#56415008 "Klebsiella pneumoniae (organism)"
+* interpretation = $v3-ObservationInterpretation#POS "Positive"
+* specimen = Reference(3Spec-Specimen)
+
+Instance: 3Spec-Specimen
+InstanceOf: Specimen
+Usage: #inline
+* type.text = "Material declared by Observation.code or non-mandatory"
+* subject = Reference(3Pat-HF)
+* collection.collectedDateTime = "2023-08-01"
+
+Instance: 3SR-Order
+InstanceOf: ServiceRequest
+Usage: #inline
+* identifier.system = "http://fhir.lab.ch/order-identifier"
+* identifier.value = "34854112365"
+* status = #completed
+* intent = #order
+* code = $loinc#85827-4 "Carbapenem resistance bla OXA-48-like gene [Presence] by Molecular method"
+* subject = Reference(3Pat-HF)
+* requester = Reference(3PR-KsAbc)
+* specimen = Reference(3Spec-Specimen)
+
+Instance: 3Org-Labor
+InstanceOf: Organization
+Usage: #inline
+* identifier.system = "urn:oid:2.51.1.3"
+* identifier.value = "7601002331470"
+* name = "SanLab"
+
+Instance: 3PR-KsAbc
+InstanceOf: PractitionerRole
+Usage: #inline
+* practitioner = Reference(3Pract-KsAbc)
+* organization = Reference(3Org-KsAbc)
+
+Instance: 3Pract-KsAbc
+InstanceOf: Practitioner
+Usage: #inline
+* identifier.system = "urn:oid:2.51.1.3"
+* identifier.value = "7601000234438"
+* name.family = "Giacometti"
+* name.given = "Monika"
+* telecom[0].system = #email
+* telecom[=].value = "[email protected]"
+* telecom[+].system = #phone
+* telecom[=].value = "+41 79 111 44 55"
+
+Instance: 3Org-KsAbc
+InstanceOf: Organization
+Usage: #inline
+* extension.url = "http://fhir.ch/ig/ch-elm/StructureDefinition/ch-elm-ext-department"
+* extension.valueString = "Abteilung 2"
+* identifier.system = "urn:oid:2.51.1.3"
+* identifier.value = "7601888888884"
+* name = "Kantonsspital ABC"
+* address.line[0] = "Aortastrasse 22"
+* address.line[+] = "Postfach 18"
+* address.city = "Bern"
+* address.postalCode = "3000"

input/fsh/invariants.fsh

@@ -3,14 +3,22 @@ Description: "At least the format YYYY-MM-DD is required."
 Severity: #error
 Expression: "$this.toString().length() >= 10"
 
-
 Invariant: ch-elm-doc-identifier
 Description: "The identifier must be an UUID."
 Severity: #error
 Expression: "startsWith('urn:uuid:')"
 
-
 Invariant: ch-elm-practrole
 Description: "Must have at least a practitioner or an organization."
 Severity: #error
 Expression: "practitioner.exists() or practitioner.exists()"
+
+Invariant: ch-elm-expecting-specimen-specification
+Description: "If Observation.code is a member of http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-expecting-specimen-specification, then Specimen.type must be a member of the mapped ValueSet in http://fhir.ch/ig/ch-elm/ConceptMap/ch-elm-expecting-specimen-specification-to-result-completion-vs"
+Severity: #error
+Expression: "code.memberOf('http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-expecting-specimen-specification') implies specimen.resolve().exists() and specimen.resolve().type.exists() and specimen.resolve().type.memberOf('http://fhir.ch/ig/ch-elm/ConceptMap/ch-elm-expecting-specimen-specification-to-result-completion-vs'.resolve().group.where(source='http://loinc.org').element.where(code=%context.code.coding.where(system='http://loinc.org').first().code).target.first().code)"
+
+Invariant: ch-elm-material
+Description: "Material declared by Observation.code or non-mandatory"
+Severity: #error
+Expression: "code.memberOf('http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-expecting-specimen-specification').not() implies specimen.resolve().exists() and specimen.resolve().type.exists() and specimen.resolve().type.text.exists() and specimen.resolve().type.text='Material declared by Observation.code or non-mandatory'"

input/fsh/profiles/Observation.fsh

@@ -3,6 +3,8 @@ Parent: ChLabObservationResultsLaboratory
 Id: ch-elm-observation-results-laboratory
 Title: "CH ELM Observation Results: Laboratory"
 Description: "This CH ELM base profile constrains the Observation resource for the purpose of laboratory test reports."
+* obeys ch-elm-expecting-specimen-specification
+* obeys ch-elm-material
 * . ^short = "CH ELM Observation Results: Laboratory"
 * status = #final
 * code from ChElmResultsLaboratoryObservation (required)
@@ -12,10 +14,15 @@ Description: "This CH ELM base profile constrains the Observation resource for t
 * effective[x] 1..
 * effectiveDateTime 1..
 * effectiveDateTime obeys ch-elm-dateTime
+
 * value[x] 1..
-* valueCodeableConcept 1..
+* valueQuantity 0..1
+// * valueQuantity only ChElmQuantity
+* valueCodeableConcept 0..1
 * valueCodeableConcept only ChElmCodeableConcept
-* valueCodeableConcept from ChElmResultsCodedValuesLaboratory (required)
+* valueCodeableConcept from ChElmResultsCodedValuesLaboratory (preferred) // (required)
+* valueCodeableConcept ^short = "Positive/Negative or code for an additional organism specification, see also 'Guidance - Laboratory Result'"
+
 * performer 1..1
 * performer only Reference(ChElmOrganizationLab)
 * specimen only Reference(ChElmSpecimen)

input/fsh/profiles/Specimen.fsh

@@ -6,11 +6,9 @@ Description: "This CH ELM base profile constrains the Specimen resource for the
 * . ^short = "CH Lab Specimen: Laboratory"
 
 * type 1.. // Req. EU LAB
-* type.coding ^short = "If the collection material is not declared by LOINC system axis (Observation.code)"
+* type ^short = "The mechanism to declare the collection material is described under 'Guidance - Laboratory Result'"
 * type.coding only ChElmCoding
-* type from ChElmLabSpecimenTypes (extensible) // 'required' not possible: No code provided, and a code is required from the value set 'CH ELM Lab Specimen Types' (http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-lab-specimen-types|0.1.0)
-* type.text ^short = "If the collection material is declared by LOINC system axis (Observation.code)"
-* type.text = "Material declared by LOINC system axis"
+* type.text = "Material declared by Observation.code or non-mandatory"
 
 * subject 1..
 * subject only Reference(ChElmPatient)