From 8804981be55e2859705150024df8f1728924fb91 Mon Sep 17 00:00:00 2001 From: KazeemHamzat Date: Thu, 23 Jan 2025 20:16:19 +0000 Subject: [PATCH 1/6] Update DiagnosticReport-GenomicReport-VariantAssessment.json Update DiagnosticReport-GenomicReport-VariantAssessment --- ...ticReport-GenomicReport-VariantAssessment.json | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/DiagnosticReport/DiagnosticReport-GenomicReport-VariantAssessment.json b/DiagnosticReport/DiagnosticReport-GenomicReport-VariantAssessment.json index 4f223b8..7b7c5ac 100644 --- a/DiagnosticReport/DiagnosticReport-GenomicReport-VariantAssessment.json +++ b/DiagnosticReport/DiagnosticReport-GenomicReport-VariantAssessment.json @@ -46,6 +46,21 @@ ], "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)." } + }, + { + "url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-DiagnosticReport.media", + "extension": [ + { + "url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-DiagnosticReport.media", + "valueString": "gdgdg" + }, + { + "url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-DiagnosticReport.media", + "valueReference": { + "reference": "http://terminology.hl7.org/CodeSystem/v3-AdministrativeGender" + } + } + ] } ], "basedOn": [ From 4dc8877a4dfb41fbcf854b14e9eadd46696fb41e Mon Sep 17 00:00:00 2001 From: KazeemHamzat Date: Mon, 27 Jan 2025 18:25:32 +0000 Subject: [PATCH 2/6] Update DiagnosticReport-GenomicVariantAssessment-Example.json Add extension-DiagnosticReport.media.link --- ...port-GenomicVariantAssessment-Example.json | 39 +++++++++++-------- 1 file changed, 23 insertions(+), 16 deletions(-) diff --git a/DiagnosticReport/DiagnosticReport-GenomicVariantAssessment-Example.json b/DiagnosticReport/DiagnosticReport-GenomicVariantAssessment-Example.json index c81cbdc..5d449ba 100644 --- a/DiagnosticReport/DiagnosticReport-GenomicVariantAssessment-Example.json +++ b/DiagnosticReport/DiagnosticReport-GenomicVariantAssessment-Example.json @@ -3,7 +3,8 @@ "id": "DiagnosticReport-GenomicVariantAssessment-Example", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report", + "https://fhir.hl7.org.uk/StructureDefinition/UKCore-DiagnosticReport" ] }, "extension": [ @@ -46,21 +47,6 @@ ], "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)." } - }, - { - "url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-DiagnosticReport.media", - "extension": [ - { - "url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-DiagnosticReport.media", - "valueString": "gdgdg" - }, - { - "url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-DiagnosticReport.media", - "valueReference": { - "reference": "http://terminology.hl7.org/CodeSystem/v3-AdministrativeGender" - } - } - ] } ], "basedOn": [ @@ -100,6 +86,27 @@ } } ], + "media": [ + { + "extension": [ + { + "url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-DiagnosticReport.media.link", + "valueReference": { + "reference": "DocumentReference/DocumentReference-StructureReporting-Example" + } + } + ], + "link": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason", + "valueCode": "unsupported" + } + ], + "display": "unsupported" + } + } + ], "result": [ { "reference": "Observation/Observation-GenomicsVariant-SLC52A2", From 2248cb15641485c88732707e22c5f118badd194b Mon Sep 17 00:00:00 2001 From: KazeemHamzat Date: Mon, 27 Jan 2025 18:35:57 +0000 Subject: [PATCH 3/6] Update DiagnosticReport-GenomicVariantAssessment-Example Update DiagnosticReport-GenomicVariantAssessment-Example --- ...port-GenomicVariantAssessment-Example.json | 20 +++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/DiagnosticReport/DiagnosticReport-GenomicVariantAssessment-Example.json b/DiagnosticReport/DiagnosticReport-GenomicVariantAssessment-Example.json