From 6364815d1f0af05c306ba10ea7709b8effe01cc3 Mon Sep 17 00:00:00 2001 From: KazeemHamzat Date: Fri, 7 Feb 2025 13:13:43 +0000 Subject: [PATCH 1/9] Create WGS -TestOderForm-Cancer Create WGS -TestOderForm-Cancer-SolidTumour --- ...cture-BodySiteLocationAbdomen-Example.json | 29 +++++ ...ion-PercentageMalignantNuclei-Example.json | 41 +++++++ ...ervation-TumourTypeDemeizaSeo-Example.json | 28 +++++ ...estOrderForm-CancerSolidTumor-Example.json | 108 ++++++++++++++++++ ...Specimen-SolidTumorDemeizaSeo-Example.json | 78 +++++++++++++ 5 files changed, 284 insertions(+) create mode 100644 BodyStructure/BodyStructure-BodySiteLocationAbdomen-Example.json create mode 100644 Observation/Observation-PercentageMalignantNuclei-Example.json create mode 100644 Observation/Observation-TumourTypeDemeizaSeo-Example.json create mode 100644 ServiceRequest/ServiceRequest-WGSTestOrderForm-CancerSolidTumor-Example.json create mode 100644 Specimen/Specimen-SolidTumorDemeizaSeo-Example.json diff --git a/BodyStructure/BodyStructure-BodySiteLocationAbdomen-Example.json b/BodyStructure/BodyStructure-BodySiteLocationAbdomen-Example.json new file mode 100644 index 00000000..2ed2a61f --- /dev/null +++ b/BodyStructure/BodyStructure-BodySiteLocationAbdomen-Example.json @@ -0,0 +1,29 @@ +{ + "resourceType": "BodyStructure", + "id": "BodyStructure-BodySiteLocationAbdomen-Example", + "morphology": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "369755005", + "display": "Multiple tumors (qualifier value)" + } + ] + }, + "location": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "818983003", + "display": "Structure of abdominopelvic cavity and/or content of abdominopelvic cavity and/or anterior abdominal wall (body structure)" + } + ] + }, + "patient": { + "reference": "Patient-DemeizaSeo-Example", + "identifier": { + "system": "https://fhir.nhs.uk/Id/nhs-number", + "value": "9449306559" + } + } +} \ No newline at end of file diff --git a/Observation/Observation-PercentageMalignantNuclei-Example.json b/Observation/Observation-PercentageMalignantNuclei-Example.json new file mode 100644 index 00000000..4268be44 --- /dev/null +++ b/Observation/Observation-PercentageMalignantNuclei-Example.json @@ -0,0 +1,41 @@ +{ + "resourceType": "Observation", + "id": "Observation-PercentageMalignantNuclei-Example", + "status": "final", + "code": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "1255076007", + "display": "Percent of cell nuclei positive for proliferation marker protein Ki-67 in primary malignant neoplasm of stomach by immunohistochemistry (observable entity)" + } + ] + }, + "subject": { + "reference": "Patient/Patient-DemeizaSeo-Example", + "identifier": { + "system": "https://fhir.nhs.uk/Id/nhs-number", + "value": "9449306559" + } + }, + "specimen": { + "reference":"Specimen/Specimen-SolidTumorDemeizaSeo-Example", + "identifier": { + "system": "https://fhir.add.nhs.uk/Id/specimenId", + "value": "RA257631", + "assigner": { + "identifier": { + "system": "https://fhir.nhs.uk/Id/ods-organization-code", + "value": "696B0" + } + } + } + }, + "valueQuantity": { + "value": 25, + "unit": "%", + "system": "http://unitsofmeasure.org", + "code": "%" + }, + "effectiveDateTime": "2023-08-29" +} \ No newline at end of file diff --git a/Observation/Observation-TumourTypeDemeizaSeo-Example.json b/Observation/Observation-TumourTypeDemeizaSeo-Example.json new file mode 100644 index 00000000..a6495d8c --- /dev/null +++ b/Observation/Observation-TumourTypeDemeizaSeo-Example.json @@ -0,0 +1,28 @@ +{ + "resourceType": "Observation", + "id": "Observation-TumourTypeDemeizaSeo-Example", + "status": "final", + "code": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "116061001", + "display": "Solid