From 3e0d13834f6d0ad7dcd5bc69c07ebe9c1ea194b5 Mon Sep 17 00:00:00 2001 From: KazeemHamzat Date: Mon, 1 Dec 2025 17:46:27 +0000 Subject: [PATCH 1/3] Recording-device/software-for-generating-Observation Recording-device/software-for-generating-Observation --- ...vation-GenomicsVariantSLC52A2-Example.json | 415 +++++++++--------- Procedure/Procedure-GenomicStudy-Example.json | 35 ++ ...edure-PGXGenomicStudyAnalysis-Example.json | 82 ++++ 3 files changed, 327 insertions(+), 205 deletions(-) create mode 100644 Procedure/Procedure-GenomicStudy-Example.json create mode 100644 Procedure/Procedure-PGXGenomicStudyAnalysis-Example.json diff --git a/Observation/Observation-GenomicsVariantSLC52A2-Example.json b/Observation/Observation-GenomicsVariantSLC52A2-Example.json index 8100a059..7a43773d 100644 --- a/Observation/Observation-GenomicsVariantSLC52A2-Example.json +++ b/Observation/Observation-GenomicsVariantSLC52A2-Example.json @@ -1,223 +1,228 @@ { - "resourceType": "Observation", - "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" - ] - }, - "status": "final", - "basedOn": [ + "resourceType": "Observation", + "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" + ] + }, + "status": "final", + "basedOn": [ + { + "reference": "ServiceRequest/ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example" + } + ], + "category": [ + { + "coding": [ { - "reference": "ServiceRequest/ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example" + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" } - ], - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - }, + ] + }, + { + "coding": [ { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/v2-0074", - "code": "GE" - } - ] + "system": "http://terminology.hl7.org/CodeSystem/v2-0074", + "code": "GE" } - ], - "code": { + ] + } + ], + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "69548-6" + }, + { + "system": "http://snomed.info/sct", + "code": "414755005", + "display": "Molecular, genetic AND/OR cellular observable" + } + ] + }, + "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" + }, + { + "system": "http://snomed.info/sct", + "code": "52101004", + "display": "Present" + } + ] + }, + "method": { + "coding": [ + { + "system": "http://loinc.org", + "code": "LA26398-0", + "display": "Sequencing" + }, + { + "system": "http://snomed.info/sct", + "code": "117040002", + "display": "Nucleic acid sequencing" + } + ] + }, + "specimen": { + "reference": "Specimen/Specimen-PheobeSmitham-Example" + }, + "component": [ + { + "code": { "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6" - }, - { - "system": "http://snomed.info/sct", - "code": "414755005", - "display": "Molecular, genetic AND/OR cellular observable" - } + { + "system": "http://loinc.org", + "code": "48004-6" + } ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://varnomen.hgvs.org", + "code": "NM_024531.4:c.9163>A p.(Gly306Arg)" + } + ] + } }, - "subject": { - "reference": "Patient/Patient-PheobeSmitham-Example" + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "81290-9" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://varnomen.hgvs.org", + "code": "Chr8:g.1455840683>A" + } + ] + } }, - "effectiveDateTime": "2023-09-16", - "performer": [ - { - "identifier": { - "system": "https://fhir.nhs.uk/Id/ods-organization-code", - "value": "R0A" - } - } - ], - "valueCodeableConcept": { + { + "code": { "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "Present" - }, - { - "system": "http://snomed.info/sct", - "code": "52101004", - "display": "Present" - } + { + "system": "http://loinc.org", + "code": "81252-9" + } ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://www.sequenceontology.org", + "code": "SO:0001583", + "display": "missense_variant" + } + ] + } }, - "method": { + { + "code": { "coding": [ - { - "system": "http://loinc.org", - "code": "LA26398-0", - "display": "Sequencing" - }, - { - "system": "http://snomed.info/sct", - "code": "117040002", - "display": "Nucleic