From d95340db115b4a824a113ceb45804f9e593c2a5b Mon Sep 17 00:00:00 2001 From: Omar Khan Date: Mon, 10 Feb 2025 14:56:22 +0000 Subject: [PATCH 01/31] HL7 EU Lab Structured Report Alignment --- Bundle/Bundle-EULabGenomicReport-Example.json | 1076 +++++++++++++++++ ...omposition-EULabGenomicReport-Example.json | 103 ++ ...port-GenomicVariantAssessment-Example.json | 30 +- .../NamingSystem-Genomics-report-number.json | 43 + ...GenomicTherapeuticImplication-Example.json | 2 +- 5 files changed, 1249 insertions(+), 5 deletions(-) create mode 100644 Bundle/Bundle-EULabGenomicReport-Example.json create mode 100644 Composition/Composition-EULabGenomicReport-Example.json create mode 100644 NamingSystem/NamingSystem-Genomics-report-number.json diff --git a/Bundle/Bundle-EULabGenomicReport-Example.json b/Bundle/Bundle-EULabGenomicReport-Example.json new file mode 100644 index 00000000..535a7ff0 --- /dev/null +++ b/Bundle/Bundle-EULabGenomicReport-Example.json @@ -0,0 +1,1076 @@ +{ + "resourceType": 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Please note that the sensitivity of this test is limited by the types of detectable pathogenic variants, regions of low read depth coverage and incomplete ascertainment of disease-gene associations. 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Not eligible for R14 or R98. Agreed with testing laboratory at Manchester. Father lives in surrey. Father to have sample taken locally and sent to MFT." + } + ] + } + }, + { + "fullURL": "https://int.api.service.nhs.uk/genomic-order-management-service/FHIR/R4/Task/Task-FollowupRecommendationReport-Example", + "resource": { + "resourceType": "Task", + "id": "Task-FollowupRecommendationReport-Example", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/followup-recommendation" + ] + }, + "status": "requested", + "intent": "proposal", + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "LA14021-2", + "display": "Confirmatory testing recommended" + } + ] + }, + "description": "Testing of Pheobe's parents is recommended (via referral to the clinical genetics service) in order to confirm that both are heterozygous carriers of the missense variant.", + "for": { + "reference": "Patient/Patient-PheobeSmitham-Example" + }, + "reasonReference": { + "reference": "Observation/Observation-GenomicImplication-Therapeutic" + }, + "input": [ + { + "type": { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/v3-RoleCode", + "code": "NFTH", + "display": "natural father" + } + ] + }, + "valueReference": { + "reference": "Patient/Patient-PheobeSmithamFather-Example" + } + }, + { + "type": { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/v3-RoleCode", + "code": "NMTH", + "display": "natural mother" + } + ] + }, + "valueReference": { + "reference": "Patient/Patient-PheobeSmithamMother-Example" + } + } + ] + } + }, + { + "fullURL": "https://int.api.service.nhs.uk/genomic-order-management-service/FHIR/R4/DocumentReference/DocumentReference-StructureReporting-Example", + "resource": { + "resourceType": "DocumentReference", + "id": "DocumentReference-StructureReporting-Example", + "status": "current", + "docStatus": "final", + "subject": { + "reference": "Patient/Patient-PheobeSmitham-Example", + "identifier": { + "system": "https://fhir.nhs.uk/Id/nhs-number", + "value": "9449307539" + } + }, + "date": "2023-10-16T09:45:00Z", + "author": [ + { + "identifier": { + "system": "https://fhir.nhs.uk/Id/ods-organization-code", + "value": "R0A" + } + } + ], + "description": "Phenotype Report", + "content": [ + { + "attachment": { + "contentType": "application/json", + "url": "drs://drs.genomicsengland.nhs.uk/ga4gh/drs/v1/objects/42375e7d-071c-4eb3-b1c8-cec11e245cf0", + "title": "-Structure Data Capture JSON report" + } + } + ], + "context": { + "related": [ + { + "reference": "ServiceRequest/ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example" + }, + { + "reference": "Specimen/Specimen-PheobeSmitham-Example" + }, + { + "reference": "Specimen/Specimen-PheobeSmithamFather-Example" + }, + { + "reference": "Specimen/Specimen-PheobeSmithamMother-Example" + } + ] + } + } + } + ] +} \ No newline at end of file diff --git a/Composition/Composition-EULabGenomicReport-Example.json b/Composition/Composition-EULabGenomicReport-Example.json new file mode 100644 index 00000000..369c9039 --- /dev/null +++ b/Composition/Composition-EULabGenomicReport-Example.json @@ -0,0 +1,103 @@ +{ + "resourceType": "Composition", + "id": "Composition-EULabGenomicReport-Example", + "meta": { + "profile": [ + "http://hl7.eu/fhir/laboratory/StructureDefinition/Composition-eu-lab" + ] + }, + "extension": [ + { + "url": "http://hl7.eu/fhir/StructureDefinition/composition-basedOn-order-or-requisition", + "valueReference": { + "reference": "ServiceRequest/ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example" + } + }, + { + "url": "http://hl7.eu/fhir/StructureDefinition/information-recipient", + "valueReference": { + "reference": "PractitionerRole/PractitionerRole-EugeneSmith-Example" + } + }, + { + "url": "http://hl7.eu/fhir/laboratory/StructureDefinition/composition-diagnosticReportReference", + "valueReference": { + "reference": "DiagnosticReport/DiagnosticReport-GenomicVariantAssessment-Example" + } + } + ], + "status": "final", + "type": { + "coding": [ + { + "system": "http://loinc.org", + "code": "51969-4", + "display": "Genetic analysis report" + } + ] + }, + "category": [ + { + "coding": [ + { + "system": "http://loinc.org", + "code": "26436-6", + "display": "Laboratory studies (set)" + } + ] + }, + { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "1236877003", + "display": "Genetic pathology" + } + ] + } + ], + "subject": { + "reference": "Patient/Patient-PheobeSmitham-Example" + }, + "author": [ + { + "identifier": { + "system": "https://fhir.nhs.uk/Id/ods-organization-code", + "value": "R0A" + } + } + ], + "title": "Example Genomic Laboratory (Single) Report", + "section": [ + { + "title": "Therapeutic Implication", + "code": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "26436-6", + "display": "Laboratory studies (set)" + } + ] + }, + "entry": { + "reference": "Observation/Observation-GenomicTherapeuticImplication-Example" + } + }, + { + "title": "Genomic Variant", + "code": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "26436-6", + "display": "Laboratory studies (set)" + } + ] + }, + "entry": { + "reference": "Observation-GenomicsVariantSLC52A2-Example" + } + } + ] +} \ No newline at end of file diff --git a/DiagnosticReport/DiagnosticReport-GenomicVariantAssessment-Example.json b/DiagnosticReport/DiagnosticReport-GenomicVariantAssessment-Example.json index d5efe0b4..ed9637d2 100644 --- a/DiagnosticReport/DiagnosticReport-GenomicVariantAssessment-Example.json +++ b/DiagnosticReport/DiagnosticReport-GenomicVariantAssessment-Example.json @@ -4,10 +4,17 @@ "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report", - "https://fhir.hl7.org.uk/StructureDefinition/UKCore-DiagnosticReport" + "https://fhir.hl7.org.uk/StructureDefinition/UKCore-DiagnosticReport", + "http://hl7.eu/fhir/laboratory/StructureDefinition/DiagnosticReport-eu-lab" ] }, "extension": [ + { + "url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-DiagnosticReport.composition", + "valueReference": { + "reference": "Composition/Composition-EULabGenomicReport-Example" + } + }, { "url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/recommended-action", "valueReference": { @@ -63,13 +70,23 @@ "code": "GE" } ] + }, + { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "1236877003", + "display": "Genetic pathology" + } + ] } ], "code": { "coding": [ { "system": "http://loinc.org", - "code": "51969-4" + "code": "51969-4", + "display": "Genetic analysis report" } ] }, @@ -86,6 +103,11 @@ } } ], + "specimen": [ + { + "reference": "Specimen/Specimen-PheobeSmitham-Example" + } + ], "media": [ { "link": { @@ -110,11 +132,11 @@ ], "result": [ { - "reference": "Observation/Observation-GenomicsVariant-SLC52A2", + "reference": "Observation/Observation-GenomicsVariantSLC52A2-Example", "display": "Brown-Vialetto-Van Laere syndrome type 2" }, { - "reference": "Observation/Observation-GenomicImplication-Therapeutic" + "reference": "Observation/Observation-GenomicTherapeuticImplication-Example" } ], "conclusion": "Pheobe is homozygous for a pathogenic SLC52A2 missense variant (details below) previously reported by Johnson et al 2012 (PMID22740598). Biallelic pathogenic SLC52A2 variants cause autosomal recessive Brown-Vialetto-Van Laere syndrome type 2 (MIM614707).", diff --git a/NamingSystem/NamingSystem-Genomics-report-number.json b/NamingSystem/NamingSystem-Genomics-report-number.json new file mode 100644 index 00000000..2d9e4b78 --- /dev/null +++ b/NamingSystem/NamingSystem-Genomics-report-number.json @@ -0,0 +1,43 @@ +{ + "resourceType": "NamingSystem", + "id": "genomics-report-number", + "name": "GenomicsReportNumber", + "status": "draft", + "kind": "identifier", + "date": "2025-02-10", + "publisher": "NHS England", + "contact": [ + { + "name": "NHS England", + "telecom": [ + { + "system": "email", + "value": "interoperabilityteam@nhs.net", + "use": "work", + "rank": 1 + } + ] + }, + { + "name": "NHS Genomic Medicine Service", + "telecom": [ + { + "system": "email", + "value": "england.genomics@nhs.net", + "use": "work", + "rank": 1 + } + ] + } + ], + "responsible": "NHS Genomic Interop Programme", + "description": "Genomic Medicine Service Unique Report Number", + "usage": "Assigned by central GMS system on receipt of a test report", + "uniqueId": [ + { + "type": "uri", + "value": "https://fhir.nhs.uk/Id/GMSReport", + "preferred": true + } + ] +} \ No newline at end of file diff --git a/Observation/Observation-GenomicTherapeuticImplication-Example.json b/Observation/Observation-GenomicTherapeuticImplication-Example.json index 8d292591..87b39079 100644 --- a/Observation/Observation-GenomicTherapeuticImplication-Example.json +++ b/Observation/Observation-GenomicTherapeuticImplication-Example.json @@ -47,7 +47,7 @@ ], "derivedFrom": [ { - "reference": "Observation/Oservation-GenomicsVariant-SLC52A2" + "reference": "Observation/Observation-GenomicsVariantSLC52A2-Example" } ], "component": [ From d80be2a43cd11987aac831721a5396a6edf6f1d1 Mon Sep 17 00:00:00 2001 From: Omar Khan Date: Mon, 10 Feb 2025 15:22:05 +0000 Subject: [PATCH 02/31] Fixes to Examples and updated dependencies --- Bundle/Bundle-EULabGenomicReport-Example.json | 18 ++++++------ ...omposition-EULabGenomicReport-Example.json | 28 ++++++------------- package.json | 5 +++- 3 files changed, 22 insertions(+), 29 deletions(-) diff --git a/Bundle/Bundle-EULabGenomicReport-Example.json b/Bundle/Bundle-EULabGenomicReport-Example.json index 535a7ff0..b3f7de10 100644 --- a/Bundle/Bundle-EULabGenomicReport-Example.json +++ b/Bundle/Bundle-EULabGenomicReport-Example.json @@ -14,7 +14,7 @@ "timestamp": "2023-10-16T00:00:00-05:00", "entry": [ { - "fullURL": "https://int.api.service.nhs.uk/genomic-order-management-service/FHIR/R4/Composition/Composition-EULabGenomicReport-Example", + "fullUrl": "https://int.api.service.nhs.uk/genomic-order-management-service/FHIR/R4/Composition/Composition-EULabGenomicReport-Example", "resource": { "resourceType": "Composition", "id": "Composition-EULabGenomicReport-Example", @@ -120,7 +120,7 @@ } }, { - "fullURL": "https://int.api.service.nhs.uk/genomic-order-management-service/FHIR/R4/DiagnosticReport/DiagnosticReport-GenomicVariantAssessment-Example", + "fullUrl": "https://int.api.service.nhs.uk/genomic-order-management-service/FHIR/R4/DiagnosticReport/DiagnosticReport-GenomicVariantAssessment-Example", "resource": { "resourceType": "DiagnosticReport", "id": "DiagnosticReport-GenomicVariantAssessment-Example", @@ -287,7 +287,7 @@ } }, { - "fullURL": "https://int.api.service.nhs.uk/genomic-order-management-service/FHIR/R4/Patient/Patient-PheobeSmitham-Example", + "fullUrl": "https://int.api.service.nhs.uk/genomic-order-management-service/FHIR/R4/Patient/Patient-PheobeSmitham-Example", "resource": { "resourceType": "Patient", "id": "Patient-PheobeSmitham-Example", @@ -395,7 +395,7 @@ } }, { - "fullURL": "https://int.api.service.nhs.uk/genomic-order-management-service/FHIR/R4/Observation/Observation-GenomicTherapeuticImplication-Example", + "fullUrl": "https://int.api.service.nhs.uk/genomic-order-management-service/FHIR/R4/Observation/Observation-GenomicTherapeuticImplication-Example", "resource": { "resourceType": "Observation", "id": "Observation-GenomicTherapeuticImplication-Example", @@ -496,7 +496,7 @@ } }, { - "fullURL": "https://int.api.service.nhs.uk/genomic-order-management-service/FHIR/R4/Observation/Observation-GenomicsVariantSLC52A2-Example", + "fullUrl": "https://int.api.service.nhs.uk/genomic-order-management-service/FHIR/R4/Observation/Observation-GenomicsVariantSLC52A2-Example", "resource": { "resourceType": "Observation", "id": "Observation-GenomicsVariantSLC52A2-Example", @@ -706,7 +706,7 @@ } }, { - "fullURL": "https://int.api.service.nhs.uk/genomic-order-management-service/FHIR/R4/Specimen/Specimen-PheobeSmitham-Example", + "fullUrl": "https://int.api.service.nhs.uk/genomic-order-management-service/FHIR/R4/Specimen/Specimen-PheobeSmitham-Example", "resource": { "resourceType": "Specimen", "id": "Specimen-PheobeSmitham-Example", @@ -765,7 +765,7 @@ } }, { - "fullURL": "https://int.api.service.nhs.uk/genomic-order-management-service/FHIR/R4/ServiceRequest/ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example", + "fullUrl": "https://int.api.service.nhs.uk/genomic-order-management-service/FHIR/R4/ServiceRequest/ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example", "resource": { "resourceType": "ServiceRequest", "id": "ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example", @@ -962,7 +962,7 @@ } }, { - "fullURL": "https://int.api.service.nhs.uk/genomic-order-management-service/FHIR/R4/Task/Task-FollowupRecommendationReport-Example", + "fullUrl": "https://int.api.service.nhs.uk/genomic-order-management-service/FHIR/R4/Task/Task-FollowupRecommendationReport-Example", "resource": { "resourceType": "Task", "id": "Task-FollowupRecommendationReport-Example", @@ -1022,7 +1022,7 @@ } }, { - "fullURL": "https://int.api.service.nhs.uk/genomic-order-management-service/FHIR/R4/DocumentReference/DocumentReference-StructureReporting-Example", + "fullUrl": "https://int.api.service.nhs.uk/genomic-order-management-service/FHIR/R4/DocumentReference/DocumentReference-StructureReporting-Example", "resource": { "resourceType": "DocumentReference", "id": "DocumentReference-StructureReporting-Example", diff --git a/Composition/Composition-EULabGenomicReport-Example.json b/Composition/Composition-EULabGenomicReport-Example.json index 369c9039..0f303391 100644 --- a/Composition/Composition-EULabGenomicReport-Example.json +++ b/Composition/Composition-EULabGenomicReport-Example.json @@ -70,7 +70,7 @@ "title": "Example Genomic Laboratory (Single) Report", "section": [ { - "title": "Therapeutic Implication", + "title": "Results", "code": { "coding": [ { @@ -80,24 +80,14 @@ } ] }, - "entry": { - "reference": "Observation/Observation-GenomicTherapeuticImplication-Example" - } - }, - { - "title": "Genomic Variant", - "code": { - "coding": [ - { - "system": "http://snomed.info/sct", - "code": "26436-6", - "display": "Laboratory studies (set)" - } - ] - }, - "entry": { - "reference": "Observation-GenomicsVariantSLC52A2-Example" - } + "entry": [ + { + "reference": "Observation/Observation-GenomicTherapeuticImplication-Example" + }, + { + "reference": "Observation-GenomicsVariantSLC52A2-Example" + } + ] } ] } \ No newline at end of file diff --git a/package.json b/package.json index e679bd07..f6a055fe 100644 --- a/package.json +++ b/package.json @@ -9,7 +9,10 @@ "dependencies": { "fhir.r4.ukcore.stu3.currentbuild": "0.0.18-pre-release", "hl7.fhir.r4.core": "4.0.1", - "hl7.fhir.uv.genomics-reporting": "3.0.0-ballot" + "hl7.fhir.uv.genomics-reporting": "3.0.0-ballot", + "hl7.fhir.eu.laboratory": "0.1.0", + "hl7.fhir.uv.ips": "1.1.0", + "hl7.fhir.eu.extensions": "0.1.0" } } From 641cba7ca1a7afaecdb37f34097333822203c694 Mon Sep 17 00:00:00 2001 From: Omar Khan Date: Mon, 10 Feb 2025 17:28:37 +0000 Subject: [PATCH 03/31] Correction to composition resource --- Bundle/Bundle-EULabGenomicReport-Example.json | 31 +++++++------------ ...omposition-EULabGenomicReport-Example.json | 3 +- 2 files changed, 13 insertions(+), 21 deletions(-) diff --git a/Bundle/Bundle-EULabGenomicReport-Example.json b/Bundle/Bundle-EULabGenomicReport-Example.json index b3f7de10..68c5ca7c 100644 --- a/Bundle/Bundle-EULabGenomicReport-Example.json +++ b/Bundle/Bundle-EULabGenomicReport-Example.json @@ -76,6 +76,7 @@ "subject": { "reference": "Patient/Patient-PheobeSmitham-Example" }, + "date": "2023-10-16T00:00:00-05:00" "author": [ { "identifier": { @@ -87,34 +88,24 @@ "title": "Example Genomic Laboratory (Single) Report", "section": [ { - "title": "Therapeutic Implication", + "title": "Results", "code": { "coding": [ { - "system": "http://snomed.info/sct", - "code": "26436-6", - "display": "Laboratory studies (set)" - } - ] - }, - "entry": { - "reference": "Observation/Observation-GenomicTherapeuticImplication-Example" - } - }, - { - "title": "Genomic Variant", - "code": { - "coding": [ - { - "system": "http://snomed.info/sct", + "system": "http://loinc.org", "code": "26436-6", "display": "Laboratory studies (set)" } ] }, - "entry": { - "reference": "Observation-GenomicsVariantSLC52A2-Example" - } + "entry": [ + { + "reference": "Observation/Observation-GenomicTherapeuticImplication-Example" + }, + { + "reference": "Observation-GenomicsVariantSLC52A2-Example" + } + ] } ] } diff --git a/Composition/Composition-EULabGenomicReport-Example.json b/Composition/Composition-EULabGenomicReport-Example.json index 0f303391..4dcc6819 100644 --- a/Composition/Composition-EULabGenomicReport-Example.json +++ b/Composition/Composition-EULabGenomicReport-Example.json @@ -59,6 +59,7 @@ "subject": { "reference": "Patient/Patient-PheobeSmitham-Example" }, + "date": "2023-10-16T00:00:00-05:00" "author": [ { "identifier": { @@ -74,7 +75,7 @@ "code": { "coding": [ { - "system": "http://snomed.info/sct", + "system": "http://loinc.org", "code": "26436-6", "display": "Laboratory studies (set)" } From 82420ba4e04d6f19941d27b48be13bd2d1f3594f Mon Sep 17 00:00:00 2001 From: Omar Khan Date: Mon, 10 Feb 2025 17:39:41 +0000 Subject: [PATCH 04/31] Typo fixes --- Bundle/Bundle-EULabGenomicReport-Example.json | 2 +- Composition/Composition-EULabGenomicReport-Example.json | 2 +- Observation/Observation-NoTransfusionProbandFather-Example.json | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/Bundle/Bundle-EULabGenomicReport-Example.json b/Bundle/Bundle-EULabGenomicReport-Example.json index 68c5ca7c..f76cc650 100644 --- a/Bundle/Bundle-EULabGenomicReport-Example.json +++ b/Bundle/Bundle-EULabGenomicReport-Example.json @@ -76,7 +76,7 @@ "subject": { "reference": "Patient/Patient-PheobeSmitham-Example" }, - "date": "2023-10-16T00:00:00-05:00" + "date": "2023-10-16T00:00:00-05:00", "author": [ { "identifier": { diff --git a/Composition/Composition-EULabGenomicReport-Example.json b/Composition/Composition-EULabGenomicReport-Example.json index 4dcc6819..46696872 100644 --- a/Composition/Composition-EULabGenomicReport-Example.json +++ b/Composition/Composition-EULabGenomicReport-Example.json @@ -59,7 +59,7 @@ "subject": { "reference": "Patient/Patient-PheobeSmitham-Example" }, - "date": "2023-10-16T00:00:00-05:00" + "date": "2023-10-16T00:00:00-05:00", "author": [ { "identifier": { diff --git a/Observation/Observation-NoTransfusionProbandFather-Example.json b/Observation/Observation-NoTransfusionProbandFather-Example.json index 5970c087..1ccd018e 100644 --- a/Observation/Observation-NoTransfusionProbandFather-Example.json +++ b/Observation/Observation-NoTransfusionProbandFather-Example.json @@ -27,5 +27,5 @@ "value": "9449307636" } }, - "effectiveDateTime": "2023-09-15T15:00:00Z", + "effectiveDateTime": "2023-09-15T15:00:00Z" } \ No newline at end of file From 32ea369f30242bbbdcd70ed06020e78ffd63193a Mon Sep 17 00:00:00 2001 From: Omar Khan Date: Tue, 11 Feb 2025 11:02:41 +0000 Subject: [PATCH 05/31] Testing fixes for EU Lab --- Bundle/Bundle-EULabGenomicReport-Example.json | 12 +++++++++--- ...vation-GenomicTherapeuticImplication-Example.json | 4 ++-- ...-WGSTestOrderFormUpdated-TrioTesting-Example.json | 6 ++++++ 3 files changed, 17 insertions(+), 5 deletions(-) diff --git a/Bundle/Bundle-EULabGenomicReport-Example.json b/Bundle/Bundle-EULabGenomicReport-Example.json index f76cc650..21c83d15 100644 --- a/Bundle/Bundle-EULabGenomicReport-Example.json +++ b/Bundle/Bundle-EULabGenomicReport-Example.json @@ -103,7 +103,7 @@ "reference": "Observation/Observation-GenomicTherapeuticImplication-Example" }, { - "reference": "Observation-GenomicsVariantSLC52A2-Example" + "reference": "Observation/Observation-GenomicsVariantSLC52A2-Example" } ] } @@ -474,8 +474,8 @@ "coding": [ { "system": "http://snomed.info/sct", - "code": "777436008", - "display": "Riboflavin" + "code": "438481000124108", + "display": "Riboflavin supplement" } ] } @@ -778,6 +778,12 @@ } } ], + "identifier": [ + { + "system": "https://fhir.nhs.uk/Id/GMSOrder", + "value": "RR8F1792" + } + ], "requisition": { "assigner": { "identifier": { diff --git a/Observation/Observation-GenomicTherapeuticImplication-Example.json b/Observation/Observation-GenomicTherapeuticImplication-Example.json index 87b39079..ff3416a2 100644 --- a/Observation/Observation-GenomicTherapeuticImplication-Example.json +++ b/Observation/Observation-GenomicTherapeuticImplication-Example.json @@ -85,8 +85,8 @@ "coding": [ { "system": "http://snomed.info/sct", - "code": "777436008", - "display": "Riboflavin" + "code": "438481000124108", + "display": "Riboflavin supplement" } ] } diff --git a/ServiceRequest/ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example.json b/ServiceRequest/ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example.json index b01a400c..2c9a6baf 100644 --- a/ServiceRequest/ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example.json +++ b/ServiceRequest/ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example.json @@ -19,6 +19,12 @@ } } ], + "identifier": [ + { + "system": "https://fhir.nhs.uk/Id/GMSOrder", + "value": "RR8F1792" + } + ], "requisition": { "assigner": { "identifier": { From a99c29fae20f2d254a5013331a633b8619cd4c4b Mon Sep 17 00:00:00 2001 From: Omar Khan Date: Tue, 11 Feb 2025 13:00:00 +0000 Subject: [PATCH 06/31] Testing adding meta profiles --- .../Observation-GenomicTherapeuticImplication-Example.json | 3 ++- Observation/Observation-GenomicsVariantSLC52A2-Example.json | 3 ++- Patient/Patient-PheobeSmitham-Example.json | 6 ++++++ Task/Task-FollowupRecommendationReport-Example.json | 2 +- 4 files changed, 11 insertions(+), 3 deletions(-) diff --git a/Observation/Observation-GenomicTherapeuticImplication-Example.json b/Observation/Observation-GenomicTherapeuticImplication-Example.json index ff3416a2..279e8cc3 100644 --- a/Observation/Observation-GenomicTherapeuticImplication-Example.json +++ b/Observation/Observation-GenomicTherapeuticImplication-Example.json @@ -3,7 +3,8 @@ "id": "Observation-GenomicTherapeuticImplication-Example", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication", + "http://hl7.eu/fhir/laboratory/StructureDefinition/Observation-eu-lab" ] }, "status": "final", diff --git a/Observation/Observation-GenomicsVariantSLC52A2-Example.json b/Observation/Observation-GenomicsVariantSLC52A2-Example.json index 7b015a5c..054a64b7 100644 --- a/Observation/Observation-GenomicsVariantSLC52A2-Example.json +++ b/Observation/Observation-GenomicsVariantSLC52A2-Example.json @@ -3,7 +3,8 @@ "id": "Observation-GenomicsVariantSLC52A2-Example", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant", + "http://hl7.eu/fhir/laboratory/StructureDefinition/Observation-eu-lab" ] }, "status": "final", diff --git a/Patient/Patient-PheobeSmitham-Example.json b/Patient/Patient-PheobeSmitham-Example.json index d00bb016..008c2c62 100644 --- a/Patient/Patient-PheobeSmitham-Example.json +++ b/Patient/Patient-PheobeSmitham-Example.json @@ -1,6 +1,12 @@ { "resourceType": "Patient", "id": "Patient-PheobeSmitham-Example", + "meta": { + "profile": [ + "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Patient", + "http://hl7.eu/fhir/laboratory/StructureDefinition/Patient-eu-lab" + ] + }, "extension": [ { "url": "https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-BirthSex", diff --git a/Task/Task-FollowupRecommendationReport-Example.json b/Task/Task-FollowupRecommendationReport-Example.json index 0a93f4b8..cf0ddec9 100644 --- a/Task/Task-FollowupRecommendationReport-Example.json +++ b/Task/Task-FollowupRecommendationReport-Example.json @@ -22,7 +22,7 @@ "reference": "Patient/Patient-PheobeSmitham-Example" }, "reasonReference": { - "reference": "Observation/Observation-GenomicImplication-Therapeutic" + "reference": "Observation/Observation-GenomicTherapeuticImplication-Example" }, "input": [ { From 221ce03440d77debc9e68b0285bcfb67050b51e1 Mon Sep 17 00:00:00 2001 From: Omar Khan Date: Wed, 12 Feb 2025 10:11:56 +0000 Subject: [PATCH 07/31] Correction to canonical URLs --- .../Observation-GenomicTherapeuticImplication-Example.json | 2 +- Observation/Observation-GenomicsVariantSLC52A2-Example.json | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/Observation/Observation-GenomicTherapeuticImplication-Example.json b/Observation/Observation-GenomicTherapeuticImplication-Example.json index 279e8cc3..cf035818 100644 --- a/Observation/Observation-GenomicTherapeuticImplication-Example.json +++ b/Observation/Observation-GenomicTherapeuticImplication-Example.json @@ -4,7 +4,7 @@ "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication", - "http://hl7.eu/fhir/laboratory/StructureDefinition/Observation-eu-lab" + "http://hl7.eu/fhir/laboratory/StructureDefinition/Observation-resultslab-eu-lab" ] }, "status": "final", diff --git a/Observation/Observation-GenomicsVariantSLC52A2-Example.json b/Observation/Observation-GenomicsVariantSLC52A2-Example.json index 054a64b7..2524e4ea 100644 --- a/Observation/Observation-GenomicsVariantSLC52A2-Example.json +++ b/Observation/Observation-GenomicsVariantSLC52A2-Example.json @@ -4,7 +4,7 @@ "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant", - "http://hl7.eu/fhir/laboratory/StructureDefinition/Observation-eu-lab" + "http://hl7.eu/fhir/laboratory/StructureDefinition/Observation-resultslab-eu-lab" ] }, "status": "final", From 98b311d7638e49f35438b4542bac1d42d18d900a Mon Sep 17 00:00:00 2001 From: Omar Khan Date: Wed, 12 Feb 2025 10:19:01 +0000 Subject: [PATCH 08/31] Changes to canonicals for testing --- .../DiagnosticReport-GenomicVariantAssessment-Example.json | 2 -- .../Observation-GenomicTherapeuticImplication-Example.json | 1 - Observation/Observation-GenomicsVariantSLC52A2-Example.json | 1 - Patient/Patient-PheobeSmitham-Example.json | 1 - 4 files changed, 5 deletions(-) diff --git a/DiagnosticReport/DiagnosticReport-GenomicVariantAssessment-Example.json b/DiagnosticReport/DiagnosticReport-GenomicVariantAssessment-Example.json index ed9637d2..01c05873 100644 --- a/DiagnosticReport/DiagnosticReport-GenomicVariantAssessment-Example.json +++ b/DiagnosticReport/DiagnosticReport-GenomicVariantAssessment-Example.json @@ -3,8 +3,6 @@ "id": "DiagnosticReport-GenomicVariantAssessment-Example", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report", - "https://fhir.hl7.org.uk/StructureDefinition/UKCore-DiagnosticReport", "http://hl7.eu/fhir/laboratory/StructureDefinition/DiagnosticReport-eu-lab" ] }, diff --git a/Observation/Observation-GenomicTherapeuticImplication-Example.json b/Observation/Observation-GenomicTherapeuticImplication-Example.json index cf035818..22d35839 100644 --- a/Observation/Observation-GenomicTherapeuticImplication-Example.json +++ b/Observation/Observation-GenomicTherapeuticImplication-Example.json @@ -3,7 +3,6 @@ "id": "Observation-GenomicTherapeuticImplication-Example", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication", "http://hl7.eu/fhir/laboratory/StructureDefinition/Observation-resultslab-eu-lab" ] }, diff --git a/Observation/Observation-GenomicsVariantSLC52A2-Example.json b/Observation/Observation-GenomicsVariantSLC52A2-Example.json index 2524e4ea..18552ad5 100644 --- a/Observation/Observation-GenomicsVariantSLC52A2-Example.json +++ b/Observation/Observation-GenomicsVariantSLC52A2-Example.json @@ -3,7 +3,6 @@ "id": "Observation-GenomicsVariantSLC52A2-Example", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant", "http://hl7.eu/fhir/laboratory/StructureDefinition/Observation-resultslab-eu-lab" ] }, diff --git a/Patient/Patient-PheobeSmitham-Example.json b/Patient/Patient-PheobeSmitham-Example.json index 008c2c62..8442b2eb 100644 --- a/Patient/Patient-PheobeSmitham-Example.json +++ b/Patient/Patient-PheobeSmitham-Example.json @@ -3,7 +3,6 @@ "id": "Patient-PheobeSmitham-Example", "meta": { "profile": [ - "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Patient", "http://hl7.eu/fhir/laboratory/StructureDefinition/Patient-eu-lab" ] }, From 0a272983a25e29f9f28d6ab2ea049f3c09fd7ca8 Mon Sep 17 00:00:00 2001 From: Omar Khan Date: Wed, 12 Feb 2025 10:27:19 +0000 Subject: [PATCH 09/31] Changes to capabilitystatement for testing --- .../CapabilityStatement-genomics-application.json | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/CapabilityStatement/CapabilityStatement-genomics-application.json b/CapabilityStatement/CapabilityStatement-genomics-application.json index 93c5d51f..4efab33c 100644 --- a/CapabilityStatement/CapabilityStatement-genomics-application.json +++ b/CapabilityStatement/CapabilityStatement-genomics-application.json @@ -953,7 +953,7 @@ }, { "type": "DiagnosticReport", - "profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-DiagnosticReport", + "profile": "http://hl7.eu/fhir/laboratory/StructureDefinition/DiagnosticReport-eu-lab", "documentation": "Endpoints for interacting with DiagnosticReport resources", "interaction": [ { @@ -1114,7 +1114,7 @@ }, { "type": "Observation", - "profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Observation", + "profile": "http://hl7.eu/fhir/laboratory/StructureDefinition/Observation-resultslab-eu-lab, "documentation": "Endpoints for interacting with Observation resources", "interaction": [ { @@ -1205,7 +1205,7 @@ }, { "type": "Patient", - "profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Patient", + "profile": "http://hl7.eu/fhir/laboratory/StructureDefinition/Patient-eu-lab", "documentation": "Endpoints for interacting with Patient resources", "interaction": [ { From 82413a86bea7e7fff22476eba3081ce9b2f9fec5 Mon Sep 17 00:00:00 2001 From: Omar Khan Date: Wed, 12 Feb 2025 10:36:07 +0000 Subject: [PATCH 10/31] Revert "Changes to capabilitystatement for testing" This reverts commit 0a272983a25e29f9f28d6ab2ea049f3c09fd7ca8. --- .../CapabilityStatement-genomics-application.json | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/CapabilityStatement/CapabilityStatement-genomics-application.json b/CapabilityStatement/CapabilityStatement-genomics-application.json index 4efab33c..93c5d51f 100644 --- a/CapabilityStatement/CapabilityStatement-genomics-application.json +++ b/CapabilityStatement/CapabilityStatement-genomics-application.json @@ -953,7 +953,7 @@ }, { "type": "DiagnosticReport", - "profile": "http://hl7.eu/fhir/laboratory/StructureDefinition/DiagnosticReport-eu-lab", + "profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-DiagnosticReport", "documentation": "Endpoints for interacting with DiagnosticReport resources", "interaction": [ { @@ -1114,7 +1114,7 @@ }, { "type": "Observation", - "profile": "http://hl7.eu/fhir/laboratory/StructureDefinition/Observation-resultslab-eu-lab, + "profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Observation", "documentation": "Endpoints for interacting with Observation resources", "interaction": [ { @@ -1205,7 +1205,7 @@ }, { "type": "Patient", - "profile": "http://hl7.eu/fhir/laboratory/StructureDefinition/Patient-eu-lab", + "profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Patient", "documentation": "Endpoints for interacting with Patient resources", "interaction": [ { From 04ea0e38eb5857bb9a2998c0cfe21c54afac21c1 Mon Sep 17 00:00:00 2001 From: Omar Khan Date: Wed, 12 Feb 2025 10:36:20 +0000 Subject: [PATCH 11/31] Revert "Changes to canonicals for testing" This reverts commit 98b311d7638e49f35438b4542bac1d42d18d900a. --- .../DiagnosticReport-GenomicVariantAssessment-Example.json | 2 ++ .../Observation-GenomicTherapeuticImplication-Example.json | 1 + Observation/Observation-GenomicsVariantSLC52A2-Example.json | 1 + Patient/Patient-PheobeSmitham-Example.json | 1 + 4 files changed, 5 insertions(+) diff --git a/DiagnosticReport/DiagnosticReport-GenomicVariantAssessment-Example.json b/DiagnosticReport/DiagnosticReport-GenomicVariantAssessment-Example.json index 01c05873..ed9637d2 100644 --- a/DiagnosticReport/DiagnosticReport-GenomicVariantAssessment-Example.json +++ b/DiagnosticReport/DiagnosticReport-GenomicVariantAssessment-Example.json @@ -3,6 +3,8 @@ "id": "DiagnosticReport-GenomicVariantAssessment-Example", "meta": { "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report", + "https://fhir.hl7.org.uk/StructureDefinition/UKCore-DiagnosticReport", "http://hl7.eu/fhir/laboratory/StructureDefinition/DiagnosticReport-eu-lab" ] }, diff --git a/Observation/Observation-GenomicTherapeuticImplication-Example.json b/Observation/Observation-GenomicTherapeuticImplication-Example.json index 22d35839..cf035818 100644 --- a/Observation/Observation-GenomicTherapeuticImplication-Example.json +++ b/Observation/Observation-GenomicTherapeuticImplication-Example.json @@ -3,6 +3,7 @@ "id": "Observation-GenomicTherapeuticImplication-Example", "meta": { "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication", "http://hl7.eu/fhir/laboratory/StructureDefinition/Observation-resultslab-eu-lab" ] }, diff --git a/Observation/Observation-GenomicsVariantSLC52A2-Example.json b/Observation/Observation-GenomicsVariantSLC52A2-Example.json index 18552ad5..2524e4ea 100644 --- a/Observation/Observation-GenomicsVariantSLC52A2-Example.json +++ b/Observation/Observation-GenomicsVariantSLC52A2-Example.json @@ -3,6 +3,7 @@ "id": "Observation-GenomicsVariantSLC52A2-Example", "meta": { "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant", "http://hl7.eu/fhir/laboratory/StructureDefinition/Observation-resultslab-eu-lab" ] }, diff --git a/Patient/Patient-PheobeSmitham-Example.json b/Patient/Patient-PheobeSmitham-Example.json index 8442b2eb..008c2c62 100644 --- a/Patient/Patient-PheobeSmitham-Example.json +++ b/Patient/Patient-PheobeSmitham-Example.json @@ -3,6 +3,7 @@ "id": "Patient-PheobeSmitham-Example", "meta": { "profile": [ + "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Patient", "http://hl7.eu/fhir/laboratory/StructureDefinition/Patient-eu-lab" ] }, From 26465a7dae414d91640fce59e6954394e17161c2 Mon Sep 17 00:00:00 2001 From: Omar Khan Date: Wed, 12 Feb 2025 11:07:45 +0000 Subject: [PATCH 12/31] Changes to capabilitystatement for testing --- .../CapabilityStatement-genomics-requirements.json | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/CapabilityStatement/CapabilityStatement-genomics-requirements.json b/CapabilityStatement/CapabilityStatement-genomics-requirements.json index 725390cb..73ac1ee9 100644 --- a/CapabilityStatement/CapabilityStatement-genomics-requirements.json +++ b/CapabilityStatement/CapabilityStatement-genomics-requirements.json @@ -117,7 +117,7 @@ }, { "type": "DiagnosticReport", - "profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-DiagnosticReport" + "profile": "http://hl7.eu/fhir/laboratory/StructureDefinition/DiagnosticReport-eu-lab" }, { "type": "FamilyMemberHistory", @@ -125,11 +125,11 @@ }, { "type": "Observation", - "profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Observation" + "profile": "http://hl7.eu/fhir/laboratory/StructureDefinition/Observation-resultslab-eu-lab" }, { "type": "Patient", - "profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Patient" + "profile": "http://hl7.eu/fhir/laboratory/StructureDefinition/Patient-eu-lab" }, { "type": "Consent", From 7b3fb16e2762675bdbad6de34a2747c62b16236e Mon Sep 17 00:00:00 2001 From: Omar Khan Date: Wed, 12 Feb 2025 11:15:02 +0000 Subject: [PATCH 13/31] Revert "Changes to capabilitystatement for testing" This reverts commit 26465a7dae414d91640fce59e6954394e17161c2. --- .../CapabilityStatement-genomics-requirements.json | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/CapabilityStatement/CapabilityStatement-genomics-requirements.json b/CapabilityStatement/CapabilityStatement-genomics-requirements.json index 73ac1ee9..725390cb 100644 --- a/CapabilityStatement/CapabilityStatement-genomics-requirements.json +++ b/CapabilityStatement/CapabilityStatement-genomics-requirements.json @@ -117,7 +117,7 @@ }, { "type": "DiagnosticReport", - "profile": "http://hl7.eu/fhir/laboratory/StructureDefinition/DiagnosticReport-eu-lab" + "profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-DiagnosticReport" }, { "type": "FamilyMemberHistory", @@ -125,11 +125,11 @@ }, { "type": "Observation", - "profile": "http://hl7.eu/fhir/laboratory/StructureDefinition/Observation-resultslab-eu-lab" + "profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Observation" }, { "type": "Patient", - "profile": "http://hl7.eu/fhir/laboratory/StructureDefinition/Patient-eu-lab" + "profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Patient" }, { "type": "Consent", From 6e1632d6918e6b939fe5799dbf91199705f4877d Mon Sep 17 00:00:00 2001 From: Omar Khan Date: Wed, 12 Feb 2025 13:10:53 +0000 Subject: [PATCH 14/31] Changes to fullUrls --- Bundle/Bundle-EULabGenomicReport-Example.json | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/Bundle/Bundle-EULabGenomicReport-Example.json b/Bundle/Bundle-EULabGenomicReport-Example.json index 21c83d15..eced36fb 100644 --- a/Bundle/Bundle-EULabGenomicReport-Example.json +++ b/Bundle/Bundle-EULabGenomicReport-Example.json @@ -14,7 +14,7 @@ "timestamp": "2023-10-16T00:00:00-05:00", "entry": [ { - "fullUrl": "https://int.api.service.nhs.uk/genomic-order-management-service/FHIR/R4/Composition/Composition-EULabGenomicReport-Example", + "fullUrl": "/Composition/Composition-EULabGenomicReport-Example", "resource": { "resourceType": "Composition", "id": "Composition-EULabGenomicReport-Example", @@ -111,7 +111,7 @@ } }, { - "fullUrl": "https://int.api.service.nhs.uk/genomic-order-management-service/FHIR/R4/DiagnosticReport/DiagnosticReport-GenomicVariantAssessment-Example", + "fullUrl": "/DiagnosticReport/DiagnosticReport-GenomicVariantAssessment-Example", "resource": { "resourceType": "DiagnosticReport", "id": "DiagnosticReport-GenomicVariantAssessment-Example", @@ -278,7 +278,7 @@ } }, { - "fullUrl": "https://int.api.service.nhs.uk/genomic-order-management-service/FHIR/R4/Patient/Patient-PheobeSmitham-Example", + "fullUrl": "/Patient/Patient-PheobeSmitham-Example", "resource": { "resourceType": "Patient", "id": "Patient-PheobeSmitham-Example", @@ -386,7 +386,7 @@ } }, { - "fullUrl": "https://int.api.service.nhs.uk/genomic-order-management-service/FHIR/R4/Observation/Observation-GenomicTherapeuticImplication-Example", + "fullUrl": "/Observation/Observation-GenomicTherapeuticImplication-Example", "resource": { "resourceType": "Observation", "id": "Observation-GenomicTherapeuticImplication-Example", @@ -487,7 +487,7 @@ } }, { - "fullUrl": "https://int.api.service.nhs.uk/genomic-order-management-service/FHIR/R4/Observation/Observation-GenomicsVariantSLC52A2-Example", + "fullUrl": "/Observation/Observation-GenomicsVariantSLC52A2-Example", "resource": { "resourceType": "Observation", "id": "Observation-GenomicsVariantSLC52A2-Example", @@ -697,7 +697,7 @@ } }, { - "fullUrl": "https://int.api.service.nhs.uk/genomic-order-management-service/FHIR/R4/Specimen/Specimen-PheobeSmitham-Example", + "fullUrl": "/Specimen/Specimen-PheobeSmitham-Example", "resource": { "resourceType": "Specimen", "id": "Specimen-PheobeSmitham-Example", @@ -756,7 +756,7 @@ } }, { - "fullUrl": "https://int.api.service.nhs.uk/genomic-order-management-service/FHIR/R4/ServiceRequest/ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example", + "fullUrl": "/ServiceRequest/ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example", "resource": { "resourceType": "ServiceRequest", "id": "ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example", @@ -959,7 +959,7 @@ } }, { - "fullUrl": "https://int.api.service.nhs.uk/genomic-order-management-service/FHIR/R4/Task/Task-FollowupRecommendationReport-Example", + "fullUrl": "/Task/Task-FollowupRecommendationReport-Example", "resource": { "resourceType": "Task", "id": "Task-FollowupRecommendationReport-Example", @@ -1019,7 +1019,7 @@ } }, { - "fullUrl": "https://int.api.service.nhs.uk/genomic-order-management-service/FHIR/R4/DocumentReference/DocumentReference-StructureReporting-Example", + "fullUrl": "/DocumentReference/DocumentReference-StructureReporting-Example", "resource": { "resourceType": "DocumentReference", "id": "DocumentReference-StructureReporting-Example", From 43ed3d463fa308232d8ace6c1fa0a832c0415c61 Mon Sep 17 00:00:00 2001 From: Omar Khan Date: Wed, 12 Feb 2025 14:09:06 +0000 Subject: [PATCH 15/31] Update Bundle-EULabGenomicReport-Example.json --- Bundle/Bundle-EULabGenomicReport-Example.json | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/Bundle/Bundle-EULabGenomicReport-Example.json b/Bundle/Bundle-EULabGenomicReport-Example.json index eced36fb..0bbe868c 100644 --- a/Bundle/Bundle-EULabGenomicReport-Example.json +++ b/Bundle/Bundle-EULabGenomicReport-Example.json @@ -14,7 +14,7 @@ "timestamp": "2023-10-16T00:00:00-05:00", "entry": [ { - "fullUrl": "/Composition/Composition-EULabGenomicReport-Example", + "fullUrl": "Composition/Composition-EULabGenomicReport-Example", "resource": { "resourceType": "Composition", "id": "Composition-EULabGenomicReport-Example", @@ -111,7 +111,7 @@ } }, { - "fullUrl": "/DiagnosticReport/DiagnosticReport-GenomicVariantAssessment-Example", + "fullUrl": "DiagnosticReport/DiagnosticReport-GenomicVariantAssessment-Example", "resource": { "resourceType": "DiagnosticReport", "id": "DiagnosticReport-GenomicVariantAssessment-Example", @@ -278,7 +278,7 @@ } }, { - "fullUrl": "/Patient/Patient-PheobeSmitham-Example", + "fullUrl": "Patient/Patient-PheobeSmitham-Example", "resource": { "resourceType": "Patient", "id": "Patient-PheobeSmitham-Example", @@ -386,7 +386,7 @@ } }, { - "fullUrl": "/Observation/Observation-GenomicTherapeuticImplication-Example", + "fullUrl": "Observation/Observation-GenomicTherapeuticImplication-Example", "resource": { "resourceType": "Observation", "id": "Observation-GenomicTherapeuticImplication-Example", @@ -487,7 +487,7 @@ } }, { - "fullUrl": "/Observation/Observation-GenomicsVariantSLC52A2-Example", + "fullUrl": "Observation/Observation-GenomicsVariantSLC52A2-Example", "resource": { "resourceType": "Observation", "id": "Observation-GenomicsVariantSLC52A2-Example", @@ -697,7 +697,7 @@ } }, { - "fullUrl": "/Specimen/Specimen-PheobeSmitham-Example", + "fullUrl": "Specimen/Specimen-PheobeSmitham-Example", "resource": { "resourceType": "Specimen", "id": "Specimen-PheobeSmitham-Example", @@ -756,7 +756,7 @@ } }, { - "fullUrl": "/ServiceRequest/ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example", + "fullUrl": "ServiceRequest/ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example", "resource": { "resourceType": "ServiceRequest", "id": "ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example", @@ -959,7 +959,7 @@ } }, { - "fullUrl": "/Task/Task-FollowupRecommendationReport-Example", + "fullUrl": "Task/Task-FollowupRecommendationReport-Example", "resource": { "resourceType": "Task", "id": "Task-FollowupRecommendationReport-Example", @@ -1019,7 +1019,7 @@ } }, { - "fullUrl": "/DocumentReference/DocumentReference-StructureReporting-Example", + "fullUrl": "DocumentReference/DocumentReference-StructureReporting-Example", "resource": { "resourceType": "DocumentReference", "id": "DocumentReference-StructureReporting-Example", From 2eb959eee4c96aa6dfdf363768899a8a08d4e1b8 Mon Sep 17 00:00:00 2001 From: Omar Khan Date: Wed, 12 Feb 2025 15:30:57 +0000 Subject: [PATCH 16/31] Revert "Update Bundle-EULabGenomicReport-Example.json" This reverts commit 43ed3d463fa308232d8ace6c1fa0a832c0415c61. --- Bundle/Bundle-EULabGenomicReport-Example.json | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/Bundle/Bundle-EULabGenomicReport-Example.json b/Bundle/Bundle-EULabGenomicReport-Example.json index 0bbe868c..eced36fb 100644 --- a/Bundle/Bundle-EULabGenomicReport-Example.json +++ b/Bundle/Bundle-EULabGenomicReport-Example.json @@ -14,7 +14,7 @@ "timestamp": "2023-10-16T00:00:00-05:00", "entry": [ { - "fullUrl": "Composition/Composition-EULabGenomicReport-Example", + "fullUrl": "/Composition/Composition-EULabGenomicReport-Example", "resource": { "resourceType": "Composition", "id": "Composition-EULabGenomicReport-Example", @@ -111,7 +111,7 @@ } }, { - "fullUrl": "DiagnosticReport/DiagnosticReport-GenomicVariantAssessment-Example", + "fullUrl": "/DiagnosticReport/DiagnosticReport-GenomicVariantAssessment-Example", "resource": { "resourceType": "DiagnosticReport", "id": "DiagnosticReport-GenomicVariantAssessment-Example", @@ -278,7 +278,7 @@ } }, { - "fullUrl": "Patient/Patient-PheobeSmitham-Example", + "fullUrl": "/Patient/Patient-PheobeSmitham-Example", "resource": { "resourceType": "Patient", "id": "Patient-PheobeSmitham-Example", @@ -386,7 +386,7 @@ } }, { - "fullUrl": "Observation/Observation-GenomicTherapeuticImplication-Example", + "fullUrl": "/Observation/Observation-GenomicTherapeuticImplication-Example", "resource": { "resourceType": "Observation", "id": "Observation-GenomicTherapeuticImplication-Example", @@ -487,7 +487,7 @@ } }, { - "fullUrl": "Observation/Observation-GenomicsVariantSLC52A2-Example", + "fullUrl": "/Observation/Observation-GenomicsVariantSLC52A2-Example", "resource": { "resourceType": "Observation", "id": "Observation-GenomicsVariantSLC52A2-Example", @@ -697,7 +697,7 @@ } }, { - "fullUrl": "Specimen/Specimen-PheobeSmitham-Example", + "fullUrl": "/Specimen/Specimen-PheobeSmitham-Example", "resource": { "resourceType": "Specimen", "id": "Specimen-PheobeSmitham-Example", @@ -756,7 +756,7 @@ } }, { - "fullUrl": "ServiceRequest/ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example", + "fullUrl": "/ServiceRequest/ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example", "resource": { "resourceType": "ServiceRequest", "id": "ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example", @@ -959,7 +959,7 @@ } }, { - "fullUrl": "Task/Task-FollowupRecommendationReport-Example", + "fullUrl": "/Task/Task-FollowupRecommendationReport-Example", "resource": { "resourceType": "Task", "id": "Task-FollowupRecommendationReport-Example", @@ -1019,7 +1019,7 @@ } }, { - "fullUrl": "DocumentReference/DocumentReference-StructureReporting-Example", + "fullUrl": "/DocumentReference/DocumentReference-StructureReporting-Example", "resource": { "resourceType": "DocumentReference", "id": "DocumentReference-StructureReporting-Example", From c20b1ee4f0bd7245fd8a0778ce5bc192fe089575 Mon Sep 17 00:00:00 2001 From: Omar Khan Date: Wed, 12 Feb 2025 16:08:59 +0000 Subject: [PATCH 17/31] Replacing URLs with example --- Bundle/Bundle-EULabGenomicReport-Example.json | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/Bundle/Bundle-EULabGenomicReport-Example.json b/Bundle/Bundle-EULabGenomicReport-Example.json index eced36fb..2474a9d0 100644 --- a/Bundle/Bundle-EULabGenomicReport-Example.json +++ b/Bundle/Bundle-EULabGenomicReport-Example.json @@ -14,7 +14,7 @@ "timestamp": "2023-10-16T00:00:00-05:00", "entry": [ { - "fullUrl": "/Composition/Composition-EULabGenomicReport-Example", + "fullUrl": "http://example.org/fhir/Composition/Composition-EULabGenomicReport-Example", "resource": { "resourceType": "Composition", "id": "Composition-EULabGenomicReport-Example", @@ -111,7 +111,7 @@ } }, { - "fullUrl": "/DiagnosticReport/DiagnosticReport-GenomicVariantAssessment-Example", + "fullUrl": "http://example.org/fhir/DiagnosticReport/DiagnosticReport-GenomicVariantAssessment-Example", "resource": { "resourceType": "DiagnosticReport", "id": "DiagnosticReport-GenomicVariantAssessment-Example", @@ -278,7 +278,7 @@ } }, { - "fullUrl": "/Patient/Patient-PheobeSmitham-Example", + "fullUrl": "http://example.org/fhir/Patient/Patient-PheobeSmitham-Example", "resource": { "resourceType": "Patient", "id": "Patient-PheobeSmitham-Example", @@ -386,7 +386,7 @@ } }, { - "fullUrl": "/Observation/Observation-GenomicTherapeuticImplication-Example", + "fullUrl": "http://example.org/fhir/Observation/Observation-GenomicTherapeuticImplication-Example", "resource": { "resourceType": "Observation", "id": "Observation-GenomicTherapeuticImplication-Example", @@ -487,7 +487,7 @@ } }, { - "fullUrl": "/Observation/Observation-GenomicsVariantSLC52A2-Example", + "fullUrl": "http://example.org/fhir/Observation/Observation-GenomicsVariantSLC52A2-Example", "resource": { "resourceType": "Observation", "id": "Observation-GenomicsVariantSLC52A2-Example", @@ -697,7 +697,7 @@ } }, { - "fullUrl": "/Specimen/Specimen-PheobeSmitham-Example", + "fullUrl": "http://example.org/fhir/Specimen/Specimen-PheobeSmitham-Example", "resource": { "resourceType": "Specimen", "id": "Specimen-PheobeSmitham-Example", @@ -756,7 +756,7 @@ } }, { - "fullUrl": "/ServiceRequest/ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example", + "fullUrl": "http://example.org/fhir/ServiceRequest/ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example", "resource": { "resourceType": "ServiceRequest", "id": "ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example", @@ -959,7 +959,7 @@ } }, { - "fullUrl": "/Task/Task-FollowupRecommendationReport-Example", + "fullUrl": "http://example.org/fhir/Task/Task-FollowupRecommendationReport-Example", "resource": { "resourceType": "Task", "id": "Task-FollowupRecommendationReport-Example", @@ -1019,7 +1019,7 @@ } }, { - "fullUrl": "/DocumentReference/DocumentReference-StructureReporting-Example", + "fullUrl": "http://example.org/fhir/DocumentReference/DocumentReference-StructureReporting-Example", "resource": { "resourceType": "DocumentReference", "id": "DocumentReference-StructureReporting-Example", From 760ba110100b55f0cc69609182262b538a976f55 Mon Sep 17 00:00:00 2001 From: Omar Khan Date: Wed, 12 Feb 2025 17:00:16 +0000 Subject: [PATCH 18/31] Updating references to URLs --- Bundle/Bundle-EULabGenomicReport-Example.json | 128 +++++++++--------- 1 file changed, 64 insertions(+), 64 deletions(-) diff --git a/Bundle/Bundle-EULabGenomicReport-Example.json b/Bundle/Bundle-EULabGenomicReport-Example.json index 2474a9d0..fffb14a1 100644 --- a/Bundle/Bundle-EULabGenomicReport-Example.json +++ b/Bundle/Bundle-EULabGenomicReport-Example.json @@ -27,19 +27,19 @@ { "url": "http://hl7.eu/fhir/StructureDefinition/composition-basedOn-order-or-requisition", "valueReference": { - "reference": "ServiceRequest/ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example" + "reference": "http://example.org/fhir/ServiceRequest/ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example" } }, { "url": "http://hl7.eu/fhir/StructureDefinition/information-recipient", "valueReference": { - "reference": "PractitionerRole/PractitionerRole-EugeneSmith-Example" + "reference": "http://example.org/fhir/PractitionerRole/PractitionerRole-EugeneSmith-Example" } }, { "url": "http://hl7.eu/fhir/laboratory/StructureDefinition/composition-diagnosticReportReference", "valueReference": { - "reference": "DiagnosticReport/DiagnosticReport-GenomicVariantAssessment-Example" + "reference": "http://example.org/fhir/DiagnosticReport/DiagnosticReport-GenomicVariantAssessment-Example" } } ], @@ -74,7 +74,7 @@ } ], "subject": { - "reference": "Patient/Patient-PheobeSmitham-Example" + "reference": "http://example.org/fhir/Patient/Patient-PheobeSmitham-Example" }, "date": "2023-10-16T00:00:00-05:00", "author": [ @@ -100,10 +100,10 @@ }, "entry": [ { - "reference": "Observation/Observation-GenomicTherapeuticImplication-Example" + "reference": "http://example.org/fhir/Observation/Observation-GenomicTherapeuticImplication-Example" }, { - "reference": "Observation/Observation-GenomicsVariantSLC52A2-Example" + "reference": "http://example.org/fhir/Observation/Observation-GenomicsVariantSLC52A2-Example" } ] } @@ -126,13 +126,13 @@ { "url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-DiagnosticReport.composition", "valueReference": { - "reference": "Composition/Composition-EULabGenomicReport-Example" + "reference": "http://example.org/fhir/Composition/Composition-EULabGenomicReport-Example" } }, { "url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/recommended-action", "valueReference": { - "reference": "Task/Task-FollowupRecommendationReport-Example", + "reference": "http://example.org/fhir/Task/Task-FollowupRecommendationReport-Example", "display": "Confirmatory testing recommended" } }, @@ -172,7 +172,7 @@ ], "basedOn": [ { - "reference": "ServiceRequest/ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example" + "reference": "http://example.org/fhir/ServiceRequest/ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example" } ], "status": "final", @@ -205,7 +205,7 @@ ] }, "subject": { - "reference": "Patient/Patient-PheobeSmitham-Example" + "reference": "http://example.org/fhir/Patient/Patient-PheobeSmitham-Example" }, "effectiveDateTime": "2023-10-16T00:00:00-05:00", "issued": "2023-09-16T00:00:00-05:00", @@ -233,7 +233,7 @@ { "url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-DiagnosticReport.media.link", "valueReference": { - "reference": "DocumentReference/DocumentReference-StructureReporting-Example" + "reference": "http://example.org/fhir/DocumentReference/DocumentReference-StructureReporting-Example" } } ] @@ -241,11 +241,11 @@ ], "result": [ { - "reference": "Observation/Observation-GenomicsVariant-SLC52A2", + "reference": "http://example.org/fhir/Observation/Observation-GenomicsVariant-SLC52A2", "display": "Brown-Vialetto-Van Laere syndrome type 2" }, { - "reference": "Observation/Observation-GenomicTherapeuticImplication-Example" + "reference": "http://example.org/fhir/Observation/Observation-GenomicTherapeuticImplication-Example" } ], "conclusion": "Pheobe is homozygous for a pathogenic SLC52A2 missense variant (details below) previously reported by Johnson et al 2012 (PMID22740598). Biallelic pathogenic SLC52A2 variants cause autosomal recessive Brown-Vialetto-Van Laere syndrome type 2 (MIM614707).", @@ -423,7 +423,7 @@ ] }, "subject": { - "reference": "Patient/Patient-PheobeSmitham-Example" + "reference": "http://example.org/fhir/Patient/Patient-PheobeSmitham-Example" }, "effectiveDateTime": "2023-09-16", "performer": [ @@ -436,7 +436,7 @@ ], "derivedFrom": [ { - "reference": "Observation/Observation-GenomicsVariantSLC52A2-Example" + "reference": "http://example.org/fhir/Observation/Observation-GenomicsVariantSLC52A2-Example" } ], "component": [ @@ -499,7 +499,7 @@ "status": "final", "basedOn": [ { - "reference": "ServiceRequest/ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example" + "reference": "http://example.org/fhir/ServiceRequest/ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example" } ], "category": [ @@ -529,7 +529,7 @@ ] }, "subject": { - "reference": "Patient/Patient-PheobeSmitham-Example" + "reference": "http://example.org/fhir/Patient/Patient-PheobeSmitham-Example" }, "effectiveDateTime": "2023-09-16", "performer": [ @@ -559,7 +559,7 @@ ] }, "specimen": { - "reference": "Specimen/Specimen-PheobeSmitham-Example" + "reference": "http://example.org/fhir/Specimen/Specimen-PheobeSmitham-Example" }, "component": [ { @@ -732,7 +732,7 @@ ] }, "subject": { - "reference": "Patient/Patient-PheobeSmitham-Example", + "reference": "http://example.org/fhir/Patient/Patient-PheobeSmitham-Example", "identifier": { "system": "https://fhir.nhs.uk/Id/nhs-number", "value": "9449307539" @@ -750,7 +750,7 @@ }, "request": [ { - "reference": "ServiceRequest/ServiceRequest-WGSTestOrderForm-TrioTestingProband-Example" + "reference": "http://example.org/fhir/ServiceRequest/ServiceRequest-WGSTestOrderForm-TrioTestingProband-Example" } ] } @@ -827,7 +827,7 @@ "text": "This is a Trio Testing, comprising 3 family members with their respective specimen`s & Record Of Discussion`s" }, "subject": { - "reference": "Patient/Patient-PheobeSmitham-Example", + "reference": "http://example.org/fhir/Patient/Patient-PheobeSmitham-Example", "identifier": { "system": "https://fhir.nhs.uk/Id/nhs-number", "value": "9449307539" @@ -835,11 +835,11 @@ }, "authoredOn": "2023-09-15T15:00:00Z", "requester": { - "reference": "PractitionerRole/PractitionerRole-EugeneSmith-Example" + "reference": "http://example.org/fhir/PractitionerRole/PractitionerRole-EugeneSmith-Example" }, "reasonReference": [ { - "reference": "Condition/Condition-InbornErrorOfMetabolism-Example" + "reference": "http://example.org/fhir/Condition/Condition-InbornErrorOfMetabolism-Example" } ], "performer": [ @@ -852,100 +852,100 @@ ], "supportingInfo": [ { - "reference": "Observation/Observation-AutisticBehaviour-Example" + "reference": "http://example.org/fhir/Observation/Observation-AutisticBehaviour-Example" }, { - "reference": "Observation/Observation-DelayedSpeechLanguageDevt-Example" + "reference": "http://example.org/fhir/Observation/Observation-DelayedSpeechLanguageDevt-Example" }, { - "reference": "Observation/Observation-DiseasePenetrancePheobeSmitham-Example" + "reference": "http://example.org/fhir/Observation/Observation-DiseasePenetrancePheobeSmitham-Example" }, { - "reference": "Observation/Observation-IntellectualDisabilityProfound-Example" + "reference": "http://example.org/fhir/Observation/Observation-IntellectualDisabilityProfound-Example" }, { - "reference": "Observation/Observation-NonConsanguinousUnionProband-Example" + "reference": "http://example.org/fhir/Observation/Observation-NonConsanguinousUnionProband-Example" }, { - "reference": "Specimen/Specimen-PheobeSmitham-Example" + "reference": "http://example.org/fhir/Specimen/Specimen-PheobeSmitham-Example" }, { - "reference": "Observation/Observation-GenomicEthnicity-Example" + "reference": "http://example.org/fhir/Observation/Observation-GenomicEthnicity-Example" }, { - "reference": "Observation/Observation-NoPregnancy-Example" + "reference": "http://example.org/fhir/Observation/Observation-NoPregnancy-Example" }, { - "reference": "Condition/Condition-MonogenicHearingLoss-Example" + "reference": "http://example.org/fhir/Condition/Condition-MonogenicHearingLoss-Example" }, { - "reference": "Observation/Observation-NoBoneMarrowTransplant-Example" + "reference": "http://example.org/fhir/Observation/Observation-NoBoneMarrowTransplant-Example" }, { - "reference": "Observation/Observation-NoTransfusion-Example" + "reference": "http://example.org/fhir/Observation/Observation-NoTransfusion-Example" }, { - "reference": "Patient/Patient-PheobeSmithamMother-Example" + "reference": "http://example.org/fhir/Patient/Patient-PheobeSmithamMother-Example" }, { - "reference": "RelatedPerson/RelatedPerson-AliceSmithamProbandMother-Example" + "reference": "http://example.org/fhir/RelatedPerson/RelatedPerson-AliceSmithamProbandMother-Example" }, { - "reference": "Specimen/Specimen-PheobeSmithamMother-Example" + "reference": "http://example.org/fhir/Specimen/Specimen-PheobeSmithamMother-Example" }, { - "reference": "Observation/Observation-NonConsanguinousUnionMother-Example" + "reference": "http://example.org/fhir/Observation/Observation-NonConsanguinousUnionMother-Example" }, { - "reference": "Observation/Observation-NoTransfusionProbandMother-Example" + "reference": "http://example.org/fhir/Observation/Observation-NoTransfusionProbandMother-Example" }, { - "reference": "Observation/Observation-NoBoneMarrowTransplantProbandMother-Example" + "reference": "http://example.org/fhir/Observation/Observation-NoBoneMarrowTransplantProbandMother-Example" }, { - "reference": "Patient/Patient-PheobeSmithamFather-Example" + "reference": "http://example.org/fhir/Patient/Patient-PheobeSmithamFather-Example" }, { - "reference": "RelatedPerson/RelatedPerson-JamesLawrenceProbandFather-Example" + "reference": "http://example.org/fhir/RelatedPerson/RelatedPerson-JamesLawrenceProbandFather-Example" }, { - "reference": "Observation/Observation-NonConsanguinousUnionProbandFather-Example" + "reference": "http://example.org/fhir/Observation/Observation-NonConsanguinousUnionProbandFather-Example" }, { - "reference": "Observation/Observation-NoTransfusionProbandFather-Example" + "reference": "http://example.org/fhir/Observation/Observation-NoTransfusionProbandFather-Example" }, { - "reference": "Observation/Observation-NoBoneMarrowTransplantProbandFather-Example" + "reference": "http://example.org/fhir/Observation/Observation-NoBoneMarrowTransplantProbandFather-Example" }, { - "reference": "Observation/Observation-IntellectualDisabilityMild-Example" + "reference": "http://example.org/fhir/Observation/Observation-IntellectualDisabilityMild-Example" }, { - "reference": "Consent/Consent-RoD-PheobeSmitham-Example" + "reference": "http://example.org/fhir/Consent/Consent-RoD-PheobeSmitham-Example" }, { - "reference": "Consent/Consent-RoD-PheobeSmithamYoungPersonAssentForm-Example" + "reference": "http://example.org/fhir/Consent/Consent-RoD-PheobeSmithamYoungPersonAssentForm-Example" }, { - "reference": "Consent/Consent-RoD-PheobeSmithamMother-Example" + "reference": "http://example.org/fhir/Consent/Consent-RoD-PheobeSmithamMother-Example" }, { - "reference": "QuestionnaireResponse/QuestionnaireResponse-RoD-PheobeSmithamCDForn-Example" + "reference": "http://example.org/fhir/QuestionnaireResponse/QuestionnaireResponse-RoD-PheobeSmithamCDForn-Example" }, { - "reference": "QuestionnaireResponse/QuestionnaireResponse-RoD-PheobeSmithamYPAForm-Example" + "reference": "http://example.org/fhir/QuestionnaireResponse/QuestionnaireResponse-RoD-PheobeSmithamYPAForm-Example" }, { - "reference": "QuestionnaireResponse/QuestionnaireResponse-RoD-PheobeSmithamMother-Example" + "reference": "http://example.org/fhir/QuestionnaireResponse/QuestionnaireResponse-RoD-PheobeSmithamMother-Example" }, { - "reference": "Consent/Consent-RoD-PheobeSmithamFather-Example" + "reference": "http://example.org/fhir/Consent/Consent-RoD-PheobeSmithamFather-Example" }, { - "reference": "QuestionnaireResponse/QuestionnaireResponse-RoD-PheobeSmithamFather-Example" + "reference": "http://example.org/fhir/QuestionnaireResponse/QuestionnaireResponse-RoD-PheobeSmithamFather-Example" }, { - "reference": "Specimen/Specimen-PheobeSmithamFather-Example" + "reference": "http://example.org/fhir/Specimen/Specimen-PheobeSmithamFather-Example" } ], "note": [ @@ -981,10 +981,10 @@ }, "description": "Testing of Pheobe's parents is recommended (via referral to the clinical genetics service) in order to confirm that both are heterozygous carriers of the missense variant.", "for": { - "reference": "Patient/Patient-PheobeSmitham-Example" + "reference": "http://example.org/fhir/Patient/Patient-PheobeSmitham-Example" }, "reasonReference": { - "reference": "Observation/Observation-GenomicImplication-Therapeutic" + "reference": "http://example.org/fhir/Observation/Observation-GenomicImplication-Therapeutic" }, "input": [ { @@ -998,7 +998,7 @@ ] }, "valueReference": { - "reference": "Patient/Patient-PheobeSmithamFather-Example" + "reference": "http://example.org/fhir/Patient/Patient-PheobeSmithamFather-Example" } }, { @@ -1012,7 +1012,7 @@ ] }, "valueReference": { - "reference": "Patient/Patient-PheobeSmithamMother-Example" + "reference": "http://example.org/fhir/Patient/Patient-PheobeSmithamMother-Example" } } ] @@ -1026,7 +1026,7 @@ "status": "current", "docStatus": "final", "subject": { - "reference": "Patient/Patient-PheobeSmitham-Example", + "reference": "http://example.org/fhir/Patient/Patient-PheobeSmitham-Example", "identifier": { "system": "https://fhir.nhs.uk/Id/nhs-number", "value": "9449307539" @@ -1054,16 +1054,16 @@ "context": { "related": [ { - "reference": "ServiceRequest/ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example" + "reference": "http://example.org/fhir/ServiceRequest/ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example" }, { - "reference": "Specimen/Specimen-PheobeSmitham-Example" + "reference": "http://example.org/fhir/Specimen/Specimen-PheobeSmitham-Example" }, { - "reference": "Specimen/Specimen-PheobeSmithamFather-Example" + "reference": "http://example.org/fhir/Specimen/Specimen-PheobeSmithamFather-Example" }, { - "reference": "Specimen/Specimen-PheobeSmithamMother-Example" + "reference": "http://example.org/fhir/Specimen/Specimen-PheobeSmithamMother-Example" } ] } From 1233096eb8be22df9fad50b55a604efbc99da6f1 Mon Sep 17 00:00:00 2001 From: Omar Khan Date: Wed, 12 Feb 2025 17:07:01 +0000 Subject: [PATCH 19/31] Revert "Updating references to URLs" This reverts commit 760ba110100b55f0cc69609182262b538a976f55. --- Bundle/Bundle-EULabGenomicReport-Example.json | 128 +++++++++--------- 1 file changed, 64 insertions(+), 64 deletions(-) diff --git a/Bundle/Bundle-EULabGenomicReport-Example.json b/Bundle/Bundle-EULabGenomicReport-Example.json index fffb14a1..2474a9d0 100644 --- a/Bundle/Bundle-EULabGenomicReport-Example.json +++ b/Bundle/Bundle-EULabGenomicReport-Example.json @@ -27,19 +27,19 @@ { "url": "http://hl7.eu/fhir/StructureDefinition/composition-basedOn-order-or-requisition", "valueReference": { - "reference": "http://example.org/fhir/ServiceRequest/ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example" + "reference": "ServiceRequest/ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example" } }, { "url": "http://hl7.eu/fhir/StructureDefinition/information-recipient", "valueReference": { - "reference": "http://example.org/fhir/PractitionerRole/PractitionerRole-EugeneSmith-Example" + "reference": "PractitionerRole/PractitionerRole-EugeneSmith-Example" } }, { "url": "http://hl7.eu/fhir/laboratory/StructureDefinition/composition-diagnosticReportReference", "valueReference": { - "reference": "http://example.org/fhir/DiagnosticReport/DiagnosticReport-GenomicVariantAssessment-Example" + "reference": "DiagnosticReport/DiagnosticReport-GenomicVariantAssessment-Example" } } ], @@ -74,7 +74,7 @@ } ], "subject": { - "reference": "http://example.org/fhir/Patient/Patient-PheobeSmitham-Example" + "reference": "Patient/Patient-PheobeSmitham-Example" }, "date": "2023-10-16T00:00:00-05:00", "author": [ @@ -100,10 +100,10 @@ }, "entry": [ { - "reference": "http://example.org/fhir/Observation/Observation-GenomicTherapeuticImplication-Example" + "reference": "Observation/Observation-GenomicTherapeuticImplication-Example" }, { - "reference": "http://example.org/fhir/Observation/Observation-GenomicsVariantSLC52A2-Example" + "reference": "Observation/Observation-GenomicsVariantSLC52A2-Example" } ] } @@ -126,13 +126,13 @@ { "url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-DiagnosticReport.composition", "valueReference": { - "reference": "http://example.org/fhir/Composition/Composition-EULabGenomicReport-Example" + "reference": "Composition/Composition-EULabGenomicReport-Example" } }, { "url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/recommended-action", "valueReference": { - "reference": "http://example.org/fhir/Task/Task-FollowupRecommendationReport-Example", + "reference": "Task/Task-FollowupRecommendationReport-Example", "display": "Confirmatory testing recommended" } }, @@ -172,7 +172,7 @@ ], "basedOn": [ { - "reference": "http://example.org/fhir/ServiceRequest/ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example" + "reference": "ServiceRequest/ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example" } ], "status": "final", @@ -205,7 +205,7 @@ ] }, "subject": { - "reference": "http://example.org/fhir/Patient/Patient-PheobeSmitham-Example" + "reference": "Patient/Patient-PheobeSmitham-Example" }, "effectiveDateTime": "2023-10-16T00:00:00-05:00", "issued": "2023-09-16T00:00:00-05:00", @@ -233,7 +233,7 @@ { "url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-DiagnosticReport.media.link", "valueReference": { - "reference": "http://example.org/fhir/DocumentReference/DocumentReference-StructureReporting-Example" + "reference": "DocumentReference/DocumentReference-StructureReporting-Example" } } ] @@ -241,11 +241,11 @@ ], "result": [ { - "reference": "http://example.org/fhir/Observation/Observation-GenomicsVariant-SLC52A2", + "reference": "Observation/Observation-GenomicsVariant-SLC52A2", "display": "Brown-Vialetto-Van Laere syndrome type 2" }, { - "reference": "http://example.org/fhir/Observation/Observation-GenomicTherapeuticImplication-Example" + "reference": "Observation/Observation-GenomicTherapeuticImplication-Example" } ], "conclusion": "Pheobe is homozygous for a pathogenic SLC52A2 missense variant (details below) previously reported by Johnson et al 2012 (PMID22740598). Biallelic pathogenic SLC52A2 variants cause autosomal recessive Brown-Vialetto-Van Laere syndrome type 2 (MIM614707).", @@ -423,7 +423,7 @@ ] }, "subject": { - "reference": "http://example.org/fhir/Patient/Patient-PheobeSmitham-Example" + "reference": "Patient/Patient-PheobeSmitham-Example" }, "effectiveDateTime": "2023-09-16", "performer": [ @@ -436,7 +436,7 @@ ], "derivedFrom": [ { - "reference": "http://example.org/fhir/Observation/Observation-GenomicsVariantSLC52A2-Example" + "reference": "Observation/Observation-GenomicsVariantSLC52A2-Example" } ], "component": [ @@ -499,7 +499,7 @@ "status": "final", "basedOn": [ { - "reference": "http://example.org/fhir/ServiceRequest/ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example" + "reference": "ServiceRequest/ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example" } ], "category": [ @@ -529,7 +529,7 @@ ] }, "subject": { - "reference": "http://example.org/fhir/Patient/Patient-PheobeSmitham-Example" + "reference": "Patient/Patient-PheobeSmitham-Example" }, "effectiveDateTime": "2023-09-16", "performer": [ @@ -559,7 +559,7 @@ ] }, "specimen": { - "reference": "http://example.org/fhir/Specimen/Specimen-PheobeSmitham-Example" + "reference": "Specimen/Specimen-PheobeSmitham-Example" }, "component": [ { @@ -732,7 +732,7 @@ ] }, "subject": { - "reference": "http://example.org/fhir/Patient/Patient-PheobeSmitham-Example", + "reference": "Patient/Patient-PheobeSmitham-Example", "identifier": { "system": "https://fhir.nhs.uk/Id/nhs-number", "value": "9449307539" @@ -750,7 +750,7 @@ }, "request": [ { - "reference": "http://example.org/fhir/ServiceRequest/ServiceRequest-WGSTestOrderForm-TrioTestingProband-Example" + "reference": "ServiceRequest/ServiceRequest-WGSTestOrderForm-TrioTestingProband-Example" } ] } @@ -827,7 +827,7 @@ "text": "This is a Trio Testing, comprising 3 family members with their respective specimen`s & Record Of Discussion`s" }, "subject": { - "reference": "http://example.org/fhir/Patient/Patient-PheobeSmitham-Example", + "reference": "Patient/Patient-PheobeSmitham-Example", "identifier": { "system": "https://fhir.nhs.uk/Id/nhs-number", "value": "9449307539" @@ -835,11 +835,11 @@ }, "authoredOn": "2023-09-15T15:00:00Z", "requester": { - "reference": "http://example.org/fhir/PractitionerRole/PractitionerRole-EugeneSmith-Example" + "reference": "PractitionerRole/PractitionerRole-EugeneSmith-Example" }, "reasonReference": [ { - "reference": "http://example.org/fhir/Condition/Condition-InbornErrorOfMetabolism-Example" + "reference": "Condition/Condition-InbornErrorOfMetabolism-Example" } ], "performer": [ @@ -852,100 +852,100 @@ ], "supportingInfo": [ { - "reference": "http://example.org/fhir/Observation/Observation-AutisticBehaviour-Example" + "reference": "Observation/Observation-AutisticBehaviour-Example" }, { - "reference": "http://example.org/fhir/Observation/Observation-DelayedSpeechLanguageDevt-Example" + "reference": "Observation/Observation-DelayedSpeechLanguageDevt-Example" }, { - "reference": "http://example.org/fhir/Observation/Observation-DiseasePenetrancePheobeSmitham-Example" + "reference": "Observation/Observation-DiseasePenetrancePheobeSmitham-Example" }, { - "reference": "http://example.org/fhir/Observation/Observation-IntellectualDisabilityProfound-Example" + "reference": "Observation/Observation-IntellectualDisabilityProfound-Example" }, { - "reference": "http://example.org/fhir/Observation/Observation-NonConsanguinousUnionProband-Example" + "reference": "Observation/Observation-NonConsanguinousUnionProband-Example" }, { - "reference": "http://example.org/fhir/Specimen/Specimen-PheobeSmitham-Example" + "reference": "Specimen/Specimen-PheobeSmitham-Example" }, { - "reference": "http://example.org/fhir/Observation/Observation-GenomicEthnicity-Example" + "reference": "Observation/Observation-GenomicEthnicity-Example" }, { - "reference": "http://example.org/fhir/Observation/Observation-NoPregnancy-Example" + "reference": "Observation/Observation-NoPregnancy-Example" }, { - "reference": "http://example.org/fhir/Condition/Condition-MonogenicHearingLoss-Example" + "reference": "Condition/Condition-MonogenicHearingLoss-Example" }, { - "reference": "http://example.org/fhir/Observation/Observation-NoBoneMarrowTransplant-Example" + "reference": "Observation/Observation-NoBoneMarrowTransplant-Example" }, { - "reference": "http://example.org/fhir/Observation/Observation-NoTransfusion-Example" + "reference": "Observation/Observation-NoTransfusion-Example" }, { - "reference": "http://example.org/fhir/Patient/Patient-PheobeSmithamMother-Example" + "reference": "Patient/Patient-PheobeSmithamMother-Example" }, { - "reference": "http://example.org/fhir/RelatedPerson/RelatedPerson-AliceSmithamProbandMother-Example" + "reference": "RelatedPerson/RelatedPerson-AliceSmithamProbandMother-Example" }, { - "reference": "http://example.org/fhir/Specimen/Specimen-PheobeSmithamMother-Example" + "reference": "Specimen/Specimen-PheobeSmithamMother-Example" }, { - "reference": "http://example.org/fhir/Observation/Observation-NonConsanguinousUnionMother-Example" + "reference": "Observation/Observation-NonConsanguinousUnionMother-Example" }, { - "reference": "http://example.org/fhir/Observation/Observation-NoTransfusionProbandMother-Example" + "reference": "Observation/Observation-NoTransfusionProbandMother-Example" }, { - "reference": "http://example.org/fhir/Observation/Observation-NoBoneMarrowTransplantProbandMother-Example" + "reference": "Observation/Observation-NoBoneMarrowTransplantProbandMother-Example" }, { - "reference": "http://example.org/fhir/Patient/Patient-PheobeSmithamFather-Example" + "reference": "Patient/Patient-PheobeSmithamFather-Example" }, { - "reference": "http://example.org/fhir/RelatedPerson/RelatedPerson-JamesLawrenceProbandFather-Example" + "reference": "RelatedPerson/RelatedPerson-JamesLawrenceProbandFather-Example" }, { - "reference": "http://example.org/fhir/Observation/Observation-NonConsanguinousUnionProbandFather-Example" + "reference": "Observation/Observation-NonConsanguinousUnionProbandFather-Example" }, { - "reference": "http://example.org/fhir/Observation/Observation-NoTransfusionProbandFather-Example" + "reference": "Observation/Observation-NoTransfusionProbandFather-Example" }, { - "reference": "http://example.org/fhir/Observation/Observation-NoBoneMarrowTransplantProbandFather-Example" + "reference": "Observation/Observation-NoBoneMarrowTransplantProbandFather-Example" }, { - "reference": "http://example.org/fhir/Observation/Observation-IntellectualDisabilityMild-Example" + "reference": "Observation/Observation-IntellectualDisabilityMild-Example" }, { - "reference": "http://example.org/fhir/Consent/Consent-RoD-PheobeSmitham-Example" + "reference": "Consent/Consent-RoD-PheobeSmitham-Example" }, { - "reference": "http://example.org/fhir/Consent/Consent-RoD-PheobeSmithamYoungPersonAssentForm-Example" + "reference": "Consent/Consent-RoD-PheobeSmithamYoungPersonAssentForm-Example" }, { - "reference": "http://example.org/fhir/Consent/Consent-RoD-PheobeSmithamMother-Example" + "reference": "Consent/Consent-RoD-PheobeSmithamMother-Example" }, { - "reference": "http://example.org/fhir/QuestionnaireResponse/QuestionnaireResponse-RoD-PheobeSmithamCDForn-Example" + "reference": "QuestionnaireResponse/QuestionnaireResponse-RoD-PheobeSmithamCDForn-Example" }, { - "reference": "http://example.org/fhir/QuestionnaireResponse/QuestionnaireResponse-RoD-PheobeSmithamYPAForm-Example" + "reference": "QuestionnaireResponse/QuestionnaireResponse-RoD-PheobeSmithamYPAForm-Example" }, { - "reference": "http://example.org/fhir/QuestionnaireResponse/QuestionnaireResponse-RoD-PheobeSmithamMother-Example" + "reference": "QuestionnaireResponse/QuestionnaireResponse-RoD-PheobeSmithamMother-Example" }, { - "reference": "http://example.org/fhir/Consent/Consent-RoD-PheobeSmithamFather-Example" + "reference": "Consent/Consent-RoD-PheobeSmithamFather-Example" }, { - "reference": "http://example.org/fhir/QuestionnaireResponse/QuestionnaireResponse-RoD-PheobeSmithamFather-Example" + "reference": "QuestionnaireResponse/QuestionnaireResponse-RoD-PheobeSmithamFather-Example" }, { - "reference": "http://example.org/fhir/Specimen/Specimen-PheobeSmithamFather-Example" + "reference": "Specimen/Specimen-PheobeSmithamFather-Example" } ], "note": [ @@ -981,10 +981,10 @@ }, "description": "Testing of Pheobe's parents is recommended (via referral to the clinical genetics service) in order to confirm that both are heterozygous carriers of the missense variant.", "for": { - "reference": "http://example.org/fhir/Patient/Patient-PheobeSmitham-Example" + "reference": "Patient/Patient-PheobeSmitham-Example" }, "reasonReference": { - "reference": "http://example.org/fhir/Observation/Observation-GenomicImplication-Therapeutic" + "reference": "Observation/Observation-GenomicImplication-Therapeutic" }, "input": [ { @@ -998,7 +998,7 @@ ] }, "valueReference": { - "reference": "http://example.org/fhir/Patient/Patient-PheobeSmithamFather-Example" + "reference": "Patient/Patient-PheobeSmithamFather-Example" } }, { @@ -1012,7 +1012,7 @@ ] }, "valueReference": { - "reference": "http://example.org/fhir/Patient/Patient-PheobeSmithamMother-Example" + "reference": "Patient/Patient-PheobeSmithamMother-Example" } } ] @@ -1026,7 +1026,7 @@ "status": "current", "docStatus": "final", "subject": { - "reference": "http://example.org/fhir/Patient/Patient-PheobeSmitham-Example", + "reference": "Patient/Patient-PheobeSmitham-Example", "identifier": { "system": "https://fhir.nhs.uk/Id/nhs-number", "value": "9449307539" @@ -1054,16 +1054,16 @@ "context": { "related": [ { - "reference": "http://example.org/fhir/ServiceRequest/ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example" + "reference": "ServiceRequest/ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example" }, { - "reference": "http://example.org/fhir/Specimen/Specimen-PheobeSmitham-Example" + "reference": "Specimen/Specimen-PheobeSmitham-Example" }, { - "reference": "http://example.org/fhir/Specimen/Specimen-PheobeSmithamFather-Example" + "reference": "Specimen/Specimen-PheobeSmithamFather-Example" }, { - "reference": "http://example.org/fhir/Specimen/Specimen-PheobeSmithamMother-Example" + "reference": "Specimen/Specimen-PheobeSmithamMother-Example" } ] } From ff7790e330811a17c025317deae39caf292f0862 Mon Sep 17 00:00:00 2001 From: Omar Khan Date: Wed, 7 May 2025 10:01:31 +0100 Subject: [PATCH 20/31] Update to Package.json --- package.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package.json b/package.json index f6a055fe..b40caa35 100644 --- a/package.json +++ b/package.json @@ -10,7 +10,7 @@ "fhir.r4.ukcore.stu3.currentbuild": "0.0.18-pre-release", "hl7.fhir.r4.core": "4.0.1", "hl7.fhir.uv.genomics-reporting": "3.0.0-ballot", - "hl7.fhir.eu.laboratory": "0.1.0", + "hl7.fhir.eu.laboratory": "0.1.1", "hl7.fhir.uv.ips": "1.1.0", "hl7.fhir.eu.extensions": "0.1.0" } From 5f05a7f525b59e34ddffb0d2cfbbc006efd988d9 Mon Sep 17 00:00:00 2001 From: KazeemHamzat Date: Fri, 18 Jul 2025 09:05:34 +0100 Subject: [PATCH 21/31] Update package.json Update package.json --- package.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package.json b/package.json index b40caa35..104edb96 100644 --- a/package.json +++ b/package.json @@ -12,7 +12,7 @@ "hl7.fhir.uv.genomics-reporting": "3.0.0-ballot", "hl7.fhir.eu.laboratory": "0.1.1", "hl7.fhir.uv.ips": "1.1.0", - "hl7.fhir.eu.extensions": "0.1.0" + "hl7.fhir.eu.extensions": "0.1.1-ballot" } } From 0e6d0f41a1241754a7689fcea394de6c779e2f17 Mon Sep 17 00:00:00 2001 From: KazeemHamzat Date: Mon, 21 Jul 2025 10:16:04 +0100 Subject: [PATCH 22/31] Added hl7.fhir.eu.extensions.r4 Added hl7.fhir.eu.extensions.r4 --- fhirpkg.lock.json | 3 ++- package.json | 2 +- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/fhirpkg.lock.json b/fhirpkg.lock.json index 1133e1b4..88c76f6e 100644 --- a/fhirpkg.lock.json +++ b/fhirpkg.lock.json @@ -5,7 +5,8 @@ "hl7.fhir.r4.core": "4.0.1", "hl7.fhir.uv.genomics-reporting": "3.0.0-ballot", "hl7.terminology.r4": "5.3.0", - "hl7.fhir.uv.extensions.r4": "1.0.0" + "hl7.fhir.uv.extensions.r4": "1.0.0", + "hl7.fhir.eu.extensions.r4": "0.1.1-ballot" }, "missing": {} } diff --git a/package.json b/package.json index 104edb96..d5b733f5 100644 --- a/package.json +++ b/package.json @@ -12,7 +12,7 @@ "hl7.fhir.uv.genomics-reporting": "3.0.0-ballot", "hl7.fhir.eu.laboratory": "0.1.1", "hl7.fhir.uv.ips": "1.1.0", - "hl7.fhir.eu.extensions": "0.1.1-ballot" + "hl7.fhir.eu.extensions.r4": "0.1.1-ballot" } } From 1223f6e180a8d3205906dd6ca76bba0df52e3dbf Mon Sep 17 00:00:00 2001 From: KazeemHamzat Date: Thu, 4 Sep 2025 14:29:45 +0100 Subject: [PATCH 23/31] Update package.json Removing "hl7.fhir.eu.laboratory": "0.1.1", --- fhirpkg.lock.json | 3 +-- package.json | 3 +-- 2 files changed, 2 insertions(+), 4 deletions(-) diff --git a/fhirpkg.lock.json b/fhirpkg.lock.json index 5e98b970..64508581 100644 --- a/fhirpkg.lock.json +++ b/fhirpkg.lock.json @@ -1,11 +1,10 @@ { "updated": "2025-05-08T09:07:12.7767319+01:00", "dependencies": { - "fhir.r4.ukcore.stu3.currentbuild": "0.0.18-pre-release", + "fhir.r4.ukcore.stu3.currentbuild": "0.24.0-pre-release", "hl7.fhir.r4.core": "4.0.1", "hl7.fhir.uv.genomics-reporting": "3.0.0-ballot", "hl7.terminology.r4": "5.3.0", - "hl7.fhir.uv.extensions.r4": "1.0.0", "hl7.fhir.eu.extensions.r4": "0.1.1-ballot" }, "missing": {} diff --git a/package.json b/package.json index d5b733f5..4e55687f 100644 --- a/package.json +++ b/package.json @@ -7,10 +7,9 @@ ], "jurisdiction": "urn:iso:std:iso:3166:-2:GB-ENG", "dependencies": { - "fhir.r4.ukcore.stu3.currentbuild": "0.0.18-pre-release", + "fhir.r4.ukcore.stu3.currentbuild": "0.24.0-pre-release", "hl7.fhir.r4.core": "4.0.1", "hl7.fhir.uv.genomics-reporting": "3.0.0-ballot", - "hl7.fhir.eu.laboratory": "0.1.1", "hl7.fhir.uv.ips": "1.1.0", "hl7.fhir.eu.extensions.r4": "0.1.1-ballot" } From 9be582fa874c0efe8d6647d8fa5403364f425fcd Mon Sep 17 00:00:00 2001 From: KazeemHamzat Date: Thu, 4 Sep 2025 19:04:24 +0100 Subject: [PATCH 24/31] Updated the EU Lab to 0.1.0-balot hl7.fhir.eu.laboratory": "0.1.0-ballot --- fhirpkg.lock.json | 13 ++++++++++--- package.json | 5 ++++- 2 files changed, 14 insertions(+), 4 deletions(-) diff --git a/fhirpkg.lock.json b/fhirpkg.lock.json index 64508581..b87d4f40 100644 --- a/fhirpkg.lock.json +++ b/fhirpkg.lock.json @@ -1,11 +1,18 @@ { - "updated": "2025-05-08T09:07:12.7767319+01:00", + "updated": "2025-09-04T19:03:17.2341729+01:00", "dependencies": { "fhir.r4.ukcore.stu3.currentbuild": "0.24.0-pre-release", "hl7.fhir.r4.core": "4.0.1", + "hl7.fhir.r5.core": "5.0.0", "hl7.fhir.uv.genomics-reporting": "3.0.0-ballot", - "hl7.terminology.r4": "5.3.0", - "hl7.fhir.eu.extensions.r4": "0.1.1-ballot" + "hl7.fhir.uv.extensions.r4": "5.2.0", + "hl7.fhir.eu.extensions": "0.1.1-ballot", + "hl7.terminology.r5": "6.2.0", + "hl7.fhir.uv.extensions.r5": "5.2.0", + "hl7.fhir.uv.ips": "1.1.0", + "fhir.dicom": "2022.4.20221006", + "hl7.terminology.r4": "6.5.0", + "hl7.fhir.eu.laboratory": "0.1.0-ballot" }, "missing": {} } diff --git a/package.json b/package.json index 4e55687f..068f0841 100644 --- a/package.json +++ b/package.json @@ -10,8 +10,11 @@ "fhir.r4.ukcore.stu3.currentbuild": "0.24.0-pre-release", "hl7.fhir.r4.core": "4.0.1", "hl7.fhir.uv.genomics-reporting": "3.0.0-ballot", + "hl7.fhir.uv.extensions.r4": "5.2.0", + "hl7.fhir.eu.extensions": "0.1.1-ballot", "hl7.fhir.uv.ips": "1.1.0", - "hl7.fhir.eu.extensions.r4": "0.1.1-ballot" + "hl7.terminology.r4": "6.5.0", + "hl7.fhir.eu.laboratory": "0.1.0-ballot" } } From 15e57f41afc658aba4f1959fac1af16a91832445 Mon Sep 17 00:00:00 2001 From: KazeemHamzat Date: Thu, 4 Sep 2025 19:17:43 +0100 Subject: [PATCH 25/31] Update Observation-GenomicsVariantSLC52A2 CodeSystem: "system": "http://purl.obolibrary.org/obo", --- Bundle/Bundle-EULabGenomicReport-Example.json | 4 ++-- Observation/Observation-GenomicsVariantSLC52A2-Example.json | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/Bundle/Bundle-EULabGenomicReport-Example.json b/Bundle/Bundle-EULabGenomicReport-Example.json index 2474a9d0..b2355cb4 100644 --- a/Bundle/Bundle-EULabGenomicReport-Example.json +++ b/Bundle/Bundle-EULabGenomicReport-Example.json @@ -610,8 +610,8 @@ "valueCodeableConcept": { "coding": [ { - "system": "http://www.sequenceontology.org", - "code": "SO:0001583", + "system": "http://purl.obolibrary.org/obo", + "code": "SO_0001583", "display": "missense_variant" } ] diff --git a/Observation/Observation-GenomicsVariantSLC52A2-Example.json b/Observation/Observation-GenomicsVariantSLC52A2-Example.json index 2524e4ea..a435ed1e 100644 --- a/Observation/Observation-GenomicsVariantSLC52A2-Example.json +++ b/Observation/Observation-GenomicsVariantSLC52A2-Example.json @@ -121,8 +121,8 @@ "valueCodeableConcept": { "coding": [ { - "system": "http://www.sequenceontology.org", - "code": "SO:0001583", + "system": "http://purl.obolibrary.org/obo", + "code": "SO_0001583", "display": "missense_variant" } ] From 6c57543b9772f15b354eab92a93ef2db029897c5 Mon Sep 17 00:00:00 2001 From: Omar Khan Date: Fri, 5 Sep 2025 12:33:59 +0100 Subject: [PATCH 26/31] Removal of size for attachment and bundle meta should allow validation of resources against any package in dependencies (not a fix but issues in Bundle are not useful) --- Bundle/Bundle-EULabGenomicReport-Example.json | 6 ------ 1 file changed, 6 deletions(-) diff --git a/Bundle/Bundle-EULabGenomicReport-Example.json b/Bundle/Bundle-EULabGenomicReport-Example.json index b2355cb4..8522c7f1 100644 --- a/Bundle/Bundle-EULabGenomicReport-Example.json +++ b/Bundle/Bundle-EULabGenomicReport-Example.json @@ -1,11 +1,6 @@ { "resourceType": "Bundle", "id": "Bundle-EULabGenomicReport-Example", - "meta": { - "profile": [ - "http://hl7.eu/fhir/laboratory/StructureDefinition/Bundle-eu-lab" - ] - }, "identifier": { "system": "https://fhir.nhs.uk/Id/GMSReport", "value": "c73ece32-b439-40c0-9659-fd51a21deef2" @@ -270,7 +265,6 @@ "contentType": "application/pdf", "language": "en-GB", "url": "https://cts5j3.axshare.com/?id=mhxwul&p=final_report_issued_test_complete&g=1", - "size": 43272, "title": "Genomic Report for Pheobe Smitham", "creation": "2023-10-16" } From 467a57944031effb7d69cef1cf7334b6ef65d943 Mon Sep 17 00:00:00 2001 From: Omar Khan Date: Fri, 5 Sep 2025 12:43:59 +0100 Subject: [PATCH 27/31] Removal of Composition profile --- Bundle/Bundle-EULabGenomicReport-Example.json | 5 ----- 1 file changed, 5 deletions(-) diff --git a/Bundle/Bundle-EULabGenomicReport-Example.json b/Bundle/Bundle-EULabGenomicReport-Example.json index 8522c7f1..42b91693 100644 --- a/Bundle/Bundle-EULabGenomicReport-Example.json +++ b/Bundle/Bundle-EULabGenomicReport-Example.json @@ -13,11 +13,6 @@ "resource": { "resourceType": "Composition", "id": "Composition-EULabGenomicReport-Example", - "meta": { - "profile": [ - "http://hl7.eu/fhir/laboratory/StructureDefinition/Composition-eu-lab" - ] - }, "extension": [ { "url": "http://hl7.eu/fhir/StructureDefinition/composition-basedOn-order-or-requisition", From dd3be43bb95d478ce7f0fab7e3187670ebacae4b Mon Sep 17 00:00:00 2001 From: Omar Khan Date: Fri, 5 Sep 2025 13:00:48 +0100 Subject: [PATCH 28/31] Removing Bundle as it will not validate Not adding anything material to the package as Composition validates fine --- .gitignore | 1 + Bundle/Bundle-EULabGenomicReport-Example.json | 1062 ----------------- 2 files changed, 1 insertion(+), 1062 deletions(-) delete mode 100644 Bundle/Bundle-EULabGenomicReport-Example.json diff --git a/.gitignore b/.gitignore index 014eff77..8bdb187a 100644 --- a/.gitignore +++ b/.gitignore @@ -8,3 +8,4 @@ IOPS-validation validation-service-fhir-r4 .idea/workspace.xml NHSDigital-DiagnosticReport-Genomics-International.StructureDefinition.json +Ignore diff --git a/Bundle/Bundle-EULabGenomicReport-Example.json b/Bundle/Bundle-EULabGenomicReport-Example.json deleted file mode 100644 index 42b91693..00000000 --- a/Bundle/Bundle-EULabGenomicReport-Example.json +++ /dev/null @@ -1,1062 +0,0 @@ -{ - "resourceType": "Bundle", - "id": "Bundle-EULabGenomicReport-Example", - "identifier": { - "system": "https://fhir.nhs.uk/Id/GMSReport", - "value": "c73ece32-b439-40c0-9659-fd51a21deef2" - }, - "type": "document", - "timestamp": "2023-10-16T00:00:00-05:00", - "entry": [ - { - "fullUrl": "http://example.org/fhir/Composition/Composition-EULabGenomicReport-Example", - "resource": { - "resourceType": "Composition", - "id": "Composition-EULabGenomicReport-Example", - "extension": [ - { - "url": "http://hl7.eu/fhir/StructureDefinition/composition-basedOn-order-or-requisition", - "valueReference": { - "reference": "ServiceRequest/ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example" - } - }, - { - "url": "http://hl7.eu/fhir/StructureDefinition/information-recipient", - "valueReference": { - "reference": "PractitionerRole/PractitionerRole-EugeneSmith-Example" - } - }, - { - "url": "http://hl7.eu/fhir/laboratory/StructureDefinition/composition-diagnosticReportReference", - "valueReference": { - "reference": "DiagnosticReport/DiagnosticReport-GenomicVariantAssessment-Example" - } - } - ], - "status": "final", - "type": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51969-4", - "display": "Genetic analysis report" - } - ] - }, - "category": [ - { - "coding": [ - { - "system": "http://loinc.org", - "code": "26436-6", - "display": "Laboratory studies (set)" - } - ] - }, - { - "coding": [ - { - "system": "http://snomed.info/sct", - "code": "1236877003", - "display": "Genetic pathology" - } - ] - } - ], - "subject": { - "reference": "Patient/Patient-PheobeSmitham-Example" - }, - "date": "2023-10-16T00:00:00-05:00", - "author": [ - { - "identifier": { - "system": "https://fhir.nhs.uk/Id/ods-organization-code", - "value": "R0A" - } - } - ], - "title": "Example Genomic Laboratory (Single) Report", - "section": [ - { - "title": "Results", - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "26436-6", - "display": "Laboratory studies (set)" - } - ] - }, - "entry": [ - { - "reference": "Observation/Observation-GenomicTherapeuticImplication-Example" - }, - { - "reference": "Observation/Observation-GenomicsVariantSLC52A2-Example" - } - ] - } - ] - } - }, - { - "fullUrl": "http://example.org/fhir/DiagnosticReport/DiagnosticReport-GenomicVariantAssessment-Example", - "resource": { - "resourceType": "DiagnosticReport", - "id": "DiagnosticReport-GenomicVariantAssessment-Example", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report", - "https://fhir.hl7.org.uk/StructureDefinition/UKCore-DiagnosticReport", - "http://hl7.eu/fhir/laboratory/StructureDefinition/DiagnosticReport-eu-lab" - ] - }, - "extension": [ - { - "url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-DiagnosticReport.composition", - "valueReference": { - "reference": "Composition/Composition-EULabGenomicReport-Example" - } - }, - { - "url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/recommended-action", - "valueReference": { - "reference": "Task/Task-FollowupRecommendationReport-Example", - "display": "Confirmatory testing recommended" - } - }, - { - "url": "http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact", - "valueRelatedArtifact": { - "type": "citation", - "display": "Johnson et al 2012 (PMID22740598)" - } - }, - { - "url": "http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact", - "valueRelatedArtifact": { - "type": "citation", - "display": "Foley et al 2014 (PMID22740598)" - } - }, - { - "url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report-note", - "valueAnnotation": { - "extension": [ - { - "url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/annotation-code", - "valueCodeableConcept": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/coded-annotation-types-cs", - "code": "test-disclaimer" - } - ] - } - } - ], - "text": "Proband whole genome sequencing by the 100,000 Genomics Project with analysis of the PanelApp Paediatric motor neuronopathies (version 1.6) gene panel followed by in-house Sanger sequencing confirmation. Please note that the sensitivity of this test is limited by the types of detectable pathogenic variants, regions of low read depth coverage and incomplete ascertainment of disease-gene associations. Further information including read depth coverage is available on request. *Variants are classified using the ACMG/AMP guidelines (Richards et al 2015 PMID25741868)." - } - } - ], - "basedOn": [ - { - "reference": "ServiceRequest/ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example" - } - ], - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/v2-0074", - "code": "GE" - } - ] - }, - { - "coding": [ - { - "system": "http://snomed.info/sct", - "code": "1236877003", - "display": "Genetic pathology" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51969-4", - "display": "Genetic analysis report" - } - ] - }, - "subject": { - "reference": "Patient/Patient-PheobeSmitham-Example" - }, - "effectiveDateTime": "2023-10-16T00:00:00-05:00", - "issued": "2023-09-16T00:00:00-05:00", - "performer": [ - { - "identifier": { - "system": "https://fhir.nhs.uk/Id/ods-organization-code", - "value": "R0A" - } - } - ], - "media": [ - { - "link": { - "type":"DocumentReference", - "display": "Reference to DocumentReferences are not supported within media.link in DiagnosticReport R4 StructureDefinition.", - "extension": [ - { - "url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason", - "valueCode": "unsupported" - } - ] - }, - "extension": [ - { - "url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-DiagnosticReport.media.link", - "valueReference": { - "reference": "DocumentReference/DocumentReference-StructureReporting-Example" - } - } - ] - } - ], - "result": [ - { - "reference": "Observation/Observation-GenomicsVariant-SLC52A2", - "display": "Brown-Vialetto-Van Laere syndrome type 2" - }, - { - "reference": "Observation/Observation-GenomicTherapeuticImplication-Example" - } - ], - "conclusion": "Pheobe is homozygous for a pathogenic SLC52A2 missense variant (details below) previously reported by Johnson et al 2012 (PMID22740598). Biallelic pathogenic SLC52A2 variants cause autosomal recessive Brown-Vialetto-Van Laere syndrome type 2 (MIM614707).", - "conclusionCode": [ - { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6576-8", - "display": "Positive" - }, - { - "system": "http://snomed.info/sct", - "code": "699866005", - "display": "Brown-Vialetto-Van Laere syndrome" - } - ] - } - ], - "presentedForm": [ - { - "contentType": "application/pdf", - "language": "en-GB", - "url": "https://cts5j3.axshare.com/?id=mhxwul&p=final_report_issued_test_complete&g=1", - "title": "Genomic Report for Pheobe Smitham", - "creation": "2023-10-16" - } - ] - } - }, - { - "fullUrl": "http://example.org/fhir/Patient/Patient-PheobeSmitham-Example", - "resource": { - "resourceType": "Patient", - "id": "Patient-PheobeSmitham-Example", - "extension": [ - { - "url": "https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-BirthSex", - "valueCodeableConcept": { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/v3-AdministrativeGender", - "code": "F", - "display": "Female" - } - ] - } - }, - { - "url": "https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-EthnicCategory", - "valueCodeableConcept": { - "coding": [ - { - "system": "https://fhir.hl7.org.uk/CodeSystem/UKCore-EthnicCategoryEngland", - "code": "A", - "display": "White - British" - } - ] - } - } - ], - "identifier": [ - { - "system": "https://fhir.nhs.uk/Id/nhs-number", - "value": "9449307539", - "extension": [ - { - "url": "https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-NHSNumberVerificationStatus", - "valueCodeableConcept": { - "coding": [ - { - "system": "https://fhir.hl7.org.uk/CodeSystem/UKCore-NHSNumberVerificationStatusEngland", - "version": "2.2.0", - "code": "01", - "display": "Number present and verified" - } - ] - } - } - ] - }, - { - "system": "urn:oid:2.16.840.1.113883.2.1.3.2.4.18.24", - "value": "RR12764", - "assigner": { - "identifier": { - "system": "https://fhir.nhs.uk/Id/ods-organization-code", - "value": "RR8" - } - } - } - ], - "name": [ - { - "given": [ - "Pheobe" - ], - "family": "Smitham" - } - ], - "birthDate": "2013-09-27", - "deceasedBoolean": true, - "address": [ - { - "line": [ - "Union Mills", - "9, Dewsbury Rd", - "Leeds" - ], - "postalCode": "LS11 5DD" - } - ], - "generalPractitioner": [ - { - "identifier": { - "system": "https://fhir.hl7.org.uk/Id/gmp-number", - "value": "G9999999" - }, - "display": "Dr. Aero Smith" - }, - { - "identifier": { - "system": "https://fhir.hl7.org.uk/Id/ODS-code", - "value": "TP123" - }, - "display": "Test GP Practice" - } - ], - "link": [ - { - "other": { - "reference": "https://api.service.nhs.uk/personal-demographics/FHIR/R4/Patient/9449307539" - }, - "type": "seealso" - } - ] - } - }, - { - "fullUrl": "http://example.org/fhir/Observation/Observation-GenomicTherapeuticImplication-Example", - "resource": { - "resourceType": "Observation", - "id": "Observation-GenomicTherapeuticImplication-Example", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - }, - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/v2-0074", - "code": "GE" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" - } - ] - }, - "subject": { - "reference": "Patient/Patient-PheobeSmitham-Example" - }, - "effectiveDateTime": "2023-09-16", - "performer": [ - { - "identifier": { - "system": "https://fhir.nhs.uk/Id/ods-organization-code", - "value": "R0A" - } - } - ], - "derivedFrom": [ - { - "reference": "Observation/Observation-GenomicsVariantSLC52A2-Example" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication", - "display": "Therapeutic Implication" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9661-5", - "display": "Presumed responsive" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "Medication assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://snomed.info/sct", - "code": "438481000124108", - "display": "Riboflavin supplement" - } - ] - } - } - ], - "note" : [{ - "text" : "High dose riboflavin supplementation has been reported to ameliorate the progression of this disorder (Foley et al 2014 PMID22740598)" - }] - } - }, - { - "fullUrl": "http://example.org/fhir/Observation/Observation-GenomicsVariantSLC52A2-Example", - "resource": { - "resourceType": "Observation", - "id": "Observation-GenomicsVariantSLC52A2-Example", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "basedOn": [ - { - "reference": "ServiceRequest/ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example" - } - ], - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - }, - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/v2-0074", - "code": "GE" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6" - } - ] - }, - "subject": { - "reference": "Patient/Patient-PheobeSmitham-Example" - }, - "effectiveDateTime": "2023-09-16", - "performer": [ - { - "identifier": { - "system": "https://fhir.nhs.uk/Id/ods-organization-code", - "value": "R0A" - } - } - ], - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "Present" - } - ] - }, - "method": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA26398-0", - "display": "Sequencing" - } - ] - }, - "specimen": { - "reference": "Specimen/Specimen-PheobeSmitham-Example" - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48004-6" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://varnomen.hgvs.org", - "code": "NM_024531.4:c.9163>A p.