pseudopapillary carcinoma (morphologic abnormality)" + } + ] + }, + "subject": { + "reference": "Patient/Patient-DemeizaSeo-Example", + "identifier": { + "system": "https://fhir.nhs.uk/Id/nhs-number", + "value": "9449306559" + } + }, + "specimen": { + "identifier": { + "system": "https://fhir.add.nhs.uk/Id/specimenId", + "value": "RA257631" + } + }, + "effectiveDateTime": "2023-11-01T11:00:00Z" +} \ No newline at end of file diff --git a/ServiceRequest/ServiceRequest-WGSTestOrderForm-CancerSolidTumor-Example.json b/ServiceRequest/ServiceRequest-WGSTestOrderForm-CancerSolidTumor-Example.json new file mode 100644 index 00000000..7901d899 --- /dev/null +++ b/ServiceRequest/ServiceRequest-WGSTestOrderForm-CancerSolidTumor-Example.json @@ -0,0 +1,108 @@ +{ + "resourceType": "ServiceRequest", + "id": "ServiceRequest-WGSTestOrderForm-CancerSolidTumor-Example", + "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" + } + ] + } + }, + { + "url": "https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-AdditionalContact", + "valueReference": { + "reference": "PractitionerRole/PractitionerRole-AnnaLaneKingstonPathology-Example" + } + } + ], + "status": "active", + "intent": "order", + "category": [ + { + "coding": [ + { + "system": "https://fhir.hl7.org.uk/CodeSystem/UKCore-GenomeSequencingCategory", + "code": "cancer-wgs", + "display": "Cancer - WGS" + } + ] + } + ], + "priority": "routine", + "code": { + "coding": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/England-GenomicTestDirectory", + "code": "M219.1", + "display": "Multi Target NGS Panel Small Variant" + } + ] + }, + "subject": { + "reference": "Patient/Patient-DemeizaSeo-Example", + "identifier": { + "system": "https://fhir.nhs.uk/Id/nhs-number", + "value": "9449306559" + } + }, + "authoredOn": "2023-09-08", + "requester": { + "reference": "PractitionerRole/PractitionerRole-HazelSmithKingstonPathology-Example" + }, + "reasonCode": [ + { + "coding": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/reasonfortesting-genomics", + "code": "diagnostic", + "display": "Diagnostic" + } + ] + } + ], + "performer": [ + { + "identifier": { + "system": "https://fhir.nhs.uk/Id/ods-organization-code", + "value": "RJZ" + }, + "display": "KING'S COLLEGE HOSPITAL NHS FOUNDATION TRUST" + } + ], + "supportingInfo": [ + + + { + "reference": "Observation/Observation-TumorType-Example" + }, + + { + "reference": "Observation/Observation-PercentageMalignantNuclei-Example" + }, + { + "reference": "BodyStructure/BodyStructure-BodySiteLocationAbdomen-Example" + }, + { + "reference": "Consent/Consent-RoDToFollow-Example" + } + ], + "specimen": [ + { + "reference": "Specimen/Specimen-SolidTumorDemeizaSeo-Example" + } + ], + "note": [ + { + "text": "Relevant Family History" + }, + { + "text": "Other Additional Information" + } + ] +} \ No newline at end of file diff --git a/Specimen/Specimen-SolidTumorDemeizaSeo-Example.json b/Specimen/Specimen-SolidTumorDemeizaSeo-Example.json new file mode 100644 index 00000000..afdf0eb6 --- /dev/null +++ b/Specimen/Specimen-SolidTumorDemeizaSeo-Example.json @@ -0,0 +1,78 @@ +{ + "resourceType": "Specimen", + "id": "Specimen-SolidTumorDemeizaSeo-Example", + "extension": [ + { + "url": "https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-SampleCategory", + "valueCodeableConcept": { + "coding": [ + { + "system": "https://fhir.hl7.org.uk/CodeSystem/UKCore-SampleCategory", + "code": "tumour", + "display": "Tumour" + } + ], + "text": "Solid Tumour" + } + } + ], + "identifier": [ + { + "system": "https://fhir.add.nhs.uk/Id/specimenId", + "value": "RA257631" + } + ], + "status": "available", + "type": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "364611000000101", + "display": "Tissue