From c9692c642e40a8d2aa7905a3fc2eebaf483830d0 Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Wed, 3 Jun 2026 10:23:32 +0100 Subject: [PATCH 01/80] Remove hl7.fhir.uv.extensions.r4 \7 \uv.tools Remove hl7.fhir.uv.extensions.r4 \7 \uv.tools --- fhirpkg.lock.json | 4 +--- package.json | 2 -- 2 files changed, 1 insertion(+), 5 deletions(-) diff --git a/fhirpkg.lock.json b/fhirpkg.lock.json index df3c15f..1e25899 100644 --- a/fhirpkg.lock.json +++ b/fhirpkg.lock.json @@ -1,8 +1,7 @@ { "updated": "2026-05-06T10:21:55.9845039+01:00", "dependencies": { - "hl7.fhir.r4.core": "4.0.1", - "hl7.fhir.uv.extensions.r4": "5.3.0-ballot-tc1", +"hl7.fhir.r4.core": "4.0.1", "hl7.fhir.uv.xver-r5.r4": "0.1.0", "hl7.fhir.uv.genomics-reporting": "3.0.0", "hl7.fhir.uv.ips": "2.0.0", @@ -10,7 +9,6 @@ "ihe.iti.pcf": "1.1.0", "hl7.fhir.us.mcode": "4.0.0", "fhir.r4.nhsengland.pathology": "0.1.4-alpha", - "hl7.fhir.uv.tools.r4": "1.1.2", "fhir.r4.nhsengland.nhse-identifiers": "0.1.1-alpha", "fhir.r4.ukcore.stu3.currentbuild": "0.28.0-pre-release" }, diff --git a/package.json b/package.json index b104930..f22152d 100644 --- a/package.json +++ b/package.json @@ -4,7 +4,6 @@ "author": "nhsdigital", "dependencies": { "hl7.fhir.r4.core": "4.0.1", - "hl7.fhir.uv.extensions.r4": "5.3.0-ballot-tc1", "hl7.fhir.uv.xver-r5.r4": "0.1.0", "hl7.fhir.uv.genomics-reporting": "3.0.0", "hl7.fhir.uv.ips": "2.0.0", @@ -12,7 +11,6 @@ "ihe.iti.pcf": "1.1.0", "hl7.fhir.us.mcode": "4.0.0", "fhir.r4.nhsengland.pathology": "0.1.4-alpha", - "hl7.fhir.uv.tools.r4": "1.1.2", "fhir.r4.nhsengland.nhse-identifiers": "0.1.1-alpha", "fhir.r4.ukcore.stu3.currentbuild": "0.28.0-pre-release" }, From 8f661f3890c4631f4dfc6505120d46fe83870063 Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Wed, 3 Jun 2026 10:35:25 +0100 Subject: [PATCH 02/80] Removing all Dependencies Removing all Dependencies --- fhirpkg.lock.json | 11 +---------- package.json | 11 +---------- 2 files changed, 2 insertions(+), 20 deletions(-) diff --git a/fhirpkg.lock.json b/fhirpkg.lock.json index 1e25899..a137f0b 100644 --- a/fhirpkg.lock.json +++ b/fhirpkg.lock.json @@ -1,16 +1,7 @@ { "updated": "2026-05-06T10:21:55.9845039+01:00", "dependencies": { -"hl7.fhir.r4.core": "4.0.1", - "hl7.fhir.uv.xver-r5.r4": "0.1.0", - "hl7.fhir.uv.genomics-reporting": "3.0.0", - "hl7.fhir.uv.ips": "2.0.0", - "hl7.fhir.eu.laboratory": "0.1.1", - "ihe.iti.pcf": "1.1.0", - "hl7.fhir.us.mcode": "4.0.0", - "fhir.r4.nhsengland.pathology": "0.1.4-alpha", - "fhir.r4.nhsengland.nhse-identifiers": "0.1.1-alpha", - "fhir.r4.ukcore.stu3.currentbuild": "0.28.0-pre-release" + }, "missing": {} } diff --git a/package.json b/package.json index f22152d..a962bce 100644 --- a/package.json +++ b/package.json @@ -3,16 +3,7 @@ "description": "FHIR Genomics Implementation Guide", "author": "nhsdigital", "dependencies": { - "hl7.fhir.r4.core": "4.0.1", - "hl7.fhir.uv.xver-r5.r4": "0.1.0", - "hl7.fhir.uv.genomics-reporting": "3.0.0", - "hl7.fhir.uv.ips": "2.0.0", - "hl7.fhir.eu.laboratory": "0.1.1", - "ihe.iti.pcf": "1.1.0", - "hl7.fhir.us.mcode": "4.0.0", - "fhir.r4.nhsengland.pathology": "0.1.4-alpha", - "fhir.r4.nhsengland.nhse-identifiers": "0.1.1-alpha", - "fhir.r4.ukcore.stu3.currentbuild": "0.28.0-pre-release" + }, "fhirVersions": [ "4.0.1" From 14a756f2ee73924457db263e8ee65ffd2965c415 Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Wed, 3 Jun 2026 10:41:48 +0100 Subject: [PATCH 03/80] Adding Base R4 Adding Base R4 --- fhirpkg.lock.json | 5 +++-- package.json | 5 +++-- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/fhirpkg.lock.json b/fhirpkg.lock.json index a137f0b..87a783c 100644 --- a/fhirpkg.lock.json +++ b/fhirpkg.lock.json @@ -1,7 +1,8 @@ { "updated": "2026-05-06T10:21:55.9845039+01:00", "dependencies": { - + "hl7.fhir.r4.core": "4.0.1", + "fhir.r4.ukcore.stu3.currentbuild": "0.28.0-pre-release" }, "missing": {} -} +} \ No newline at end of file diff --git a/package.json b/package.json index a962bce..bbeec8b 100644 --- a/package.json +++ b/package.json @@ -3,10 +3,11 @@ "description": "FHIR Genomics Implementation Guide", "author": "nhsdigital", "dependencies": { - + "hl7.fhir.r4.core": "4.0.1", + "fhir.r4.ukcore.stu3.currentbuild": "0.28.0-pre-release" }, "fhirVersions": [ "4.0.1" ], "jurisdiction": "urn:iso:std:iso:3166:-2#GB" -} +} \ No newline at end of file From 9600da1bf74a8f6f1ff8594b47498d0ad57e076d Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Wed, 3 Jun 2026 10:49:56 +0100 Subject: [PATCH 04/80] Update CapabilityStatement-genomics-requirements Update CapabilityStatement-genomics-requirements --- .../CapabilityStatement-genomics-requirements.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CapabilityStatement/CapabilityStatement-genomics-requirements.json b/CapabilityStatement/CapabilityStatement-genomics-requirements.json index 718e6ed..250cffb 100644 --- a/CapabilityStatement/CapabilityStatement-genomics-requirements.json +++ b/CapabilityStatement/CapabilityStatement-genomics-requirements.json @@ -45,7 +45,7 @@ }, { "type": "DocumentReference", - "profile": "https://fhir.nhs.uk/StructureDefinition/NHSEngland-DocumentReference-GenomicDataFile + "profile": "https://fhir.nhs.uk/StructureDefinition/NHSEngland-DocumentReference-GenomicDataFile" }, { "type": "CodeSystem", From 32aec2c6d6c51c92c189e26ef3b1731b34ec046e Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Wed, 3 Jun 2026 11:02:51 +0100 Subject: [PATCH 05/80] Added Genomics reporting & EU_Lab Added Genomics reporting & EU_Lab --- fhirpkg.lock.json | 4 +++- package.json | 4 +++- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/fhirpkg.lock.json b/fhirpkg.lock.json index 87a783c..c5747ec 100644 --- a/fhirpkg.lock.json +++ b/fhirpkg.lock.json @@ -2,7 +2,9 @@ "updated": "2026-05-06T10:21:55.9845039+01:00", "dependencies": { "hl7.fhir.r4.core": "4.0.1", - "fhir.r4.ukcore.stu3.currentbuild": "0.28.0-pre-release" + "fhir.r4.ukcore.stu3.currentbuild": "0.28.0-pre-release", + "hl7.fhir.uv.genomics-reporting": "3.0.0", + "hl7.fhir.eu.laboratory": "0.1.1" }, "missing": {} } \ No newline at end of file diff --git a/package.json b/package.json index bbeec8b..30fcac6 100644 --- a/package.json +++ b/package.json @@ -4,7 +4,9 @@ "author": "nhsdigital", "dependencies": { "hl7.fhir.r4.core": "4.0.1", - "fhir.r4.ukcore.stu3.currentbuild": "0.28.0-pre-release" + "fhir.r4.ukcore.stu3.currentbuild": "0.28.0-pre-release", + "hl7.fhir.uv.genomics-reporting": "3.0.0", + "hl7.fhir.eu.laboratory": "0.1.1" }, "fhirVersions": [ "4.0.1" From 470d0b6a1f1e8484b7b8b3ba8f96ed0f9d21a1c0 Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Wed, 3 Jun 2026 11:15:36 +0100 Subject: [PATCH 06/80] Setting Eu-lab to "0.1.0-ballot" Setting Eu-lab to "0.1.0-ballot" --- fhirpkg.lock.json | 3 ++- package.json | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/fhirpkg.lock.json b/fhirpkg.lock.json index c5747ec..9a4e92f 100644 --- a/fhirpkg.lock.json +++ b/fhirpkg.lock.json @@ -2,9 +2,10 @@ "updated": "2026-05-06T10:21:55.9845039+01:00", "dependencies": { "hl7.fhir.r4.core": "4.0.1", + "hl7.fhir.uv.xver-r5.r4": "0.1.0", "fhir.r4.ukcore.stu3.currentbuild": "0.28.0-pre-release", "hl7.fhir.uv.genomics-reporting": "3.0.0", - "hl7.fhir.eu.laboratory": "0.1.1" + "hl7.fhir.eu.laboratory": "0.1.0-ballot" }, "missing": {} } \ No newline at end of file diff --git a/package.json b/package.json index 30fcac6..98ef381 100644 --- a/package.json +++ b/package.json @@ -4,9 +4,10 @@ "author": "nhsdigital", "dependencies": { "hl7.fhir.r4.core": "4.0.1", + "hl7.fhir.uv.xver-r5.r4": "0.1.0", "fhir.r4.ukcore.stu3.currentbuild": "0.28.0-pre-release", "hl7.fhir.uv.genomics-reporting": "3.0.0", - "hl7.fhir.eu.laboratory": "0.1.1" + "hl7.fhir.eu.laboratory": "0.1.0-ballot" }, "fhirVersions": [ "4.0.1" From 682ff105a42f5db63b49ba849fb72220cd2de337 Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Wed, 3 Jun 2026 11:29:20 +0100 Subject: [PATCH 07/80] Update EU-Lab to 2..0.0 Update EU-Lab to 2..0.0 --- 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 9a4e92f..c2dfd50 100644 --- a/fhirpkg.lock.json +++ b/fhirpkg.lock.json @@ -5,7 +5,7 @@ "hl7.fhir.uv.xver-r5.r4": "0.1.0", "fhir.r4.ukcore.stu3.currentbuild": "0.28.0-pre-release", "hl7.fhir.uv.genomics-reporting": "3.0.0", - "hl7.fhir.eu.laboratory": "0.1.0-ballot" + "hl7.fhir.eu.laboratory": "2.0.0" }, "missing": {} } \ No newline at end of file diff --git a/package.json b/package.json index 98ef381..0cbe611 100644 --- a/package.json +++ b/package.json @@ -7,7 +7,7 @@ "hl7.fhir.uv.xver-r5.r4": "0.1.0", "fhir.r4.ukcore.stu3.currentbuild": "0.28.0-pre-release", "hl7.fhir.uv.genomics-reporting": "3.0.0", - "hl7.fhir.eu.laboratory": "0.1.0-ballot" + "hl7.fhir.eu.laboratory": "2.0.0" }, "fhirVersions": [ "4.0.1" From d52e8878978f048b77bf7bf5712ebc433628d842 Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Wed, 3 Jun 2026 17:13:24 +0100 Subject: [PATCH 08/80] Feedback Issues Feedback Issues --- .../ConceptMap-Genomics-chromosomal-sex.json | 6 +++--- ...omics-fetal-maternal-screening-genotype.json | 6 +++--- ...isk-reason-for-specimen-specialhandling.json | 6 +++--- Patient/Patient-PheobeSmitham-Example.json | 2 +- ...England-Composition-GenomicsEULabReport.json | 16 ++++++++++++---- ...SEngland-DiagnosticReport-GenomicReport.json | 10 ++-------- .../NHSEngland-Patient-Genomics.json | 7 ++----- .../NHSEngland-ServiceRequest-Genomics.json | 7 ++----- .../NHSEngland-Specimen-Genomics.json | 17 ++--------------- fhirpkg.lock.json | 2 +- package.json | 2 +- 11 files changed, 32 insertions(+), 49 deletions(-) diff --git a/ConceptMap/ConceptMap-Genomics-chromosomal-sex.json b/ConceptMap/ConceptMap-Genomics-chromosomal-sex.json index b69bc8a..d86a701 100644 --- a/ConceptMap/ConceptMap-Genomics-chromosomal-sex.json +++ b/ConceptMap/ConceptMap-Genomics-chromosomal-sex.json @@ -2,11 +2,11 @@ "resourceType": "ConceptMap", "id": "genomics-chromosomal-sex", "url": "https://fhir.nhs.uk/ConceptMap/genomics-chromosomal-sex", - "version": "0.1.0", + "version": "0.2.0", "name": "GenomicsChromosomalSex", "title": "Genomics Chromosomal Sex", "status": "draft", - "date": "2025-09-05T10:33:00.000Z", + "date": "2026-06-03T00:00:00.000Z", "publisher": "NHS England", "contact": [ { @@ -22,7 +22,7 @@ "description": "A ConceptMap used for the translation and recording of concepts from MDS source data(code-options) to equivalent Snomed CT codes, and FHIR spec.", "purpose": "ConceptMap used for the translation and recording of chromosomal sex. This is intended for the element Observation.code. An appropriate SNOMED CT code or free text should be used to record the sex of other is selected.", "copyright": "Copyright © 2025+ NHS England Licensed under the Apache License, Version 2.0 (the \\\"License\\\"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \\\"AS IS\\\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. HL7® FHIR® standard Copyright © 2011+ HL7 The HL7® FHIR® standard is used under the FHIR license. You may obtain a copy of the FHIR license at https://www.hl7.org/fhir/license.html.", - "targetUri": "http://snomed.info/sct", + "targetUri": "http://snomed.info/sct?fhir_vs", "group": [ { "source": "https://future.nhs.uk/NHSgenomics/view?objectId=222250117", diff --git a/ConceptMap/ConceptMap-Genomics-fetal-maternal-screening-genotype.json b/ConceptMap/ConceptMap-Genomics-fetal-maternal-screening-genotype.json index 80049a7..bf1f22d 100644 --- a/ConceptMap/ConceptMap-Genomics-fetal-maternal-screening-genotype.json +++ b/ConceptMap/ConceptMap-Genomics-fetal-maternal-screening-genotype.json @@ -2,11 +2,11 @@ "resourceType": "ConceptMap", "id": "genomics-fetal-maternal-screening-genotype", "url": "https://fhir.nhs.uk/ConceptMap/genomics-fetal-maternal-screening-genotype", - "version": "0.3.0", + "version": "0.4.0", "name": "GenomicsFetalMaternalScreeningGenotype", "title": "Genomics Fetal Maternal Screening Genotype", "status": "draft", - "date": "2025-10-05T21:00:00.000Z", + "date": "2026-06-03T00:00:00.000Z", "publisher": "NHS England", "contact": [ { @@ -22,7 +22,7 @@ "description": "A ConceptMap used for the translation and recording of concepts from MDS source data(code-options) to equivalent Snomed CT codes, and FHIR spec.", "purpose": "ConceptMap used for the translation and recording of concepts for fetal maternal screening genotype. This is intended for the element Condition.code. An appropriate SNOMED