diff --git a/input/fsh/examples/1-NeisseriaGonorrhoeae-Broker/1bSpec-NeisseriaGonorrhoeae.fsh b/input/fsh/examples/1-NeisseriaGonorrhoeae-Broker/1bSpec-NeisseriaGonorrhoeae.fsh index 7150c5a..fb96843 100644 --- a/input/fsh/examples/1-NeisseriaGonorrhoeae-Broker/1bSpec-NeisseriaGonorrhoeae.fsh +++ b/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" diff --git a/input/fsh/examples/1-NeisseriaGonorrhoeae/1Spec-NeisseriaGonorrhoeae.fsh b/input/fsh/examples/1-NeisseriaGonorrhoeae/1Spec-NeisseriaGonorrhoeae.fsh index 72ab502..c72ea80 100644 --- a/input/fsh/examples/1-NeisseriaGonorrhoeae/1Spec-NeisseriaGonorrhoeae.fsh +++ b/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" diff --git a/input/fsh/examples/2-ChlamydiaTrachomatis/2Doc-ChlamydiaTrachomatis.fsh b/input/fsh/examples/2Doc-ChlamydiaTrachomatis.fsh similarity index 100% rename from input/fsh/examples/2-ChlamydiaTrachomatis/2Doc-ChlamydiaTrachomatis.fsh rename to input/fsh/examples/2Doc-ChlamydiaTrachomatis.fsh diff --git a/input/fsh/examples/3Doc-CPE.fsh b/input/fsh/examples/3Doc-CPE.fsh new file mode 100644 index 0000000..8405311 --- /dev/null +++ b/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 = $loinc#85827-4 "Carbapenem resistance bla OXA-48-like gene [Presence] by Molecular method" +* subject = Reference(3Pat-HF) +* requester = Reference(3PR-KsAbc) +* specimen = Reference(3Spec-Specimen) + +Instance: 3Org-Labor +InstanceOf: Organization +Usage: #inline +* identifier.system = "urn:oid:2.51.1.3" +* identifier.value = "7601002331470" +* name = "SanLab" + +Instance: 3PR-KsAbc +InstanceOf: PractitionerRole +Usage: #inline +* practitioner = Reference(3Pract-KsAbc) +* organization = Reference(3Org-KsAbc) + +Instance: 3Pract-KsAbc +InstanceOf: Practitioner +Usage: #inline +* identifier.system = "urn:oid:2.51.1.3" +* identifier.value = "7601000234438" +* name.family = "Giacometti" +* name.given = "Monika" +* telecom[0].system = #email +* telecom[=].value = "m.giacometti@ks-abc.ch" +* telecom[+].system = #phone +* telecom[=].value = "+41 79 111 44 55" + +Instance: 3Org-KsAbc +InstanceOf: Organization +Usage: #inline +* extension.url = "http://fhir.ch/ig/ch-elm/StructureDefinition/ch-elm-ext-department" +* extension.valueString = "Abteilung 2" +* identifier.system = "urn:oid:2.51.1.3" +* identifier.value = "7601888888884" +* name = "Kantonsspital ABC" +* address.line[0] = "Aortastrasse 22" +* address.line[+] = "Postfach 18" +* address.city = "Bern" +* address.postalCode = "3000" diff --git a/input/fsh/invariants.fsh b/input/fsh/invariants.fsh index 0b23575..daa6ce3 100644 --- a/input/fsh/invariants.fsh +++ b/input/fsh/invariants.fsh @@ -3,14 +3,22 @@ Description: "At least the format YYYY-MM-DD is required." Severity: #error Expression: "$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'" diff --git a/input/fsh/profiles/Observation.fsh b/input/fsh/profiles/Observation.fsh index 1f048a5..275660e 100644 --- a/input/fsh/profiles/Observation.fsh +++ b/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) diff --git a/input/fsh/profiles/Specimen.fsh b/input/fsh/profiles/Specimen.fsh index d0a5c8a..25576e2 100644 --- a/input/fsh/profiles/Specimen.fsh +++ b/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) diff --git a/input/fsh/terminology/LabSpecimenTypes.fsh b/input/fsh/terminology/LabSpecimenTypes.fsh deleted file mode 100644 index 34292f6..0000000 --- a/input/fsh/terminology/LabSpecimenTypes.fsh +++ /dev/null @@ -1,79 +0,0 @@ -ValueSet: ChElmLabSpecimenTypes -Id: ch-elm-lab-specimen-types -Title: "CH ELM Lab Specimen Types" -Description: "This CH ELM value set includes the codes for the laboratory specimen." -* ^status = #active -* ^experimental = false - -* $sct#257261003 "Swab" // 1=swab -* $sct#123038009 "Specimen" // 2=other -* $sct#258500001 "Nasopharyngeal swab" // 3=nasopharyngeal swab -* $sct#461911000124106 "Oropharyngeal swab" // 4=oropharyngeal swab -* $sct#258529004 "Throat swab" // 5=throat swab -* $sct#258607008 "Bronchoalveolar lavage fluid" // 6=bronchoalveolar lavage -* $sct#119339001 "Faeces specimen" // 7=faeces -* $sct#119334006 "Sputum specimen" // 8=sputum -* $sct#119297000 "Blood specimen" // 9=full blood -* $sct#119342007 "Saliva specimen" // 10=saliva -* $sct#447154002 "Specimen from nose" // 11=specimen from nose -* $sct#119371008 "Specimen from abscess" // 12 abscess -* $sct#447955000 "Specimen from rectum" // 13 anal/rectum -* $sct#168139001 "Peritoneal fluid" // 14 peritoneal fluid -* $sct#119399004 "Specimen from eye" // 15 eye -* $sct#119401005 "Specimen from conjunctiva" // 16 conjunctival specimen -* $sct#258415003 "Biopsy specimen" // 17 biopsy -* $sct#119395005 "Specimen from uterine cervix" // 18 cervix -* $sct#119344008 "Specimen from genital system" // 19 genital -* $sct#258450006 "Cerebrospinal fluid specimen" // 20 cerebrospinal fluid -* $sct#258589002 "Lymph node specimen" // 21 lymph node -* $sct#258426009 "Placental membrane tissue specimen" // 22 placental tissue -* $sct#57711000052109 "Specimen obtained by puncture procedure" // 23 punctate -* $sct#119347001 "Seminal fluid" // 24 seminal fluid -* $sct#122575003 "Urine specimen" // 25 urine -* $sct#119394009 "Specimen from vagina" // 26 vaginal -* $sct#119365002 "Specimen from wound" // 27 wound -* $sct#119393003 "Specimen from urethra" // 28 urethra -* $sct#119364003 "Serum specimen" // 29 serum -* $sct#309051001 "Body fluid specimen" // 30 unspecified body fluid -* $sct#430304001 "Specimen from unspecified body site" // 31 unspecified -* $sct#309132009 "Prostate biopsy specimen" // 32 prostate biopsy - -* $sct#472904006 "Swab from abdomen" -* $sct#258527002 "Anal swab" -* $sct#445160003 "Swab of eye" -* $sct#119300005 "Specimen from blood product" -* $sct#119391001 "Specimen from bronchus" -* $sct#258454002 "Dialysis fluid specimen" -* $sct#122643008 "Tissue specimen from large intestine" -* $sct#119323008 "Pus specimen" -* $sct#119378002 "Endocardial specimen" -* $sct#119373006 "Amniotic fluid specimen" -* $sct#119341000 "Bile specimen" -* $sct#119332005 "Synovial fluid specimen" -* $sct#258508008 "Genital swab" -* $sct#119376003 "Tissue specimen" -* $sct#608969007 "Specimen from skin" -* $sct#119398007 "Specimen from brain" -* $sct#119303007 "Microbial isolate specimen" -* $sct#430268003 "Specimen