index 5d449ba..f7130f1 100644 --- a/DiagnosticReport/DiagnosticReport-GenomicVariantAssessment-Example.json +++ b/DiagnosticReport/DiagnosticReport-GenomicVariantAssessment-Example.json @@ -88,6 +88,15 @@ ], "media": [ { + "link": { + "display": "unsupported", + "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", @@ -95,16 +104,7 @@ "reference": "DocumentReference/DocumentReference-StructureReporting-Example" } } - ], - "link": { - "extension": [ - { - "url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason", - "valueCode": "unsupported" - } - ], - "display": "unsupported" - } + ] } ], "result": [ From 8654970c84ff89675f441de8c993f2c70c33d562 Mon Sep 17 00:00:00 2001 From: KazeemHamzat Date: Tue, 28 Jan 2025 15:01:37 +0000 Subject: [PATCH 4/6] Update Dependency UKCore Package Update the UKCore Dependency package to fhir.r4.ukcore.stu3.currentbuild 0.0.18-pre-release UK Core FHIR profiles and Assets --- fhirpkg.lock.json | 2 +- package.json | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/fhirpkg.lock.json b/fhirpkg.lock.json index cf246c4..1133e1b 100644 --- a/fhirpkg.lock.json +++ b/fhirpkg.lock.json @@ -1,7 +1,7 @@ { "updated": "2024-05-16T10:18:19.8963748+01:00", "dependencies": { - "fhir.r4.ukcore.stu3.currentbuild": "0.0.17-pre-release", + "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.terminology.r4": "5.3.0", diff --git a/package.json b/package.json index b88c24e..e679bd0 100644 --- a/package.json +++ b/package.json @@ -7,7 +7,7 @@ ], "jurisdiction": "urn:iso:std:iso:3166:-2:GB-ENG", "dependencies": { - "fhir.r4.ukcore.stu3.currentbuild": "0.0.17-pre-release", + "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" } From 0f2c6df79a43914e7e56aa51cad4aea45264e05c Mon Sep 17 00:00:00 2001 From: KazeemHamzat Date: Thu, 30 Jan 2025 14:11:15 +0000 Subject: [PATCH 5/6] Update DiagnosticReport-GenomicVariantAssessment-Example.json Update to include type --- .../DiagnosticReport-GenomicVariantAssessment-Example.json | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/DiagnosticReport/DiagnosticReport-GenomicVariantAssessment-Example.json b/DiagnosticReport/DiagnosticReport-GenomicVariantAssessment-Example.json index f7130f1..262d739 100644 --- a/DiagnosticReport/DiagnosticReport-GenomicVariantAssessment-Example.json +++ b/DiagnosticReport/DiagnosticReport-GenomicVariantAssessment-Example.json @@ -89,7 +89,8 @@ "media": [ { "link": { - "display": "unsupported", + "type":"DocumentReference", + "display": "Reference to DocumentReferences are not supported within media.link in DiagnosticReport R4 resource", "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason", From de3395f3bc9b859e35082c05f30c565c3ea90af2 Mon Sep 17 00:00:00 2001 From: KazeemHamzat Date: Fri, 31 Jan 2025 09:55:53 +0000 Subject: [PATCH 6/6] Update DiagnosticReport-GenomicVariantAssessment-Example Update DiagnosticReport-GenomicVariantAssessment-Example --- .../DiagnosticReport-GenomicVariantAssessment-Example.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DiagnosticReport/DiagnosticReport-GenomicVariantAssessment-Example.json b/DiagnosticReport/DiagnosticReport-GenomicVariantAssessment-Example.json index 262d739..d5efe0b 100644 --- a/DiagnosticReport/DiagnosticReport-GenomicVariantAssessment-Example.json +++ b/DiagnosticReport/DiagnosticReport-GenomicVariantAssessment-Example.json @@ -90,7 +90,7 @@ { "link": { "type":"DocumentReference", - "display": "Reference to DocumentReferences are not supported within media.link in DiagnosticReport R4 resource", + "display": "Reference to DocumentReferences are not supported within media.link in DiagnosticReport R4 StructureDefinition.", "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason",