From 72b53be3a45cc6bc19765eb0228bb98bf9e7401a Mon Sep 17 00:00:00 2001 From: Omar Khan Date: Thu, 24 Apr 2025 16:26:23 +0100 Subject: [PATCH 01/10] Consent examples for UGR --- ...Consent-UGRConsentForResearch-Example.json | 63 +++++++++++++++ Consent/Consent-UGRGenomicData-Example.json | 81 +++++++++++++++++++ 2 files changed, 144 insertions(+) create mode 100644 Consent/Consent-UGRConsentForResearch-Example.json create mode 100644 Consent/Consent-UGRGenomicData-Example.json diff --git a/Consent/Consent-UGRConsentForResearch-Example.json b/Consent/Consent-UGRConsentForResearch-Example.json new file mode 100644 index 00000000..00c002ef --- /dev/null +++ b/Consent/Consent-UGRConsentForResearch-Example.json @@ -0,0 +1,63 @@ +{ + "resourceType" : "Consent", + "id" : "Consent-UGRConsentForResearch-Example", + "meta" : { + "profile" : [ + "https://profiles.ihe.net/ITI/PCF/StructureDefinition/IHE.PCF.consentBasic" + ] + }, + "status" : "active", + "scope" : { + "coding" : [ + { + "system" : "http://terminology.hl7.org/CodeSystem/consentscope", + "code" : "patient-privacy" + } + ] + }, + "category" : [ + { + "coding" : [ + { + "system" : "http://loinc.org", + "code" : "59284-0", + "display" : "Consent" + } + ] + } + ], + "patient" : { + "reference" : "Patient/Patient-MeirLieberman-Example" + }, + "dateTime" : "2025-04-24", + "performer" : [ + { + "reference" : "Patient/Patient-MeirLieberman-Example" + } + ], + "organization" : [ + { + "identifier" : { + "system": "https://fhir.hl7.org.uk/Id/ODS-code", + "value": "X26" + } + } + ], + "sourceReference" : { + "reference" : "QuestionnaireResponse/QuestionnaireResponse-ConsentQuestionnaire-Example" + }, + "policy" : [ + { + "uri" : "https://www.england.nhs.uk/wp-content/uploads/2018/05/nhs-england-privacy-notice-v1.77.pdf" + } + ], + "provision" : { + "type" : "permit", + "purpose" : [ + { + "system" : "http://terminology.hl7.org/CodeSystem/v3-ActReason", + "code" : "HRESCH" + } + ] + } +} \ No newline at end of file diff --git a/Consent/Consent-UGRGenomicData-Example.json b/Consent/Consent-UGRGenomicData-Example.json new file mode 100644 index 00000000..d651203d --- /dev/null +++ b/Consent/Consent-UGRGenomicData-Example.json @@ -0,0 +1,81 @@ +{ + "resourceType" : "Consent", + "id" : "Consent-UGRGenomicData-Example", + "status" : "active", + "scope" : { + "coding" : [ + { + "system" : "http://terminology.hl7.org/CodeSystem/consentscope", + "code" : "patient-privacy" + } + ] + }, + "category" : [ + { + "coding" : [ + { + "system" : "http://loinc.org", + "code" : "59284-0", + "display" : "Consent" + } + ] + } + ], + "patient" : { + "reference" : "Patient/Patient-MeirLieberman-Example" + }, + "dateTime" : "2025-04-24", + "performer" : [ + { + "reference" : "Patient/Patient-MeirLieberman-Example" + } + ], + "organization" : [ + { + "identifier" : { + "system": "https://fhir.hl7.org.uk/Id/ODS-code", + "value": "X26" + } + } + ], + "sourceReference" : { + "reference" : "QuestionnaireResponse/QuestionnaireResponse-ConsentQuestionnaire-Example" + }, + "policy" : [ + { + "uri" : "https://www.england.nhs.uk/wp-content/uploads/2018/05/nhs-england-privacy-notice-v1.77.pdf" + } + ], + "provision" : { + "type" : "permit", + "purpose" : [ + { + "system" : "http://terminology.hl7.org/CodeSystem/v3-ActReason", + "code" : "POPHLTH" + }, + { + "system" : "http://terminology.hl7.org/CodeSystem/v3-ActReason", + "code" : "HRESCH" + }, + { + "system" : "http://terminology.hl7.org/CodeSystem/v3-ActReason", + "code" : "HOPERAT" + } + ], + "class" : [ + { + "system" : "http://hl7.org/fhir/resource-types", + "code" : "DocumentReference", + "display" : "DocumentReference" + } + ], + "data" : [ + { + "meaning" : "instance", + "reference" : { + "reference" : "DocumentReference/DocumentReference-PharmCAT-Example" + } + } + ] + } +} \ No newline at end of file From 0d4b445bf889db710e641279d656368eeac95197 Mon Sep 17 00:00:00 2001 From: Omar Khan Date: Tue, 22 Apr 2025 13:46:19 +0100 Subject: [PATCH 02/10] Correction to SNOMED display term --- Bundle/UKCore-Bundle-MichaelJonesRequest-Example_minimal.json | 2 +- .../UKCore-Bundle-MichaelJonesRequest-Example_v3_message.json | 2 +- .../UKCore-ServiceRequest-MichaelJonesDYPDRequest-Example.json | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/Bundle/UKCore-Bundle-MichaelJonesRequest-Example_minimal.json b/Bundle/UKCore-Bundle-MichaelJonesRequest-Example_minimal.json index efe489f4..02c54a77 100644 --- a/Bundle/UKCore-Bundle-MichaelJonesRequest-Example_minimal.json +++ b/Bundle/UKCore-Bundle-MichaelJonesRequest-Example_minimal.json @@ -158,7 +158,7 @@ { "system": "http://snomed.info/sct", "code": "363418001", - "display": "Malignant tumor of pancreas (disorder)" + "display": "Malignant neoplasm of pancreas" } ] } diff --git a/Bundle/UKCore-Bundle-MichaelJonesRequest-Example_v3_message.json b/Bundle/UKCore-Bundle-MichaelJonesRequest-Example_v3_message.json index d530951d..776fbe3b 100644 --- a/Bundle/UKCore-Bundle-MichaelJonesRequest-Example_v3_message.json +++ b/Bundle/UKCore-Bundle-MichaelJonesRequest-Example_v3_message.json @@ -596,7 +596,7 @@ { "system": "http://snomed.info/sct", "code": "363418001", - "display": "Malignant tumor of pancreas (disorder)" + "display": "Malignant neoplasm of pancreas" } ] } diff --git a/ServiceRequest/UKCore-ServiceRequest-MichaelJonesDYPDRequest-Example.json b/ServiceRequest/UKCore-ServiceRequest-MichaelJonesDYPDRequest-Example.json index 811560f0..4f3c171b 100644 --- a/ServiceRequest/UKCore-ServiceRequest-MichaelJonesDYPDRequest-Example.json +++ b/ServiceRequest/UKCore-ServiceRequest-MichaelJonesDYPDRequest-Example.json @@ -88,7 +88,7 @@ { "system": "http://snomed.info/sct", "code": "363418001", - "display": "Malignant tumor of pancreas (disorder)" + "display": "Malignant neoplasm of pancreas" } ] } From 694e3b0c4588371986e10eabf8d3ce0bb124b81d Mon Sep 17 00:00:00 2001 From: Omar Khan Date: Thu, 24 Apr 2025 16:34:17 +0100 Subject: [PATCH 03/10] Update to dependency list To include IHE PCF --- package.json | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/package.json b/package.json index e679bd07..5b211e40 100644 --- a/package.json +++ b/package.json @@ -9,7 +9,8 @@ "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", + "ihe.iti.pcf": "1.1.0" } } From 0b959e4d8fd4189db096a6fbf414a6a379167f3c Mon Sep 17 00:00:00 2001 From: Omar Khan Date: Thu, 24 Apr 2025 16:40:20 +0100 Subject: [PATCH 04/10] Additional inclusion of BALP package To try to correct validator issue --- package.json | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/package.json b/package.json index 5b211e40..fe4e0dd4 100644 --- a/package.json +++ b/package.json @@ -10,7 +10,8 @@ "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", - "ihe.iti.pcf": "1.1.0" + "ihe.iti.pcf": "1.1.0", + "ihe.iti.balp": "1.1.3" } } From 20d6bc82a201d355c3d9865c923a85dd0e873749 Mon Sep 17 00:00:00 2001 From: Omar Khan Date: Mon, 28 Apr 2025 09:35:53 +0100 Subject: [PATCH 05/10] Correction to invalid Observation --- Observation/Observation-NoTransfusionProbandFather-Example.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 889d229e2635083cc7cce71109463ecd2d658995 Mon Sep 17 00:00:00 2001 From: KazeemHamzat Date: Fri, 5 Sep 2025 12:26:59 +0100 Subject: [PATCH 06/10] Testing "ihe.iti.balp": "1.1.3" Update fhirpkg.lock.json --- fhirpkg.lock.json | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/fhirpkg.lock.json b/fhirpkg.lock.json index 5f2bc664..b03e01d5 100644 --- a/fhirpkg.lock.json +++ b/fhirpkg.lock.json @@ -1,11 +1,14 @@ { - "updated": "2025-05-08T09:07:12.7767319+01:00", + "updated": "2025-09-05T12:25:10.566496+01:00", "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.terminology.r4": "5.3.0", - "hl7.fhir.uv.extensions.r4": "1.0.0" + "hl7.fhir.uv.extensions.r4": "1.0.0", + "ihe.iti.pcf": "1.1.0", + "us.nlm.vsac": "0.9.0", + "ihe.iti.balp": "1.1.3" }, "missing": {} } From 5ccf6a3e30269d1a059089e5308086e2b01eea45 Mon Sep 17 00:00:00 2001 From: KazeemHamzat Date: Fri, 5 Sep 2025 12:39:45 +0100 Subject: [PATCH 07/10] Testing "ihe.iti.balp": "1.1.2" Testing "ihe.iti.balp": "1.1.2" --- fhirpkg.lock.json | 2 +- package.json | 14 ++++++-------- 2 files changed, 7 insertions(+), 9 deletions(-) diff --git a/fhirpkg.lock.json b/fhirpkg.lock.json index b03e01d5..5218d511 100644 --- a/fhirpkg.lock.json +++ b/fhirpkg.lock.json @@ -1,5 +1,5 @@ { - "updated": "2025-09-05T12:25:10.566496+01:00", + "updated": "2025-09-05T12:37:12.6177925+01:00", "dependencies": { "fhir.r4.ukcore.stu3.currentbuild": "0.0.18-pre-release", "hl7.fhir.r4.core": "4.0.1", diff --git a/package.json b/package.json index fe4e0dd4..78de4a62 100644 --- a/package.json +++ b/package.json @@ -2,17 +2,15 @@ "name": "uk.nhsdigital.r4.genomics", "description": "FHIR Genomics Implementation Guide", "author": "nhsdigital", - "fhirVersions": [ - "4.0.1" - ], - "jurisdiction": "urn:iso:std:iso:3166:-2:GB-ENG", "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", "ihe.iti.pcf": "1.1.0", - "ihe.iti.balp": "1.1.3" - } + "ihe.iti.balp": "1.1.2" + }, + "fhirVersions": [ + "4.0.1" + ], + "jurisdiction": "urn:iso:std:iso:3166:-2:GB-ENG" } - - From 02fa7df7ec26fb11a7f894aad304eba12fe161dc Mon Sep 17 00:00:00 2001 From: KazeemHamzat Date: Fri, 5 Sep 2025 12:59:23 +0100 Subject: [PATCH 08/10] Testing "ihe.iti.balp": "1.1.3" Testing "ihe.iti.balp": "1.1.3" --- fhirpkg.lock.json | 4 +--- package.json | 3 +-- 2 files changed, 2 insertions(+), 5 deletions(-) diff --git a/fhirpkg.lock.json b/fhirpkg.lock.json index 5218d511..738b5691 100644 --- a/fhirpkg.lock.json +++ b/fhirpkg.lock.json @@ -1,13 +1,11 @@ { - "updated": "2025-09-05T12:37:12.6177925+01:00", + "updated": "2025-09-05T12:58:00.6661158+01:00", "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.terminology.r4": "5.3.0", "hl7.fhir.uv.extensions.r4": "1.0.0", - "ihe.iti.pcf": "1.1.0", - "us.nlm.vsac": "0.9.0", "ihe.iti.balp": "1.1.3" }, "missing": {} diff --git a/package.json b/package.json index 78de4a62..05c1e101 100644 --- a/package.json +++ b/package.json @@ -6,8 +6,7 @@ "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", - "ihe.iti.pcf": "1.1.0", - "ihe.iti.balp": "1.1.2" + "ihe.iti.balp": "1.1.3" }, "fhirVersions": [ "4.0.1" From c24b8b4911ad2376d7447c7d021a3f24664ecb48 Mon Sep 17 00:00:00 2001 From: KazeemHamzat Date: Fri, 5 Sep 2025 15:44:17 +0100 Subject: [PATCH 09/10] Testing "ihe.iti.pcf": "1.1.0" Testing "ihe.iti.pcf": "1.1.0" --- fhirpkg.lock.json | 4 +++- package.json | 2 +- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/fhirpkg.lock.json b/fhirpkg.lock.json index 738b5691..92a09196 100644 --- a/fhirpkg.lock.json +++ b/fhirpkg.lock.json @@ -1,11 +1,13 @@ { - "updated": "2025-09-05T12:58:00.6661158+01:00", + "updated": "2025-09-05T15:43:25.6984082+01:00", "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.terminology.r4": "5.3.0", "hl7.fhir.uv.extensions.r4": "1.0.0", + "ihe.iti.pcf": "1.1.0", + "us.nlm.vsac": "0.9.0", "ihe.iti.balp": "1.1.3" }, "missing": {} diff --git a/package.json b/package.json index 05c1e101..f44384d5 100644 --- a/package.json +++ b/package.json @@ -6,7 +6,7 @@ "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", - "ihe.iti.balp": "1.1.3" + "ihe.iti.pcf": "1.1.0" }, "fhirVersions": [ "4.0.1" From 20e5991ac4a159488b8528114365f4f737e06c25 Mon Sep 17 00:00:00 2001 From: KazeemHamzat Date: Fri, 5 Sep 2025 15:50:42 +0100 Subject: [PATCH 10/10] Testing "ihe.iti.pcf": "1.0.0-comment" Testing "ihe.iti.pcf": "1.0.0-comment" --- fhirpkg.lock.json | 7 ++++--- package.json | 3 ++- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/fhirpkg.lock.json b/fhirpkg.lock.json index 92a09196..445b05cd 100644 --- a/fhirpkg.lock.json +++ b/fhirpkg.lock.json @@ -1,14 +1,15 @@ { - "updated": "2025-09-05T15:43:25.6984082+01:00", + "updated": "2025-09-05T15:50:23.3766758+01:00", "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.terminology.r4": "5.3.0", "hl7.fhir.uv.extensions.r4": "1.0.0", - "ihe.iti.pcf": "1.1.0", + "ihe.iti.pcf": "1.0.0-comment", + "hl7.fhir.r4b.core": "4.3.0", "us.nlm.vsac": "0.9.0", - "ihe.iti.balp": "1.1.3" + "ihe.iti.balp": "1.1.1" }, "missing": {} } diff --git a/package.json b/package.json index f44384d5..9f273180 100644 --- a/package.json +++ b/package.json @@ -6,7 +6,8 @@ "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", - "ihe.iti.pcf": "1.1.0" + "ihe.iti.pcf": "1.0.0-comment" + }, "fhirVersions": [ "4.0.1"