acid sequencing" - } + { + "system": "http://loinc.org", + "code": "48018-6" + } ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://www.genenames.org/", + "code": "HGNC:30224", + "display": "SLC52A2" + } + ] + } }, - "specimen": { - "reference": "Specimen/Specimen-PheobeSmitham-Example" + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "53034-5" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://loinc.org", + "code": "LA6705-3", + "display": "homozygous" + } + ] + } }, - "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://www.sequenceontology.org", - "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" - } - ] - } - } + { + "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" + } + ] + } + } + ], + "partOf": [ + { + "reference": "Procedure/Procedure-GenomicStudy-Example" + } ] } \ No newline at end of file diff --git a/Procedure/Procedure-GenomicStudy-Example.json b/Procedure/Procedure-GenomicStudy-Example.json new file mode 100644 index 00000000..be71b0c2 --- /dev/null +++ b/Procedure/Procedure-GenomicStudy-Example.json @@ -0,0 +1,35 @@ +{ + "resourceType": "Procedure", + "id": "Procedure-GenomicStudy-Example", + "extension": [ + { + "url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-ext", + "valueReference": { + "reference": "Procedure/Procedure-PGXGenomicStudyAnalysis-Example", + "display": "PGX Genomic Study Analysis" + } + } + ], + "status": "completed", + "category": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "405824009", + "display": "Genetic test" + } + ] + }, + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-type-cs", + "code": "struc-var", + "display": "Structural variation detection" + } + ] + }, + "subject": { + "reference": "Patient/Patient-PheobeSmitham-Example" + } +} \ No newline at end of file diff --git a/Procedure/Procedure-PGXGenomicStudyAnalysis-Example.json b/Procedure/Procedure-PGXGenomicStudyAnalysis-Example.json new file mode 100644 index 00000000..ebe3d5d9 --- /dev/null +++ b/Procedure/Procedure-PGXGenomicStudyAnalysis-Example.json @@ -0,0 +1,82 @@ +{ + "resourceType": "Procedure", + "id": "Procedure-PGXGenomicStudyAnalysis-Example", + "extension": [ + { + "url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-device", + "extension": [ + { + "url": "device", + "valueReference": { + "reference": "Device/Device-SampleCollectionKit-Example", + "display": "DNA Sample Collection Kit (Saliva/Buccal Swab)" + } + }, + { + "url": "device", + "valueReference": { + "reference": "Device/Device-DNAExtractionSystem-Example", + "display": "Automated DNA Extraction System" + } + }, + { + "url": "device", + "valueReference": { + "reference": "Device/Device-BioAnalyzerSystem-Example", + "display": "Quality Control System (Bioanalyzer/Qubit)" + } + }, + { + "url": "device", + "valueReference": { + "reference": "Device/Device-Sequencerillumina-Example", + "display": "Illumina NextSeq 2000 Sequencer" + } + }, + { + "url": "device", + "valueReference": { + "reference": "Device/Device-BioinformaticsPipeline-Example", + "display": "Bioinformatics Analysis Pipeline v5.2" + } + }, + { + "url": "device", + "valueReference": { + "reference": "Device/Device-VariantSnnotationTool-Example", + "display": "Variant Annotation & Interpretation Software" + } + }, + { + "url": "device", + "valueReference": { + "reference": "Device/Device-GenomicReportingSystem-Example", + "display": "Genomic Reporting System" + } + } + ] + } + ], + "status": "completed", + "category": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "405824009", + "display": "Genetic test" + } + ] + }, + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-type-cs", + "code": "struc-var", + "display": "Structural variation detection" + } + ] + }, + "subject": { + "reference": "Patient/Patient-PheobeSmitham-Example" + } +} \ No newline at end of file From 