CT code or free text should be used to record the Genotype.", "copyright": "Copyright © 2023+ NHS England Licensed under the Apache License, Version 2.0 (the \\\"License\\\"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \\\"AS IS\\\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. HL7® FHIR® standard Copyright © 2011+ HL7 The HL7® FHIR® standard is used under the FHIR license. You may obtain a copy of the FHIR license at https://www.hl7.org/fhir/license.html.", - "targetUri": "http://snomed.info/sct", + "targetUri": "http://snomed.info/sct?fhir_vs", "group": [ { "source": "https://future.nhs.uk/NHSgenomics/view?objectId=222250117", diff --git a/ConceptMap/ConceptMap-Genomics-risk-reason-for-specimen-specialhandling.json b/ConceptMap/ConceptMap-Genomics-risk-reason-for-specimen-specialhandling.json index e9825b3..e08cddb 100644 --- a/ConceptMap/ConceptMap-Genomics-risk-reason-for-specimen-specialhandling.json +++ b/ConceptMap/ConceptMap-Genomics-risk-reason-for-specimen-specialhandling.json @@ -2,11 +2,11 @@ "resourceType": "ConceptMap", "id": "genomics-risk-reason-for-specimen-specialhandling", "url": "https://fhir.nhs.uk/ConceptMap/genomics-risk-reason-for-specimen-specialhandling", - "version": "0.3.0", + "version": "0.4.0", "name": "GenomicsRiskReasonForSpecimenSpecialHandling", "title": "Genomics Risk Reason for Specimen Special Handling", "status": "draft", - "date": "2025-09-05T11:00:00.000Z", + "date": "2026-06-03T00:00:00.000Z", "publisher": "NHS England", "contact": [ { @@ -22,7 +22,7 @@ "description": "A ConceptMap used for the translation and recording of concepts from MDS source data(code-options) to equivalent Snomed CT codes, and FHIR spec.", "purpose": "ConceptMap used for the translation and recording of the risk reason for specimen special handling . This is intended for the element Specimen.collection.extension:specimen-specialHandling.valueCoding.code", "copyright": "Copyright © 2023+ NHS England Licensed under the Apache License, Version 2.0 (the \\\"License\\\"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \\\"AS IS\\\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. HL7® FHIR® standard Copyright © 2011+ HL7 The HL7® FHIR® standard is used under the FHIR license. You may obtain a copy of the FHIR license at https://www.hl7.org/fhir/license.html.", - "targetUri": "http://snomed.info/sct", + "targetUri": "http://snomed.info/sct?fhir_vs", "group": [ { "source": "https://future.nhs.uk/NHSgenomics/view?objectId=222250117", diff --git a/Patient/Patient-PheobeSmitham-Example.json b/Patient/Patient-PheobeSmitham-Example.json index 181eb7c..94281a7 100644 --- a/Patient/Patient-PheobeSmitham-Example.json +++ b/Patient/Patient-PheobeSmitham-Example.json @@ -4,7 +4,7 @@ "meta": { "profile": [ "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Patient", - "http://hl7.eu/fhir/laboratory/StructureDefinition/Patient-eu-lab" + "http://hl7.eu/fhir/laboratory/StructureDefinition/Patient-animal-eu-lab" ] }, "extension": [ diff --git a/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json