(Gly306Arg)" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81290-9" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://varnomen.hgvs.org", - "code": "Chr8:g.1455840683>A" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://purl.obolibrary.org/obo", - "code": "SO_0001583", - "display": "missense_variant" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48018-6" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.genenames.org/", - "code": "HGNC:30224", - "display": "SLC52A2" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "94186-4" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA4489-6", - "display": "Unknown" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "Germline" - } - ] - } - } - ] - } - }, - { - "fullUrl": "http://example.org/fhir/Specimen/Specimen-PheobeSmitham-Example", - "resource": { - "resourceType": "Specimen", - "id": "Specimen-PheobeSmitham-Example", - "extension": [ - { - "url": "https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-SampleCategory", - "valueCodeableConcept": { - "coding": [ - { - "system": "https://fhir.hl7.org.uk/CodeSystem/UKCore-SampleCategory", - "code": "germline", - "display": "Germline" - } - ] - } - } - ], - "identifier": [ - { - "system": "https://fhir.leedssth.nhs.uk//Id/specimenId", - "value": "RGD-69050-P-RR12764" - } - ], - "status": "available", - "type": { - "coding": [ - { - "system": "http://snomed.info/sct", - "code": "445295009", - "display": "Blood specimen with EDTA" - } - ] - }, - "subject": { - "reference": "Patient/Patient-PheobeSmitham-Example", - "identifier": { - "system": "https://fhir.nhs.uk/Id/nhs-number", - "value": "9449307539" - } - }, - "collection": { - "collector": { - "identifier": { - "system": "https://fhir.nhs.uk/Id/sds-user-id", - "value": "9999999998" - }, - "display": "Phletobomist-Lois Lane" - }, - "collectedDateTime": "2023-09-17" - }, - "request": [ - { - "reference": "ServiceRequest/ServiceRequest-WGSTestOrderForm-TrioTestingProband-Example" - } - ] - } - }, - { - "fullUrl": "http://example.org/fhir/ServiceRequest/ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example", - "resource": { - "resourceType": "ServiceRequest", - "id": "ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example", - "meta": { - "versionId": "2", - "lastUpdated": "2023-10-09T09:15:00Z" - }, - "extension": [ - { - "url": "https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-Coverage", - "valueCodeableConcept": { - "coding": [ - { - "system": "https://fhir.hl7.org.uk/CodeSystem/UKCore-FundingCategory", - "code": "nhs-england", - "display": "NHS England" - } - ] - } - } - ], - "identifier": [ - { - "system": "https://fhir.nhs.uk/Id/GMSOrder", - "value": "RR8F1792" - } - ], - "requisition": { - "assigner": { - "identifier": { - "system": "https://fhir.leedsth.nhs.uk/Id/grouptestId", - "value": "RR8F1792" - } - } - }, - "status": "active", - "intent": "order", - "category": [ - { - "coding": [ - { - "system": "https://fhir.hl7.org.uk/CodeSystem/UKCore-GenomeSequencingCategory", - "code": "rare-disease-wgs", - "display": "Rare Disease - WGS" - } - ] - }, - { - "coding": [ - { - "system": "https://fhir.nhs.uk/CodeSystem/reasonfortesting-genomics", - "code": "diagnostic", - "display": "Diagnostic" - } - ] - } - ], - "priority": "routine", - "code": { - "coding": [ - { - "system": "https://fhir.nhs.uk/CodeSystem/England-GenomicTestDirectory", - "code": "R98.2", - "display": "Likely inborn error of metabolism", - "version": "7" - } - ], - "text": "This is a Trio Testing, comprising 3 family members with their respective specimen`s & Record Of Discussion`s" - }, - "subject": { - "reference": "Patient/Patient-PheobeSmitham-Example", - "identifier": { - "system": "https://fhir.nhs.uk/Id/nhs-number", - "value": "9449307539" - } - }, - "authoredOn": "2023-09-15T15:00:00Z", - "requester": { - "reference": "PractitionerRole/PractitionerRole-EugeneSmith-Example" - }, - "reasonReference": [ - { - "reference": "Condition/Condition-InbornErrorOfMetabolism-Example" - } - ], - "performer": [ - { - "identifier": { - "system": "https://fhir.nhs.uk/Id/ods-organization-code", - "value": "R0A" - } - } - ], - "supportingInfo": [ - { - "reference": "Observation/Observation-AutisticBehaviour-Example" - }, - { - "reference": "Observation/Observation-DelayedSpeechLanguageDevt-Example" - }, - { - "reference": "Observation/Observation-DiseasePenetrancePheobeSmitham-Example" - }, - { - "reference": "Observation/Observation-IntellectualDisabilityProfound-Example" - }, - { - "reference": "Observation/Observation-NonConsanguinousUnionProband-Example" - }, - { - "reference": "Specimen/Specimen-PheobeSmitham-Example" - }, - { - "reference": "Observation/Observation-GenomicEthnicity-Example" - }, - { - "reference": "Observation/Observation-NoPregnancy-Example" - }, - { - "reference": "Condition/Condition-MonogenicHearingLoss-Example" - }, - { - "reference": "Observation/Observation-NoBoneMarrowTransplant-Example" - }, - { - "reference": "Observation/Observation-NoTransfusion-Example" - }, - { - "reference": "Patient/Patient-PheobeSmithamMother-Example" - }, - { - "reference": "RelatedPerson/RelatedPerson-AliceSmithamProbandMother-Example" - }, - { - "reference": "Specimen/Specimen-PheobeSmithamMother-Example" - }, - { - "reference": "Observation/Observation-NonConsanguinousUnionMother-Example" - }, - { - "reference": "Observation/Observation-NoTransfusionProbandMother-Example" - }, - { - "reference": "Observation/Observation-NoBoneMarrowTransplantProbandMother-Example" - }, - { - "reference": "Patient/Patient-PheobeSmithamFather-Example" - }, - { - "reference": "RelatedPerson/RelatedPerson-JamesLawrenceProbandFather-Example" - }, - { - "reference": "Observation/Observation-NonConsanguinousUnionProbandFather-Example" - }, - { - "reference": "Observation/Observation-NoTransfusionProbandFather-Example" - }, - { - "reference": "Observation/Observation-NoBoneMarrowTransplantProbandFather-Example" - }, - { - "reference": "Observation/Observation-IntellectualDisabilityMild-Example" - }, - { - "reference": "Consent/Consent-RoD-PheobeSmitham-Example" - }, - { - "reference": "Consent/Consent-RoD-PheobeSmithamYoungPersonAssentForm-Example" - }, - { - "reference": "Consent/Consent-RoD-PheobeSmithamMother-Example" - }, - { - "reference": "QuestionnaireResponse/QuestionnaireResponse-RoD-PheobeSmithamCDForn-Example" - }, - { - "reference": "QuestionnaireResponse/QuestionnaireResponse-RoD-PheobeSmithamYPAForm-Example" - }, - { - "reference": "QuestionnaireResponse/QuestionnaireResponse-RoD-PheobeSmithamMother-Example" - }, - { - "reference": "Consent/Consent-RoD-PheobeSmithamFather-Example" - }, - { - "reference": "QuestionnaireResponse/QuestionnaireResponse-RoD-PheobeSmithamFather-Example" - }, - { - "reference": "Specimen/Specimen-PheobeSmithamFather-Example" - } - ], - "note": [ - { - "text": "No family history of genomic testing" - }, - { - "text": "Free text for diagnosis/reason for referral, relevant information including family history, phenotypic details/ HPO Terms/ E.g. Not eligible for R14 or R98. Agreed with testing laboratory at Manchester. Father lives in surrey. Father to have sample taken locally and sent to MFT." - } - ] - } - }, - { - "fullUrl": "http://example.org/fhir/Task/Task-FollowupRecommendationReport-Example", - "resource": { - "resourceType": "Task", - "id": "Task-FollowupRecommendationReport-Example", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/followup-recommendation" - ] - }, - "status": "requested", - "intent": "proposal", - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA14021-2", - "display": "Confirmatory testing recommended" - } - ] - }, - "description": "Testing of Pheobe's parents is recommended (via referral to the clinical genetics service) in order to confirm that both are heterozygous carriers of the missense variant.", - "for": { - "reference": "Patient/Patient-PheobeSmitham-Example" - }, - "reasonReference": { - "reference": "Observation/Observation-GenomicImplication-Therapeutic" - }, - "input": [ - { - "type": { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/v3-RoleCode", - "code": "NFTH", - "display": "natural father" - } - ] - }, - "valueReference": { - "reference": "Patient/Patient-PheobeSmithamFather-Example" - } - }, - { - "type": { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/v3-RoleCode", - "code": "NMTH", - "display": "natural mother" - } - ] - }, - "valueReference": { - "reference": "Patient/Patient-PheobeSmithamMother-Example" - } - } - ] - } - }, - { - "fullUrl": "http://example.org/fhir/DocumentReference/DocumentReference-StructureReporting-Example", - "resource": { - "resourceType": "DocumentReference", - "id": "DocumentReference-StructureReporting-Example", - "status": "current", - "docStatus": "final", - "subject": { - "reference": "Patient/Patient-PheobeSmitham-Example", - "identifier": { - "system": "https://fhir.nhs.uk/Id/nhs-number", - "value": "9449307539" - } - }, - "date": "2023-10-16T09:45:00Z", - "author": [ - { - "identifier": { - "system": "https://fhir.nhs.uk/Id/ods-organization-code", - "value": "R0A" - } - } - ], - "description": "Phenotype Report", - "content": [ - { - "attachment": { - "contentType": "application/json", - "url": "drs://drs.genomicsengland.nhs.uk/ga4gh/drs/v1/objects/42375e7d-071c-4eb3-b1c8-cec11e245cf0", - "title": "-Structure Data Capture JSON report" - } - } - ], - "context": { - "related": [ - { - "reference": "ServiceRequest/ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example" - }, - { - "reference": "Specimen/Specimen-PheobeSmitham-Example" - }, - { - "reference": "Specimen/Specimen-PheobeSmithamFather-Example" - }, - { - "reference": "Specimen/Specimen-PheobeSmithamMother-Example" - } - ] - } - } - } - ] -} \ No newline at end of file From 66ac9d6b196941ad20b2cb4a44445d48ceb48cef Mon Sep 17 00:00:00 2001 From: KazeemHamzat Date: Fri, 5 Sep 2025 16:31:18 +0100 Subject: [PATCH 29/31] Removed EU Extensions Removed EU Extensions --- fhirpkg.lock.json | 9 +++------ package.json | 3 --- 2 files changed, 3 insertions(+), 9 deletions(-) diff --git a/fhirpkg.lock.json b/fhirpkg.lock.json index b87d4f40..5619249a 100644 --- a/fhirpkg.lock.json +++ b/fhirpkg.lock.json @@ -1,17 +1,14 @@ { - "updated": "2025-09-04T19:03:17.2341729+01:00", + "updated": "2025-09-05T16:30:58.9974559+01:00", "dependencies": { "fhir.r4.ukcore.stu3.currentbuild": "0.24.0-pre-release", "hl7.fhir.r4.core": "4.0.1", "hl7.fhir.r5.core": "5.0.0", "hl7.fhir.uv.genomics-reporting": "3.0.0-ballot", - "hl7.fhir.uv.extensions.r4": "5.2.0", - "hl7.fhir.eu.extensions": "0.1.1-ballot", - "hl7.terminology.r5": "6.2.0", - "hl7.fhir.uv.extensions.r5": "5.2.0", + "hl7.terminology.r4": "5.3.0", + "hl7.fhir.uv.extensions.r4": "1.0.0", "hl7.fhir.uv.ips": "1.1.0", "fhir.dicom": "2022.4.20221006", - "hl7.terminology.r4": "6.5.0", "hl7.fhir.eu.laboratory": "0.1.0-ballot" }, "missing": {} diff --git a/package.json b/package.json index 068f0841..63ed107b 100644 --- a/package.json +++ b/package.json @@ -10,10 +10,7 @@ "fhir.r4.ukcore.stu3.currentbuild": "0.24.0-pre-release", "hl7.fhir.r4.core": "4.0.1", "hl7.fhir.uv.genomics-reporting": "3.0.0-ballot", - "hl7.fhir.uv.extensions.r4": "5.2.0", - "hl7.fhir.eu.extensions": "0.1.1-ballot", "hl7.fhir.uv.ips": "1.1.0", - "hl7.terminology.r4": "6.5.0", "hl7.fhir.eu.laboratory": "0.1.0-ballot" } } From 10dab47ec8471f0cc01d5bfc5f7561050d8cb345 Mon Sep 17 00:00:00 2001 From: Omar Khan Date: Mon, 8 Sep 2025 10:20:09 +0100 Subject: [PATCH 30/31] Revert of example to use SO CS --- Observation/Observation-GenomicsVariantSLC52A2-Example.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Observation/Observation-GenomicsVariantSLC52A2-Example.json b/Observation/Observation-GenomicsVariantSLC52A2-Example.json index a435ed1e..2524e4ea 100644 --- a/Observation/Observation-GenomicsVariantSLC52A2-Example.json +++ b/Observation/Observation-GenomicsVariantSLC52A2-Example.json @@ -121,8 +121,8 @@ "valueCodeableConcept": { "coding": [ { - "system": "http://purl.obolibrary.org/obo", - "code": "SO_0001583", + "system": "http://www.sequenceontology.org", + "code": "SO:0001583", "display": "missense_variant" } ] From dce8590695100b132616bca80af77a27d4bf8a10 Mon Sep 17 00:00:00 2001 From: Omar Khan Date: Mon, 8 Sep 2025 12:48:48 +0100 Subject: [PATCH 31/31] Corrected issues Updated Observation reference Updated date on NamingSystem Added EU Profiles to ServiceRequest --- Composition/Composition-EULabGenomicReport-Example.json | 2 +- NamingSystem/NamingSystem-Genomics-report-number.json | 2 +- ...Request-WGSTestOrderFormUpdated-TrioTesting-Example.json | 6 +++++- 3 files changed, 7 insertions(+), 3 deletions(-) diff --git a/Composition/Composition-EULabGenomicReport-Example.json b/Composition/Composition-EULabGenomicReport-Example.json index 46696872..8d849926 100644 --- a/Composition/Composition-EULabGenomicReport-Example.json +++ b/Composition/Composition-EULabGenomicReport-Example.json @@ -86,7 +86,7 @@ "reference": "Observation/Observation-GenomicTherapeuticImplication-Example" }, { - "reference": "Observation-GenomicsVariantSLC52A2-Example" + "reference": "Observation/Observation-GenomicsVariantSLC52A2-Example" } ] } diff --git a/NamingSystem/NamingSystem-Genomics-report-number.json b/NamingSystem/NamingSystem-Genomics-report-number.json index 2d9e4b78..0a1c5332 100644 --- a/NamingSystem/NamingSystem-Genomics-report-number.json +++ b/NamingSystem/NamingSystem-Genomics-report-number.json @@ -4,7 +4,7 @@ "name": "GenomicsReportNumber", "status": "draft", "kind": "identifier", - "date": "2025-02-10", + "date": "2025-09-08", "publisher": "NHS England", "contact": [ { diff --git a/ServiceRequest/ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example.json b/ServiceRequest/ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example.json index 2c9a6baf..78c5ad88 100644 --- a/ServiceRequest/ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example.json +++ b/ServiceRequest/ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example.json @@ -3,7 +3,11 @@ "id": "ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example", "meta": { "versionId": "2", - "lastUpdated": "2023-10-09T09:15:00Z" + "lastUpdated": "2023-10-09T09:15:00Z", + "profile": [ + "http://hl7.eu/fhir/laboratory/StructureDefinition/ServiceRequest-eu-lab", + "https://fhir.hl7.org.uk/StructureDefinition/UKCore-ServiceRequest" + ] }, "extension": [ {