845e16fadd0ea415598428bda851dea725106210 Mon Sep 17 00:00:00 2001 From: KazeemHamzat Date: Mon, 1 Dec 2025 18:22:46 +0000 Subject: [PATCH 2/3] Update Procedure-PGXGenomicStudyAnalysis-Example Update Procedure-PGXGenomicStudyAnalysis-Example --- ...edure-PGXGenomicStudyAnalysis-Example.json | 42 ++++++++++++++++--- 1 file changed, 36 insertions(+), 6 deletions(-) diff --git a/Procedure/Procedure-PGXGenomicStudyAnalysis-Example.json b/Procedure/Procedure-PGXGenomicStudyAnalysis-Example.json index ebe3d5d9..e594b2c9 100644 --- a/Procedure/Procedure-PGXGenomicStudyAnalysis-Example.json +++ b/Procedure/Procedure-PGXGenomicStudyAnalysis-Example.json @@ -11,42 +11,72 @@ "reference": "Device/Device-SampleCollectionKit-Example", "display": "DNA Sample Collection Kit (Saliva/Buccal Swab)" } - }, + } + ] + }, + { + "url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-device", + "extension": [ { "url": "device", "valueReference": { "reference": "Device/Device-DNAExtractionSystem-Example", "display": "Automated DNA Extraction System" } - }, + } + ] + }, + { + "url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-device", + "extension": [ { "url": "device", "valueReference": { "reference": "Device/Device-BioAnalyzerSystem-Example", "display": "Quality Control System (Bioanalyzer/Qubit)" } - }, + } + ] + }, + { + "url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-device", + "extension": [ { "url": "device", "valueReference": { "reference": "Device/Device-Sequencerillumina-Example", "display": "Illumina NextSeq 2000 Sequencer" } - }, + } + ] + }, + { + "url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-device", + "extension": [ { "url": "device", "valueReference": { "reference": "Device/Device-BioinformaticsPipeline-Example", "display": "Bioinformatics Analysis Pipeline v5.2" } - }, + } + ] + }, + { + "url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-device", + "extension": [ { "url": "device", "valueReference": { "reference": "Device/Device-VariantSnnotationTool-Example", "display": "Variant Annotation & Interpretation Software" } - }, + } + ] + }, + { + "url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-device", + "extension": [ { "url": "device", "valueReference": { From ad5f4b4f9a1d4dab6517838cc736854ff5d73167 Mon Sep 17 00:00:00 2001 From: KazeemHamzat Date: Tue, 2 Dec 2025 11:04:31 +0000 Subject: [PATCH 3/3] Feedback Issues Changing mapping for Procedure.category --- Procedure/Procedure-GenomicStudy-Example.json | 15 +++------------ ...Procedure-PGXGenomicStudyAnalysis-Example.json | 15 +++------------ 2 files changed, 6 insertions(+), 24 deletions(-) diff --git a/Procedure/Procedure-GenomicStudy-Example.json b/Procedure/Procedure-GenomicStudy-Example.json index be71b0c2..b9b676b5 100644 --- a/Procedure/Procedure-GenomicStudy-Example.json +++ b/Procedure/Procedure-GenomicStudy-Example.json @@ -14,18 +14,9 @@ "category": { "coding": [ { - "system": "http://snomed.info/sct", - "code": "405824009", - "display": "Genetic test" - } - ] - }, - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-type-cs", - "code": "struc-var", - "display": "Structural variation detection" + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory", + "display": "Laboratory" } ] }, diff --git a/Procedure/Procedure-PGXGenomicStudyAnalysis-Example.json b/Procedure/Procedure-PGXGenomicStudyAnalysis-Example.json index e594b2c9..f48fc517 100644 --- a/Procedure/Procedure-PGXGenomicStudyAnalysis-Example.json +++ b/Procedure/Procedure-PGXGenomicStudyAnalysis-Example.json @@ -91,18 +91,9 @@ "category": { "coding": [ { - "system": "http://snomed.info/sct", - "code": "405824009", - "display": "Genetic test" - } - ] - }, - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-type-cs", - "code": "struc-var", - "display": "Structural variation detection" + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory", + "display": "Laboratory" } ] },