resection sample" + } + ] + }, + "subject": { + "reference": "Patient/Patient-DemeizaSeo-Example", + "identifier": { + "system": "https://fhir.nhs.uk/Id/nhs-number", + "value": "9449306559" + } + }, + "collection": { + "collector": { + "identifier": { + "system": "https://fhir.nhs.uk/Id/sds-user-id", + "value": "9999999998" + }, + "display": "ClinicalScientist-John Taylor" + }, + "collectedDateTime": "2023-09-09T11:00:00Z", + "bodySite": { + "extension": [ + { + "url": "https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-BodySiteReference", + "valueReference": { + "reference": "BodyStructure/BodyStructure-BodySiteLocationAbdomen-Example" + } + } + ] + } + }, + "condition": [ + { + "coding": [ + { + "system": "https://fhir.hl7.org.uk/CodeSystem/UKCore-BiopsyState", + "code": "fresh-frozen", + "display": "Fresh Frozen" + } + ] + } + ], + "request": [ + { + "reference": "ServiceRequest/ServiceRequest-WGS" + } + ] +} \ No newline at end of file From e4e57c53549b18fd2749fbc2dbde651b77ff3d69 Mon Sep 17 00:00:00 2001 From: KazeemHamzat Date: Fri, 7 Feb 2025 14:20:48 +0000 Subject: [PATCH 2/9] Update ServiceRequest-WGSTestOrderForm-CancerSolidTumor-Example.json update --- ...uest-WGSTestOrderForm-CancerSolidTumor-Example.json | 10 ++-------- 1 file changed, 2 insertions(+), 8 deletions(-) diff --git a/ServiceRequest/ServiceRequest-WGSTestOrderForm-CancerSolidTumor-Example.json b/ServiceRequest/ServiceRequest-WGSTestOrderForm-CancerSolidTumor-Example.json index 7901d899..daf2a1e1 100644 --- a/ServiceRequest/ServiceRequest-WGSTestOrderForm-CancerSolidTumor-Example.json +++ b/ServiceRequest/ServiceRequest-WGSTestOrderForm-CancerSolidTumor-Example.json @@ -76,21 +76,15 @@ } ], "supportingInfo": [ - - { "reference": "Observation/Observation-TumorType-Example" }, - { "reference": "Observation/Observation-PercentageMalignantNuclei-Example" }, { - "reference": "BodyStructure/BodyStructure-BodySiteLocationAbdomen-Example" - }, - { - "reference": "Consent/Consent-RoDToFollow-Example" - } + "reference": "Consent/Consent-RoDToFollow-Example" + } ], "specimen": [ { From e6ce8f5b8b9038f3c5e54d98e718eecbef713b1f Mon Sep 17 00:00:00 2001 From: KazeemHamzat Date: Fri, 7 Feb 2025 15:15:47 +0000 Subject: [PATCH 3/9] Add a Task Resource Add a Task Resource --- ...ion-PercentageMalignantNuclei-Example.json | 2 +- ...ervation-TumourTypeDemeizaSeo-Example.json | 2 +- ...Specimen-SolidTumorDemeizaSeo-Example.json | 2 +- ...GSCancerTestOrder-SolidTumour-Example.json | 30 +++++++++++++++++++ 4 files changed, 33 insertions(+), 3 deletions(-) create mode 100644 Task/Task-WGSCancerTestOrder-SolidTumour-Example.json diff --git a/Observation/Observation-PercentageMalignantNuclei-Example.json b/Observation/Observation-PercentageMalignantNuclei-Example.json index 4268be44..ab1df124 100644 --- a/Observation/Observation-PercentageMalignantNuclei-Example.json +++ b/Observation/Observation-PercentageMalignantNuclei-Example.json @@ -37,5 +37,5 @@ "system": "http://unitsofmeasure.org", "code": "%" }, - "effectiveDateTime": "2023-08-29" + "effectiveDateTime": "2023-08-09" } \ No newline at end of file diff --git a/Observation/Observation-TumourTypeDemeizaSeo-Example.json b/Observation/Observation-TumourTypeDemeizaSeo-Example.json index a6495d8c..cec810bb 100644 --- a/Observation/Observation-TumourTypeDemeizaSeo-Example.json +++ b/Observation/Observation-TumourTypeDemeizaSeo-Example.json @@ -24,5 +24,5 @@ "value": "RA257631" } }, - "effectiveDateTime": "2023-11-01T11:00:00Z" + "effectiveDateTime": "2023-09-08T11:00:00Z" } \ No newline at end of file diff --git a/Specimen/Specimen-SolidTumorDemeizaSeo-Example.json b/Specimen/Specimen-SolidTumorDemeizaSeo-Example.json index afdf0eb6..132a4e6d 100644 --- a/Specimen/Specimen-SolidTumorDemeizaSeo-Example.json +++ b/Specimen/Specimen-SolidTumorDemeizaSeo-Example.json @@ -72,7 +72,7 @@ ], "request": [ { - "reference": "ServiceRequest/ServiceRequest-WGS" + "reference": "ServiceRequest/ServiceRequest-WGSTestOrderForm-CancerSolidTumor-Example" } ] } \ No newline at end of file diff --git a/Task/Task-WGSCancerTestOrder-SolidTumour-Example.json b/Task/Task-WGSCancerTestOrder-SolidTumour-Example.json new file mode 100644 index 00000000..dd85d6a6 --- /dev/null +++ b/Task/Task-WGSCancerTestOrder-SolidTumour-Example.json @@ -0,0 +1,30 @@ +{ + "resourceType": "Task", + "id": "Task-WGSCancerTestOrder-SolidTumor-Example", + "status": "requested", + "intent": "order", + "priority": "routine", + "code": { + "coding": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/task-code-genomics", + "code": "process-genomic-test-request", + "display": "Process Genomic Test Request" + } + ] + }, + "focus": { + "reference": "ServiceRequest/ServiceRequest-WGSTestOrderForm-CancerSolidTumor-Example" + }, + "for": { + "reference": "Patient/Patient-DemeizaSeo-Example", + "identifier": { + "system": "https://fhir.nhs.uk/Id/nhs-number", + "value": "9449306559" + } + }, + "authoredOn": "2023-09-09", + "requester": { + "reference": "PractitionerRole/PractitionerRole-HazelSmithRenal-Example" + } +} From 6880b81ec5d6de1c95084377d1ffaaa1b5e85684 Mon Sep 17 00:00:00 2001 From: KazeemHamzat Date: Fri, 7 Feb 2025 17:51:17 +0000 Subject: [PATCH 4/9] Update Task-WGSCancerTestOrder-SolidTumour-Example.json Update Task Requester reference --- Task/Task-WGSCancerTestOrder-SolidTumour-Example.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Task/Task-WGSCancerTestOrder-SolidTumour-Example.json b/Task/Task-WGSCancerTestOrder-SolidTumour-Example.json index dd85d6a6..870a68c3 100644 --- a/Task/Task-WGSCancerTestOrder-SolidTumour-Example.json +++ b/Task/Task-WGSCancerTestOrder-SolidTumour-Example.json @@ -25,6 +25,6 @@ }, "authoredOn": "2023-09-09", "requester": { - "reference": "PractitionerRole/PractitionerRole-HazelSmithRenal-Example" + "reference": "PractitionerRole/PractitionerRole-HazelSmithKingstonPathology-Example" } } From d99f3250a65ea4d2f7a28ce88218ff5eefc574fc Mon Sep 17 00:00:00 2001 From: KazeemHamzat Date: Mon, 10 Feb 2025 13:57:53 +0000 Subject: [PATCH 5/9] Update ServiceRequest-WGSTestOrderForm-CancerSolidTumor-Example.json Update SR to reflect new mapping of reason-for-testing --- ...iceRequest-WGSTestOrderForm-CancerSolidTumor-Example.json | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/ServiceRequest/ServiceRequest-WGSTestOrderForm-CancerSolidTumor-Example.json b/ServiceRequest/ServiceRequest-WGSTestOrderForm-CancerSolidTumor-Example.json index daf2a1e1..d9f2c4a0 100644 --- a/ServiceRequest/ServiceRequest-WGSTestOrderForm-CancerSolidTumor-Example.json +++ b/ServiceRequest/ServiceRequest-WGSTestOrderForm-CancerSolidTumor-Example.json @@ -30,6 +30,11 @@ "system": "https://fhir.hl7.org.uk/CodeSystem/UKCore-GenomeSequencingCategory", "code": "cancer-wgs", "display": "Cancer - WGS" + }, + { + "system": "https://fhir.nhs.uk/CodeSystem/reasonfortesting-genomics", + "code": "diagnostic", + "display": "Diagnostic" } ] } From 675ed53487982207e5a61dfd1fce711912b16f23 Mon Sep 17 00:00:00 2001 From: KazeemHamzat Date: Mon, 10 Feb 2025 14:45:42 +0000 Subject: [PATCH 6/9] Update ServiceRequest-WGSTestOrderForm-CancerSolidTumor-Example.json new mapping --- ...ceRequest-WGSTestOrderForm-CancerSolidTumor-Example.json | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/ServiceRequest/ServiceRequest-WGSTestOrderForm-CancerSolidTumor-Example.json b/ServiceRequest/ServiceRequest-WGSTestOrderForm-CancerSolidTumor-Example.json index d9f2c4a0..0eb11142 100644 --- a/ServiceRequest/ServiceRequest-WGSTestOrderForm-CancerSolidTumor-Example.json +++ b/ServiceRequest/ServiceRequest-WGSTestOrderForm-CancerSolidTumor-Example.json @@ -30,7 +30,11 @@ "system": "https://fhir.hl7.org.uk/CodeSystem/UKCore-GenomeSequencingCategory", "code": "cancer-wgs", "display": "Cancer - WGS" - }, + } + ] + }, + { + "coding": [ { "system": "https://fhir.nhs.uk/CodeSystem/reasonfortesting-genomics", "code": "diagnostic", From b7fff851877c5cef2ebc4d5112fa6432dde6b5aa Mon Sep 17 00:00:00 2001 From: KazeemHamzat Date: Tue, 11 Feb 2025 18:04:33 +0000 Subject: [PATCH 7/9] Feedback Issues Update SR.code value --- ...viceRequest-WGSTestOrderForm-CancerSolidTumor-Example.json | 4 ++-- Specimen/Specimen-SolidTumorDemeizaSeo-Example.json | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/ServiceRequest/ServiceRequest-WGSTestOrderForm-CancerSolidTumor-Example.json b/ServiceRequest/ServiceRequest-WGSTestOrderForm-CancerSolidTumor-Example.json index 0eb11142..ae5c5e74 100644 --- a/ServiceRequest/ServiceRequest-WGSTestOrderForm-CancerSolidTumor-Example.json +++ b/ServiceRequest/ServiceRequest-WGSTestOrderForm-CancerSolidTumor-Example.json @@ -48,8 +48,8 @@ "coding": [ { "system": "https://fhir.nhs.uk/CodeSystem/England-GenomicTestDirectory", - "code": "M219.1", - "display": "Multi Target NGS Panel Small Variant" + "code": "M233.1", + "display": "WGS Germline and Tumour" } ] }, diff --git a/Specimen/Specimen-SolidTumorDemeizaSeo-Example.json b/Specimen/Specimen-SolidTumorDemeizaSeo-Example.json index 132a4e6d..5885e97d 100644 --- a/Specimen/Specimen-SolidTumorDemeizaSeo-Example.json +++ b/Specimen/Specimen-SolidTumorDemeizaSeo-Example.json @@ -8,8 +8,8 @@ "coding": [ { "system": "https://fhir.hl7.org.uk/CodeSystem/UKCore-SampleCategory", - "code": "tumour", - "display": "Tumour" + "code": "solid-tumour", + "display": "Solid Tumour" } ], "text": "Solid Tumour" From 0ccb6917f01f2fec4f6ded639cd8e1c5d4a9f1a7 Mon Sep 17 00:00:00 2001 From: KazeemHamzat Date: Tue, 11 Feb 2025 18:12:10 +0000 Subject: [PATCH 8/9] Update Specimen-SolidTumorDemeizaSeo-Example.json Update Specimen.code value --- Specimen/Specimen-SolidTumorDemeizaSeo-Example.json | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/Specimen/Specimen-SolidTumorDemeizaSeo-Example.json b/Specimen/Specimen-SolidTumorDemeizaSeo-Example.json index 5885e97d..41671158 100644 --- a/Specimen/Specimen-SolidTumorDemeizaSeo-Example.json +++ b/Specimen/Specimen-SolidTumorDemeizaSeo-Example.json @@ -11,8 +11,7 @@ "code": "solid-tumour", "display": "Solid Tumour" } - ], - "text": "Solid Tumour" + ] } } ], From c16af60a92f1e3485a851a05b430fa6c32df4b07 Mon Sep 17 00:00:00 2001 From: KazeemHamzat Date: Wed, 12 Feb 2025 13:42:40 +0000 Subject: [PATCH 9/9] Update Specimen-SolidTumorDemeizaSeo-Example.json Update value for Specimen.condition --- Specimen/Specimen-SolidTumorDemeizaSeo-Example.json | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Specimen/Specimen-SolidTumorDemeizaSeo-Example.json b/Specimen/Specimen-SolidTumorDemeizaSeo-Example.json index 41671158..2d21ca33 100644 --- a/Specimen/Specimen-SolidTumorDemeizaSeo-Example.json +++ b/Specimen/Specimen-SolidTumorDemeizaSeo-Example.json @@ -62,9 +62,9 @@ { "coding": [ { - "system": "https://fhir.hl7.org.uk/CodeSystem/UKCore-BiopsyState", - "code": "fresh-frozen", - "display": "Fresh Frozen" + "system": "https://fhir.hl7.org.uk/CodeSystem/UKCore-PrimarySampleState", + "code": "fresh", + "display": "Fresh" } ] }