from bone" -* $sct#445447003 "Specimen from trachea obtained by aspiration" -* $sct#399492000 "Tissue specimen from lung" -* $sct#258459007 "Gastric fluid sample" -* $sct#119359002 "Bone marrow specimen" -* $sct#122556008 "Cord blood specimen" -* $sct#309165001 "Ear sample" -* $sct#119343002 "Pancreatic fluid specimen" -* $sct#119361006 "Plasma specimen" -* $sct#122736005 "Tissue specimen from placenta" -* $sct#418564007 "Pleural fluid specimen" -* $sct#119386002 "Specimen from prostate" -* $sct#119295008 "Specimen obtained by aspiration" -* $sct#119389009 "Specimen from throat" -* $sct#119396006 "Specimen from endometrium" -* $sct#258465007 "Lacrimal fluid sample" -* $sct#119369008 "Specimen from ulcer" -* $sct#119324002 "Specimen of unknown material" -* $sct#258520000 "Vaginal swab" -* $sct#258580003 "Whole blood sample" -* $sct#258531008 "Wound swab" -* $sct#119368000 "Specimen from cyst" diff --git a/input/fsh/terminology/LabSpecimenTypesChlamydiaTrachomatis.fsh b/input/fsh/terminology/LabSpecimenTypesChlamydiaTrachomatis.fsh deleted file mode 100644 index ea2925f..0000000 --- a/input/fsh/terminology/LabSpecimenTypesChlamydiaTrachomatis.fsh +++ /dev/null @@ -1,15 +0,0 @@ -ValueSet: ChElmLabSpecimenTypesChlamydiaTrachomatis -Id: ch-elm-lab-specimen-types-chlamydia-trachomatis -Title: "CH ELM Lab Specimen Types: Chlamydia Trachomatis" -Description: "This restricted CH ELM value set includes the codes for the laboratory specimen if, in addition to the leading LOINC code, the collection material must be given in coded form." -* ^status = #active -* ^experimental = false - -* $sct#119395005 "Specimen from uterine cervix" -* $sct#258527002 "Anal swab" -* $sct#258508008 "Genital swab" -* $sct#258520000 "Vaginal swab" -* $sct#119393003 "Specimen from urethra" -* $sct#119347001 "Seminal fluid" -* $sct#119396006 "Specimen from endometrium" - diff --git a/input/fsh/terminology/ResultsLaboratoryObservation.fsh b/input/fsh/terminology/ResultsLaboratoryObservation.fsh deleted file mode 100644 index 80e4ccc..0000000 --- a/input/fsh/terminology/ResultsLaboratoryObservation.fsh +++ /dev/null @@ -1,61 +0,0 @@ -ValueSet: ChElmResultsLaboratoryObservation -Id: ch-elm-results-laboratory-observation -Title: "CH ELM Results Laboratory Observation" -Description: "This CH ELM value set includes the codes for the laboratory test results (organism)." -* ^status = #active -* ^experimental = false - -* $loinc#14127-5 "Neisseria gonorrhoeae [Presence] in Anal by Organism specific culture" -* $loinc#21415-5 "Neisseria gonorrhoeae DNA [Presence] in Urethra by NAA with probe detection" -* $loinc#21416-3 "Neisseria gonorrhoeae DNA [Presence] in Urine by NAA with probe detection" -* $loinc#24111-7 "Neisseria gonorrhoeae DNA [Presence] in Specimen by NAA with probe detection" -* $loinc#32705-6 "Neisseria gonorrhoeae DNA [Presence] in Vaginal fluid by NAA with probe detection" -* $loinc#43305-2 "Neisseria gonorrhoeae rRNA [Presence] in Specimen by NAA with probe detection" -* $loinc#47387-6 "Neisseria gonorrhoeae DNA [Presence] in Genital specimen by NAA with probe detection" -* $loinc#50388-8 "Neisseria gonorrhoeae rRNA [Presence] in Cervix by NAA with probe detection" -* $loinc#53879-3 "Neisseria gonorrhoeae rRNA [Presence] in Vaginal fluid by NAA with probe detection" -* $loinc#53927-0 "Neisseria gonorrhoeae rRNA [Presence] in Urethra by NAA with probe detection" -* $loinc#57458-2 "Neisseria gonorrhoeae rRNA [Presence] in Anal by NAA with probe detection" -* $loinc#60255-7 "Neisseria gonorrhoeae rRNA [Presence] in Throat by NAA with probe detection" -* $loinc#60256-5 "Neisseria gonorrhoeae rRNA [Presence] in Urine by NAA with probe detection" -* $loinc#688-2 "Neisseria gonorrhoeae [Presence] in Cervix by Organism specific culture" -* $loinc#691-6 "Neisseria gonorrhoeae [Presence] in Genital specimen by Organism specific culture" -* $loinc#693-2 "Neisseria gonorrhoeae [Presence] in Vaginal fluid by Organism specific culture" -* $loinc#694-0 "Neisseria gonorrhoeae [Presence] in Semen by Organism specific culture" -* $loinc#696-5 "Neisseria gonorrhoeae [Presence] in Throat by Organism specific culture" -* $loinc#697-3 "Neisseria gonorrhoeae [Presence] in Urethra by Organism specific culture" -* $loinc#698-1 "Neisseria gonorrhoeae [Presence] in Specimen by Organism specific culture" -* $loinc#80366-8 "Neisseria gonorrhoeae rRNA [Presence] in Anorectal by NAA with probe detection" -* $loinc#80368-4 "Neisseria gonorrhoeae [Presence] in Anorectal by Organism specific culture" -* $loinc#88224-1 "Neisseria gonorrhoeae DNA [Presence] in Anorectal by NAA with probe detection" -* $loinc#88225-8 "Neisseria gonorrhoeae DNA [Presence] in Throat by NAA with probe detection" -* $loinc#96599-6 "Neisseria gonorrhoeae DNA [Presence] in Cervix by NAA with probe detection" - -* $loinc#14463-4 "Chlamydia trachomatis [Presence] in Cervix by Organism specific culture" -* $loinc#14464-2 "Chlamydia trachomatis [Presence] in Vaginal fluid by Organism specific culture" -* $loinc#14465-9 "Chlamydia trachomatis [Presence] in Urethra by Organism specific culture" -* $loinc#16600-9 "Chlamydia trachomatis rRNA [Presence] in Genital specimen by probe" -* $loinc#21190-4 "Chlamydia trachomatis DNA [Presence] in Cervix by NAA with probe detection" -* $loinc#21191-2 "Chlamydia trachomatis DNA [Presence] in Urethra by NAA with probe detection" -* $loinc#21613-5 "Chlamydia trachomatis DNA [Presence] in Specimen by NAA with probe detection" -* $loinc#23838-6 "Chlamydia trachomatis rRNA [Presence] in Genital fluid by probe" -* $loinc#31777-6 "Chlamydia trachomatis Ag [Presence] in Specimen" -* $loinc#42931-6 "Chlamydia trachomatis rRNA [Presence] in Urine by NAA with probe detection" -* $loinc#43304-5 "Chlamydia trachomatis rRNA [Presence] in Specimen by NAA with probe detection" -* $loinc#45084-1 "Chlamydia trachomatis DNA [Presence] in Vaginal fluid by NAA with probe detection" -* $loinc#45090-8 "Chlamydia trachomatis DNA [Presence] in Anal by NAA with probe detection" -* $loinc#45093-2 "Chlamydia trachomatis [Presence] in Anal by Organism specific culture" -* $loinc#45095-7 "Chlamydia trachomatis [Presence] in Genital specimen by Organism specific culture" -* $loinc#50387-0 "Chlamydia trachomatis rRNA [Presence] in Cervix by NAA with probe detection" -* $loinc#51578-3 "Chlamydia trachomatis DNA [Presence] in Semen by NAA with probe detection" -* $loinc#53925-4 "Chlamydia trachomatis rRNA [Presence] in Urethra by NAA with probe detection" -* $loinc#53926-2 "Chlamydia trachomatis rRNA [Presence] in Vaginal fluid by NAA with probe detection" -* $loinc#57287-5 "Chlamydia trachomatis rRNA [Presence] in Anal by NAA with probe detection" -* $loinc#6349-5 "Chlamydia trachomatis [Presence] in Specimen by Organism specific culture" -* $loinc#6356-0 "Chlamydia trachomatis DNA [Presence] in Genital specimen by NAA with probe detection" -* $loinc#6357-8 "Chlamydia trachomatis DNA [Presence] in Urine by NAA with probe detection" -* $loinc#80363-5 "Chlamydia trachomatis DNA [Presence] in Anorectal by NAA with probe detection" -* $loinc#80364-3 "Chlamydia trachomatis rRNA [Presence] in Anorectal by NAA with probe detection" -* $loinc#80367-6 "Chlamydia trachomatis [Presence] in Anorectal by Organism specific culture" - - diff --git a/input/fsh/terminology/LabStudyTypes.fsh b/input/fsh/terminology/VS_LabStudyTypes.fsh similarity index 100% rename from input/fsh/terminology/LabStudyTypes.fsh rename to input/fsh/terminology/VS_LabStudyTypes.fsh diff --git a/input/fsh/terminology/ObservationInterpretationCodes.fsh b/input/fsh/terminology/VS_ObservationInterpretationCodes.fsh similarity index 100% rename from input/fsh/terminology/ObservationInterpretationCodes.fsh rename to input/fsh/terminology/VS_ObservationInterpretationCodes.fsh diff --git a/input/fsh/terminology/ResultsCodedValuesLaboratory.fsh b/input/fsh/terminology/VS_ResultsCodedValuesLaboratory.fsh similarity index 100% rename from input/fsh/terminology/ResultsCodedValuesLaboratory.fsh rename to input/fsh/terminology/VS_ResultsCodedValuesLaboratory.fsh diff --git a/input/ignoreWarnings.txt b/input/ignoreWarnings.txt index 7f71a47..55d6cd1 100644 --- a/input/ignoreWarnings.txt +++ b/input/ignoreWarnings.txt @@ -1,9 +1,10 @@ == Suppressed Messages == -# Based on the design choice from HL7 Europe Laboratory Report (https://build.fhir.org/ig/hl7-eu/laboratory/branches/master/background.html#design-choices) +# Based on the design choice from HL7 Europe Laboratory Report (https://hl7.eu/fhir/laboratory/design-choice.html) Entry 'http://test.fhir.ch/r4/DiagnosticReport/1DR-NeisseriaGonorrhoeae' isn't reachable by traversing forwards from the Composition. Only Provenance is approved to be used this way (R4 section 3.3.1) Entry 'http://test.fhir.ch/r4/DiagnosticReport/1bDR-NeisseriaGonorrhoeae' isn't reachable by traversing forwards from the Composition. Only Provenance is approved to be used this way (R4 section 3.3.1) Entry 'urn:uuid:2f69f609-e3bf-4863-bc42-3cbf0568cab1' isn't reachable by traversing forwards from the Composition. Only Provenance is approved to be used this way (R4 section 3.3.1) +Entry 'http://test.fhir.ch/r4/DiagnosticReport/3DR-CPE' isn't reachable by traversing forwards from the Composition. Only Provenance is approved to be used this way (R4 section 3.3.1) # Caused by the underlying profiles The repeating element has a pattern. The pattern will apply to all the repeats (this has not been clear to all users) @@ -20,3 +21,6 @@ The link 'StructureDefinition-LaboratoryReport-mappings.html#mappings-for-ch-elm # Narrative Rule dom-6: 'A resource should have narrative for robust management' Failed (defined in http://hl7.org/fhir/StructureDefinition/DomainResource) (Best Practice Recommendation) + +# https://chat.fhir.org/#narrow/stream/179252-IG-creation/topic/New.20ConceptMap.20Warning.20--.20induced.20by.20IG.20Publisher +The modifier extension http://hl7.org/fhir/1.0/StructureDefinition/extension-ConceptMap.element.target.equivalence from FHIR version {3} is not allowed to be used at this point (allowed = e:ConceptMap.element.target; this element is [[BackboneElement, ConceptMap.group.element.target]; this is a warning since contexts may be renamed between FHIR versions) diff --git a/input/pagecontent/changelog.md b/input/pagecontent/changelog.md index 6c787e5..304975b 100644 --- a/input/pagecontent/changelog.md +++ b/input/pagecontent/changelog.md @@ -3,6 +3,7 @@ All significant changes to this FHIR implementation guide will be documented on ### 1.0.0-release #### Added +* New examples: Carbapenemase-producing Enterobacteriaceae (CPE) #### Changed / Updated * [#15](https://github.com/ahdis/ch-elm/issues/15): API update for search capabilities @@ -12,6 +13,11 @@ All significant changes to this FHIR implementation guide will be documented on * [#19](https://github.com/ahdis/ch-elm/issues/19): Require DiagnosticReport.identifier (equal to Composition.identifier) * [#13](https://github.com/ahdis/ch-elm/issues/13): Update *Fig. 6: Resource Overview* with cardinalities * [#21](https://github.com/ahdis/ch-elm/issues/21): Usage of the IDN instead of the OASI for Patient.identifier Liechtenstein. +* Add a computable way for the concept of leading code and in some cases necessary addition of additional codes to the leading code, see [Guidance - Laboratory Result](guidance.html#laboratory-result) + * [#23](https://github.com/ahdis/ch-elm/issues/23): Include rules to check if the described mechanism is applied correctly + * [#25](https://github.com/ahdis/ch-elm/issues/25): Renaming of the specimen-specific ValueSet 'CH ELM Lab Specimen Types: Chlamydia Trachomatis' to ValueSet 'CH ELM Results Geni Spec' + * [#26](https://github.com/ahdis/ch-elm/issues/26)/[#8](https://github.com/ahdis/ch-elm/issues/8): Remove ValueSet 'CH ELM Lab Specimen Types'; now handled via the newly introduced mechanism + * [#8](https://github.com/ahdis/ch-elm/issues/8): Change the fixed value for Specimen.type.text to a more general version: 'Material declared by LOINC system axis' -> 'Material declared by Observation.code or non-mandatory' #### Fixed * [#9](https://github.com/ahdis/ch-elm/issues/9): Set minimum cardinality of Patient.gender to 1 (according to the logical model) diff --git a/input/pagecontent/document.md b/input/pagecontent/document.md index bc7f9ad..c297037 100644 --- a/input/pagecontent/document.md +++ b/input/pagecontent/document.md @@ -15,5 +15,8 @@ Each CH ELM document requires The profile [CH ELM Document](StructureDefinition-ch-elm-document.html) is a **generic profile** for all types of laboratory reports. Here are examples of laboratory reports for different organisms that have different requirements (see also use case ([DE](usecase-german.html)) or [guidance](guidance.html)): -* Neisseria Gonorrhoeae [JSON](Bundle-1Doc-NeisseriaGonorrhoeae.json.html), [XML](Bundle-1Doc-NeisseriaGonorrhoeae.xml.html) +* Neisseria Gonorrhoeae: [JSON](Bundle-1Doc-NeisseriaGonorrhoeae.json.html), [XML](Bundle-1Doc-NeisseriaGonorrhoeae.xml.html) + * Neisseria gonorrhoeae - Broker Szenario: [JSON](Bundle-1bDoc-NeisseriaGonorrhoeae.json.html), [XML](Bundle-1bDoc-NeisseriaGonorrhoeae.xml.html) +* Chlamydia trachomatis: [JSON](Bundle-2Doc-ChlamydiaTrachomatis.json.html), [XML](Bundle-2Doc-ChlamydiaTrachomatis.xml.html) +* Carbapenemase-producing Enterobacteriaceae (CPE): [JSON](Bundle-3Doc-CPE.json.html), [XML](Bundle-3Doc-CPE.xml.html) diff --git a/input/pagecontent/guidance.md b/input/pagecontent/guidance.md index e00d236..6cac2e4 100644 --- a/input/pagecontent/guidance.md +++ b/input/pagecontent/guidance.md @@ -34,31 +34,52 @@ The laboratory report is currently either of the type [organism detection](#orga * `Observation.interpretation` = Resistant/Susceptible ([CH ELM Observation Interpretation Codes](ValueSet-ch-elm-observation-interpretation-codes.html)) ### Laboratory Result -The laboratory result is represented by a so called leading LOINC code and laboratories are requested to choose the code from the provided ValueSet ([CH ELM Results Laboratory Observation](ValueSet-ch-elm-results-laboratory-observation.html)) that corresponds to the test parameters performed. The LOINC code reflects a 4-axis model and ideally, the chosen LOINC code covers all 4 axes. -[Example](Bundle-1Doc-NeisseriaGonorrhoeae.html): LOINC [697-3 Neisseria gonorrhoeae [Presence] in Urethra by Organism specific culture](https://loinc.org/697-3/): +#### Leading Code +The laboratory result is represented by a so called leading code (in most cases LOINC) and laboratories are requested to choose the code from the provided ([ValueSet CH ELM Results Laboratory Observation](ValueSet-ch-elm-results-laboratory-observation.html)) that corresponds to the test parameters performed. The leading code reflects a 4-axis model and ideally, the chosen code covers all 4 axes. + +[Example Neisseria gonorrhoeae](Bundle-1Doc-NeisseriaGonorrhoeae.html): The leading LOINC code [697-3 Neisseria gonorrhoeae [Presence] in Urethra by Organism specific culture](https://loinc.org/697-3/) covering all 4 axes: * **Organism**: Neisseria gonorrhoeae * **Detection**: organism growth * **Detection method**: organism specific culture * **Collection material**: urethra -If the leading LOINC code does not cover all axes, the missing axis must be complemented by a SNOMED CT code (see below “Collection Material“). +Note: The Specimen.type.text element in this case contains a fixed text as value: “Material declared by Observation.code or non-mandatory”. -[Example](Bundle-2Doc-ChlamydiaTrachomatis.html): The leading LOINC code (Observation.code = LOINC 6349-5), complemented by a SNOMED CT code for the collection material (Specimen.type = SNOMED CT 119393003) +Important note: +The ([ValueSet CH ELM Results Laboratory Observation](ValueSet-ch-elm-results-laboratory-observation.html)) is a selection of LOINC codes related to notifiable diseases and their legal basis. The ValueSet can be adapted according to laboratory-specific needs - please contact the FOPH in this regard. -**Important note**: The [ValueSet](ValueSet-ch-elm-results-laboratory-observation.html) is a selection of LOINC codes related to notifiable diseases and their legal basis. The [ValueSet](ValueSet-ch-elm-results-laboratory-observation.html) can be adapted according to laboratory-specific needs - please contact the FOPH in this regard. +#### Completion of the Leading Code +If the leading code does not cover all axes, the missing axis must be completed by an additional code. -#### Collection Material -In the cases described below, the collection material must be explicitly specified. +##### Expecting Specimen Specification +In some cases, the collection material must be explicitly specified. -* Chlamydia trachomatis - * if Observation.code = LOINC 21613-5 / 31777-6 / 43304-5 / 6349-5 - * use a Specimen.type form the [ValueSet CH ELM Lab Specimen Types: Chlamydia Trachomatis](ValueSet-ch-elm-lab-specimen-types-chlamydia-trachomatis.html) +[Example Chlamydia trachomatis](Bundle-2Doc-ChlamydiaTrachomatis.html): The leading code (Observation.code = LOINC 6349-5) is completed by an additional code for the collection material (Specimen.type = SNOMED CT 119393003). -In all other cases, the Specimen.type has to be defined as fixed text: “Material declared by LOINC system axis”. +1. Check if Observation.code is a member of the [CH ELM Expecting Specimen Specification To Result Completion ValueSets Mapping](ConceptMap-ch-elm-expecting-specimen-specification-to-result-completion-vs.html) (Source Code) + * NO: Observation.code does cover all axes, see section [Leading Code](#leading-code) + * YES: The collection material must be explicitly specified, continue with step 2 + * Example Chlamydia trachomatis: LOINC 6349-5 is a member of the ConceptMap +2. The mapping shows from which ValueSet the code for Specimen.type has to come from (Target Code) + * Example Chlamydia trachomatis: http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-results-geni-spec +3. Define Specimen.type with a code from the ValueSet from step 2 + * Example Chlamydia trachomatis: Speciment.type = SNOMED CT 119393003 from [ValueSet CH ELM Results Geni Spec](ValueSet-ch-elm-results-geni-spec.html) -### Multiplex Cases -The exchange format defines the [FHIR document](document.html) for reporting to the FOPH so that **one document per organism per patient** is submitted. +##### Expecting Organism Specification +In some cases, an additional organism must be specified. +[Example Carbapenemase-producing Enterobacteriaceae (CPE)](Bundle-3Doc-CPE.html): The leading code (Observation.code = LOINC 85827-4) is completed by an additional code for the organism (Observation.valueCodeableConcept = SNOMED CT 56415008). +1. Check if Observation.code is a member of the [CH ELM Expecting Organism Specification To Result Completion ValueSets Mapping](ConceptMap-ch-elm-expecting-organism-specification-to-result-completion-vs.html) (Source Code) + * NO: Observation.code does cover all axes, see section [Leading Code](#leading-code) + * YES: An additional code for the organism must be specified, continue with step 2 + * Example Carbapenemase-producing Enterobacteriaceae (CPE): LOINC 85827-4 is a member of the ConceptMap +2. The mapping shows from which ValueSet the code for Observation.valueCodeableConcept has to come from (Target Code) + * Example Carbapenemase-producing Enterobacteriaceae (CPE): http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-results-cpe-org +3. Define Observation.valueCodeableConcept with a code from the ValueSet from step 2 + * Example Carbapenemase-producing Enterobacteriaceae (CPE): Observation.valueCodeableConcept = SNOMED CT 56415008 from [ValueSet CH ELM Results CPE Org](ValueSet-ch-elm-results-cpe-org.html) + +### Multiplex Cases +The exchange format defines the [FHIR document](document.html) for reporting to the FOPH so that **one document per organism per patient** is submitted. diff --git a/input/pagecontent/terminology.md b/input/pagecontent/terminology.md index e42d728..f3c3363 100644 --- a/input/pagecontent/terminology.md +++ b/input/pagecontent/terminology.md @@ -2,7 +2,14 @@ {% include list-simple-valuesets.xhtml %} +### CodeSystems + +{% include list-simple-codesystems.xhtml %} + +### ConceptMaps + +{% include list-simple-conceptmaps.xhtml %} + ### NamingSystems {% include list-simple-namingsystems.xhtml %} - diff --git a/input/resources/CodeSystem-ch-elm-result-completion-vs.json b/input/resources/CodeSystem-ch-elm-result-completion-vs.json new file mode 100644 index 0000000..772b924 --- /dev/null +++ b/input/resources/CodeSystem-ch-elm-result-completion-vs.json @@ -0,0 +1,93 @@ +{ + "resourceType": "CodeSystem", + "id": "ch-elm-result-completion-vs", + "url": "http://fhir.ch/ig/ch-elm/CodeSystem/ch-elm-result-completion-vs", + "version": "2023-10-30", + "name": "ChElmResultCompletionValueSets", + "title": "CH ELM Result Completion ValueSets", + "status": "active", + "experimental": false, + "description": "This CH ELM code system defines the value set URLs as codes to map in the concept maps the leading codes, which must be completed with additional codes.", + "caseSensitive": false, + "content": "complete", + "concept": [ + { + "code": "http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-results-sterile-spec" + }, + { + "code": "http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-results-geni-spec" + }, + { + "code": "http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-results-bot-spec" + }, + { + "code": "http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-results-diph-spec" + }, + { + "code": "http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-results-tub-spec" + }, + { + "code": "http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-results-mpx-sash" + }, + { + "code": "http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-results-mpx-ctng" + }, + { + "code": "http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-results-inf-org" + }, + { + "code": "http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-results-mea-org" + }, + { + "code": "http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-results-ehec-org" + }, + { + "code": "http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-results-shi-org" + }, + { + "code": "http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-results-diph-org" + }, + { + "code": "http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-results-pneu-org" + }, + { + "code": "http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-results-tub-org" + }, + { + "code": "http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-results-sal-org" + }, + { + "code": "http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-results-haem-org" + }, + { + "code": "http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-results-lis-org" + }, + { + "code": "http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-results-chol-org" + }, + { + "code": "http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-results-hiv-org" + }, + { + "code": "http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-results-bru-org" + }, + { + "code": "http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-results-mpx-sashec" + }, + { + "code": "http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-results-men-org" + }, + { + "code": "http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-results-cpe-org" + }, + { + "code": "http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-results-mal-org" + }, + { + "code": "http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-results-bot-org" + }, + { + "code": "http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-results-tub-gen-org" + } + ] +} diff --git a/input/resources/ConceptMap-ch-elm-expecting-organism-specification-to-result-completion-vs.json b/input/resources/ConceptMap-ch-elm-expecting-organism-specification-to-result-completion-vs.json new file mode 100644 index 0000000..d518a66 --- /dev/null +++ b/input/resources/ConceptMap-ch-elm-expecting-organism-specification-to-result-completion-vs.json @@ -0,0 +1,31 @@ +{ + "resourceType": "ConceptMap", + "id": "ch-elm-expecting-organism-specification-to-result-completion-vs", + "url": "http://fhir.ch/ig/ch-elm/ConceptMap/ch-elm-expecting-organism-specification-to-result-completion-vs", + "version": "2023-10-30", + "name": "ChElmExpectingOrganismSpecificationToResultCompletionValueSets", + "title": "CH ELM Expecting Organism Specification To Result Completion ValueSets Mapping", + "status": "active", + "experimental": false, + "description": "This CH ELM concept map shows which leading codes have to be completed by an additional code. The target code shows the URL of the value set from which the completing codes for the expecting specimen must come from.", + "sourceCanonical": "http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-expecting-organism-specification", + "targetCanonical": "http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-result-completion-vs", + "group": [ + { + "source": "http://loinc.org", + "target": "http://fhir.ch/ig/ch-elm/CodeSystem/ch-elm-result-completion-vs", + "element": [ + { + "code": "85827-4", + "display": "Carbapenem resistance bla OXA-48-like gene [Presence] by Molecular method", + "target": [ + { + "code": "http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-results-cpe-org", + "equivalence": "relatedto" + } + ] + } + ] + } + ] +} \ No newline at end of file diff --git a/input/resources/ConceptMap-ch-elm-expecting-specimen-specification-to-result-completion-vs.json b/input/resources/ConceptMap-ch-elm-expecting-specimen-specification-to-result-completion-vs.json new file mode 100644 index 0000000..876c9b8 --- /dev/null +++ b/input/resources/ConceptMap-ch-elm-expecting-specimen-specification-to-result-completion-vs.json @@ -0,0 +1,61 @@ +{ + "resourceType": "ConceptMap", + "id": "ch-elm-expecting-specimen-specification-to-result-completion-vs", + "url": "http://fhir.ch/ig/ch-elm/ConceptMap/ch-elm-expecting-specimen-specification-to-result-completion-vs", + "version": "2023-10-30", + "name": "ChElmExpectingSpecimenSpecificationToResultCompletionValueSets", + "title": "CH ELM Expecting Specimen Specification To Result Completion ValueSets Mapping", + "status": "active", + "experimental": false, + "description": "This CH ELM concept map shows which leading codes have to be completed by an additional code. The target code shows the URL of the value set from which the completing codes for the expecting specimen must come from.", + "sourceCanonical": "http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-expecting-specimen-specification", + "targetCanonical": "http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-result-completion-vs", + "group": [ + { + "source": "http://loinc.org", + "target": "http://fhir.ch/ig/ch-elm/CodeSystem/ch-elm-result-completion-vs", + "element": [ + { + "code": "21613-5", + "display": "Chlamydia trachomatis DNA [Presence] in Specimen by NAA with probe detection", + "target": [ + { + "code": "http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-results-geni-spec", + "equivalence": "relatedto" + } + ] + }, + { + "code": "31777-6", + "display": "Chlamydia trachomatis Ag [Presence] in Specimen", + "target": [ + { + "code": "http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-results-geni-spec", + "equivalence": "relatedto" + } + ] + }, + { + "code": "43304-5", + "display": "Chlamydia trachomatis rRNA [Presence] in Specimen by NAA with probe detection", + "target": [ + { + "code": "http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-results-geni-spec", + "equivalence": "relatedto" + } + ] + }, + { + "code": "6349-5", + "display": "Chlamydia trachomatis [Presence] in Specimen by Organism specific culture", + "target": [ + { + "code": "http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-results-geni-spec", + "equivalence": "relatedto" + } + ] + } + ] + } + ] +} \ No newline at end of file diff --git a/input/resources/ValueSet-ch-elm-expecting-organism-specification.json b/input/resources/ValueSet-ch-elm-expecting-organism-specification.json new file mode 100644 index 0000000..232efa4 --- /dev/null +++ b/input/resources/ValueSet-ch-elm-expecting-organism-specification.json @@ -0,0 +1,24 @@ +{ + "resourceType": "ValueSet", + "id": "ch-elm-expecting-organism-specification", + "url": "http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-expecting-organism-specification", + "version": "2023-10-30", + "name": "ChElmExpectingOrganismSpecification", + "title": "CH ELM Expecting Organism Specification", + "status": "active", + "experimental": false, + "description": "This CH ELM value set includes the leading codes for the laboratory test results, which have to be completed by another code for the expecting organism.", + "compose": { + "include": [ + { + "system": "http://loinc.org", + "concept": [ + { + "code": "85827-4", + "display": "Carbapenem resistance bla OXA-48-like gene [Presence] by Molecular method" + } + ] + } + ] + } +} \ No newline at end of file diff --git a/input/resources/ValueSet-ch-elm-expecting-specimen-specification.json b/input/resources/ValueSet-ch-elm-expecting-specimen-specification.json new file mode 100644 index 0000000..d9f84d2 --- /dev/null +++ b/input/resources/ValueSet-ch-elm-expecting-specimen-specification.json @@ -0,0 +1,36 @@ +{ + "resourceType": "ValueSet", + "id": "ch-elm-expecting-specimen-specification", + "url": "http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-expecting-specimen-specification", + "version": "2023-10-30", + "name": "ChElmExpectingSpecimenSpecification", + "title": "CH ELM Expecting Specimen Specification", + "status": "active", + "experimental": false, + "description": "This CH ELM value set includes the leading codes for the laboratory test results, which have to be completed by another code for the expecting specimen.", + "compose": { + "include": [ + { + "system": "http://loinc.org", + "concept": [ + { + "code": "21613-5", + "display": "Chlamydia trachomatis DNA [Presence] in Specimen by NAA with probe detection" + }, + { + "code": "31777-6", + "display": "Chlamydia trachomatis Ag [Presence] in Specimen" + }, + { + "code": "43304-5", + "display": "Chlamydia trachomatis rRNA [Presence] in Specimen by NAA with probe detection" + }, + { + "code": "6349-5", + "display": "Chlamydia trachomatis [Presence] in Specimen by Organism specific culture" + } + ] + } + ] + } +} \ No newline at end of file diff --git a/input/resources/ValueSet-ch-elm-result-completion-vs.json b/input/resources/ValueSet-ch-elm-result-completion-vs.json new file mode 100644 index 0000000..d553b05 --- /dev/null +++ b/input/resources/ValueSet-ch-elm-result-completion-vs.json @@ -0,0 +1,98 @@ +{ + "resourceType": "ValueSet", + "id": "ch-elm-result-completion-vs", + "url": "http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-result-completion-vs", + "version": "2023-10-18", + "name": "ChElmResultCompletionValueSets", + "title": "CH ELM Result Completion ValueSets", + "status": "active", + "experimental": false, + "description": "This CH ELM value set includes the value set URLs as codes to map in the concept maps the leading codes, which must be completed with additional codes.", + "compose": { + "include": [ + { + "system": "http://fhir.ch/ig/ch-elm/CodeSystem/ch-elm-result-completion-vs", + "concept": [ + { + "code": "http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-results-sterile-spec" + }, + { + "code": "http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-results-geni-spec" + }, + { + "code": "http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-results-bot-spec" + }, + { + "code": "http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-results-diph-spec" + }, + { + "code": "http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-results-tub-spec" + }, + { + "code": "http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-results-mpx-sash" + }, + { + "code": "http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-results-mpx-ctng" + }, + { + "code": "http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-results-inf-org" + }, + { + "code": "http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-results-mea-org" + }, + { + "code": "http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-results-ehec-org" + }, + { + "code": "http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-results-shi-org" + }, + { + "code": "http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-results-diph-org" + }, + { + "code": "http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-results-pneu-org" + }, + { + "code": "http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-results-tub-org" + }, + { + "code": "http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-results-sal-org" + }, + { + "code": "http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-results-haem-org" + }, + { + "code": "http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-results-lis-org" + }, + { + "code": "http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-results-chol-org" + }, + { + "code": "http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-results-hiv-org" + }, + { + "code": "http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-results-bru-org" + }, + { + "code": "http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-results-mpx-sashec" + }, + { + "code": "http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-results-men-org" + }, + { + "code": "http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-results-cpe-org" + }, + { + "code": "http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-results-mal-org" + }, + { + "code": "http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-results-bot-org" + }, + { + "code": "http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-results-tub-gen-org" + } + ] + } + ] + } +} diff --git a/input/resources/ValueSet-ch-elm-results-cpe-org.json b/input/resources/ValueSet-ch-elm-results-cpe-org.json new file mode 100644 index 0000000..74f5f4d --- /dev/null +++ b/input/resources/ValueSet-ch-elm-results-cpe-org.json @@ -0,0 +1,24 @@ +{ + "resourceType": "ValueSet", + "id": "ch-elm-results-cpe-org", + "url": "http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-results-cpe-org", + "version": "2023-10-31", + "name": "ChElmResultsCpeOrg", + "title": "CH ELM Results CPE Org", + "status": "active", + "experimental": false, + "description": "This CH ELM value set includes the codes for the laboratory test results to complete the leading code with an additional code.", + "compose": { + "include": [ + { + "system": "http://snomed.info/sct", + "concept": [ + { + "code": "56415008", + "display": "Klebsiella pneumoniae (organism)" + } + ] + } + ] + } +} \ No newline at end of file diff --git a/input/resources/ValueSet-ch-elm-results-geni-spec.json b/input/resources/ValueSet-ch-elm-results-geni-spec.json new file mode 100644 index 0000000..21201dd --- /dev/null +++ b/input/resources/ValueSet-ch-elm-results-geni-spec.json @@ -0,0 +1,48 @@ +{ + "resourceType": "ValueSet", + "id": "ch-elm-results-geni-spec", + "url": "http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-results-geni-spec", + "version": "2023-10-18", + "name": "ChElmResultsGeniSpec", + "title": "CH ELM Results Geni Spec", + "status": "active", + "experimental": false, + "description": "This CH ELM value set includes the codes for the laboratory test results to complete the leading code with an additional code.", + "compose": { + "include": [ + { + "system": "http://snomed.info/sct", + "concept": [ + { + "code": "119395005", + "display": "Specimen from uterine cervix" + }, + { + "code": "258527002", + "display": "Anal swab" + }, + { + "code": "258508008", + "display": "Genital swab" + }, + { + "code": "258520000", + "display": "Vaginal swab" + }, + { + "code": "119393003", + "display": "Specimen from urethra" + }, + { + "code": "119347001", + "display": "Seminal fluid" + }, + { + "code": "119396006", + "display": "Specimen from endometrium" + } + ] + } + ] + } +} \ No newline at end of file diff --git a/input/resources/ValueSet-ch-elm-results-laboratory-observation.json b/input/resources/ValueSet-ch-elm-results-laboratory-observation.json new file mode 100644 index 0000000..2396652 --- /dev/null +++ b/input/resources/ValueSet-ch-elm-results-laboratory-observation.json @@ -0,0 +1,228 @@ +{ + "resourceType": "ValueSet", + "id": "ch-elm-results-laboratory-observation", + "url": "http://fhir.ch/ig/ch-elm/ValueSet/ch-elm-results-laboratory-observation", + "version": "2023-10-18", + "name": "ChElmResultsLaboratoryObservation", + "title": "CH ELM Results Laboratory Observation", + "status": "active", + "experimental": false, + "description": "This CH ELM value set includes the codes for the laboratory test results (organism).", + "compose": { + "include": [ + { + "system": "http://loinc.org", + "concept": [ + { + "code": "14127-5", + "display": "Neisseria gonorrhoeae [Presence] in Anal by Organism specific culture" + }, + { + "code": "21415-5", + "display": "Neisseria gonorrhoeae DNA [Presence] in Urethra by NAA with probe detection" + }, + { + "code": "21416-3", + "display": "Neisseria gonorrhoeae DNA [Presence] in Urine by NAA with probe detection" + }, + { + "code": "24111-7", + "display": "Neisseria gonorrhoeae DNA [Presence] in Specimen by NAA with probe detection" + }, + { + "code": "32705-6", + "display": "Neisseria gonorrhoeae DNA [Presence] in Vaginal fluid by NAA with probe detection" + }, + { + "code": "43305-2", + "display": "Neisseria gonorrhoeae rRNA [Presence] in Specimen by NAA with probe detection" + }, + { + "code": "47387-6", + "display": "Neisseria gonorrhoeae DNA [Presence] in Genital specimen by NAA with probe detection" + }, + { + "code": "50388-8", + "display": "Neisseria gonorrhoeae rRNA [Presence] in Cervix by NAA with probe detection" + }, + { + "code": "53879-3", + "display": "Neisseria gonorrhoeae rRNA [Presence] in Vaginal fluid by NAA with probe detection" + }, + { + "code": "53927-0", + "display": "Neisseria gonorrhoeae rRNA [Presence] in Urethra by NAA with probe detection" + }, + { + "code": "57458-2", + "display": "Neisseria gonorrhoeae rRNA [Presence] in Anal by NAA with probe detection" + }, + { + "code": "60255-7", + "display": "Neisseria gonorrhoeae rRNA [Presence] in Throat by NAA with probe detection" + }, + { + "code": "60256-5", + "display": "Neisseria gonorrhoeae rRNA [Presence] in Urine by NAA with probe detection" + }, + { + "code": "688-2", + "display": "Neisseria gonorrhoeae [Presence] in Cervix by Organism specific culture" + }, + { + "code": "691-6", + "display": "Neisseria gonorrhoeae [Presence] in Genital specimen by Organism specific culture" + }, + { + "code": "693-2", + "display": "Neisseria gonorrhoeae [Presence] in Vaginal fluid by Organism specific culture" + }, + { + "code": "694-0", + "display": "Neisseria gonorrhoeae [Presence] in Semen by Organism specific culture" + }, + { + "code": "696-5", + "display": "Neisseria gonorrhoeae [Presence] in Throat by Organism specific culture" + }, + { + "code": "697-3", + "display": "Neisseria gonorrhoeae [Presence] in Urethra by Organism specific culture" + }, + { + "code": "698-1", + "display": "Neisseria gonorrhoeae [Presence] in Specimen by Organism specific culture" + }, + { + "code": "80366-8", + "display": "Neisseria gonorrhoeae rRNA [Presence] in Anorectal by NAA with probe detection" + }, + { + "code": "80368-4", + "display": "Neisseria gonorrhoeae [Presence] in Anorectal by Organism specific culture" + }, + { + "code": "88224-1", + "display": "Neisseria gonorrhoeae DNA [Presence] in Anorectal by NAA with probe detection" + }, + { + "code": "88225-8", + "display": "Neisseria gonorrhoeae DNA [Presence] in Throat by NAA with probe detection" + }, + { + "code": "96599-6", + "display": "Neisseria gonorrhoeae DNA [Presence] in Cervix by NAA with probe detection" + }, + { + "code": "14463-4", + "display": "Chlamydia trachomatis [Presence] in Cervix by Organism specific culture" + }, + { + "code": "14464-2", + "display": "Chlamydia trachomatis [Presence] in Vaginal fluid by Organism specific culture" + }, + { + "code": "14465-9", + "display": "Chlamydia trachomatis [Presence] in Urethra by Organism specific culture" + }, + { + "code": "16600-9", + "display": "Chlamydia trachomatis rRNA [Presence] in Genital specimen by probe" + }, + { + "code": "21190-4", + "display": "Chlamydia trachomatis DNA [Presence] in Cervix by NAA with probe detection" + }, + { + "code": "21191-2", + "display": "Chlamydia trachomatis DNA [Presence] in Urethra by NAA with probe detection" + }, + { + "code": "21613-5", + "display": "Chlamydia trachomatis DNA [Presence] in Specimen by NAA with probe detection" + }, + { + "code": "23838-6", + "display": "Chlamydia trachomatis rRNA [Presence] in Genital fluid by probe" + }, + { + "code": "31777-6", + "display": "Chlamydia trachomatis Ag [Presence] in Specimen" + }, + { + "code": "42931-6", + "display": "Chlamydia trachomatis rRNA [Presence] in Urine by NAA with probe detection" + }, + { + "code": "43304-5", + "display": "Chlamydia trachomatis rRNA [Presence] in Specimen by NAA with probe detection" + }, + { + "code": "45084-1", + "display": "Chlamydia trachomatis DNA [Presence] in Vaginal fluid by NAA with probe detection" + }, + { + "code": "45090-8", + "display": "Chlamydia trachomatis DNA [Presence] in Anal by NAA with probe detection" + }, + { + "code": "45093-2", + "display": "Chlamydia trachomatis [Presence] in Anal by Organism specific culture" + }, + { + "code": "45095-7", + "display": "Chlamydia trachomatis [Presence] in Genital specimen by Organism specific culture" + }, + { + "code": "50387-0", + "display": "Chlamydia trachomatis rRNA [Presence] in Cervix by NAA with probe detection" + }, + { + "code": "51578-3", + "display": "Chlamydia trachomatis DNA [Presence] in Semen by NAA with probe detection" + }, + { + "code": "53925-4", + "display": "Chlamydia trachomatis rRNA [Presence] in Urethra by NAA with probe detection" + }, + { + "code": "53926-2", + "display": "Chlamydia trachomatis rRNA [Presence] in Vaginal fluid by NAA with probe detection" + }, + { + "code": "57287-5", + "display": "Chlamydia trachomatis rRNA [Presence] in Anal by NAA with probe detection" + }, + { + "code": "6349-5", + "display": "Chlamydia trachomatis [Presence] in Specimen by Organism specific culture" + }, + { + "code": "6356-0", + "display": "Chlamydia trachomatis DNA [Presence] in Genital specimen by NAA with probe detection" + }, + { + "code": "6357-8", + "display": "Chlamydia trachomatis DNA [Presence] in Urine by NAA with probe detection" + }, + { + "code": "80363-5", + "display": "Chlamydia trachomatis DNA [Presence] in Anorectal by NAA with probe detection" + }, + { + "code": "80364-3", + "display": "Chlamydia trachomatis rRNA [Presence] in Anorectal by NAA with probe detection" + }, + { + "code": "80367-6", + "display": "Chlamydia trachomatis [Presence] in Anorectal by Organism specific culture" + }, + { + "code": "85827-4", + "display": "Carbapenem resistance bla OXA-48-like gene [Presence] by Molecular method" + } + ] + } + ] + } +} \ No newline at end of file diff --git a/sushi-config.yaml b/sushi-config.yaml index b91235e..6aae957 100644 --- a/sushi-config.yaml +++ b/sushi-config.yaml @@ -8,7 +8,7 @@ canonical: http://fhir.ch/ig/ch-elm name: CH_ELM title: "CH ELM (R4)" description: FHIR® Implementation Guide for the Electronic Laboratory Report of the Swiss Federal Office of Public Health -status: draft +status: draft # draft | active | retired | unknown license: CC0-1.0 copyright: CC0-1.0 jurisdiction: urn:iso:std:iso:3166#CHE @@ -75,4 +75,6 @@ parameters: - input/resources - fsh-generated/resources no-narrative: Bundle/* - excludettl: true \ No newline at end of file + excludettl: true + apply-version: false + default-version: true