b/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json index c31e397..ffd9207 100644 --- a/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json +++ b/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json @@ -2,11 +2,11 @@ "resourceType": "StructureDefinition", "id": "NHSEngland-Composition-GenomicsEULabReport", "url": "https://fhir.nhs.uk/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport", - "version": "0.3.0", + "version": "0.4.0", "name": "NHSEngland_Composition_GenomicsEULabReport", "title": "NHSEngland Composition GenomicsEULabReport", "status": "active", - "date": "2026-04-16", + "date": "2026-06-03", "publisher": "NHS England", "contact": [ { @@ -46,7 +46,6 @@ { "code": "Reference", "targetProfile": [ - "https://fhir.nhs.uk/StructureDefinition/NHSEngland-ServiceRequest-Genomics", "http://hl7.eu/fhir/laboratory/StructureDefinition/ServiceRequest-eu-lab" ], "aggregation": [ @@ -175,6 +174,11 @@ "id": "Composition.category", "path": "Composition.category", "slicing": { + "discriminator": [ + { + "type": "pattern", + "path": "$this" + }], "rules": "open" }, "definition": "Fixed codes for conformance to the EU Lab Composition profile (for cross border sharing of lab reports)." @@ -235,7 +239,6 @@ { "code": "Reference", "targetProfile": [ - "https://fhir.nhs.uk/StructureDefinition/NHSEngland-Patient-Genomics", "http://hl7.eu/fhir/laboratory/StructureDefinition/Patient-eu-lab", "http://hl7.eu/fhir/laboratory/StructureDefinition/Patient-animal-eu-lab", "http://hl7.org/fhir/StructureDefinition/Group", @@ -269,6 +272,11 @@ "id": "Composition.section", "path": "Composition.section", "slicing": { + "discriminator": [ + { + "type": "pattern", + "path": "$this" + }], "rules": "open" }, "definition": "To conform to EU Lab, SHOULD include references to the results that form part of the genomic report. For the UGR, will include sections that conform to the UGR folders, this work is currently in development." diff --git a/StructureDefinition/NHSEngland-DiagnosticReport-GenomicReport.json b/StructureDefinition/NHSEngland-DiagnosticReport-GenomicReport.json index abcc4ca..57f184f 100644 --- a/StructureDefinition/NHSEngland-DiagnosticReport-GenomicReport.json +++ b/StructureDefinition/NHSEngland-DiagnosticReport-GenomicReport.json @@ -2,11 +2,11 @@ "resourceType": "StructureDefinition", "id": "NHSEngland-DiagnosticReport-GenomicReport", "url": "https://fhir.nhs.uk/StructureDefinition/NHSEngland-DiagnosticReport-GenomicReport", - "version": "0.3.0", + "version": "0.4.0", "name": "NHSEngland_DiagnosticReport_GenomicReport", "title": "NHSEngland DiagnosticReport GenomicReport", "status": "active", - "date": "2026-04-16", + "date": "2026-06-03", "publisher": "NHS England", "contact": [ { @@ -169,7 +169,6 @@ { "code": "Reference", "targetProfile": [ - "https://fhir.nhs.uk/StructureDefinition/NHSEngland-ServiceRequest-Genomics", "http://hl7.org/fhir/StructureDefinition/CarePlan", "http://hl7.org/fhir/StructureDefinition/ImmunizationRecommendation", "http://hl7.org/fhir/StructureDefinition/MedicationRequest", @@ -245,7 +244,6 @@ { "code": "Reference", "targetProfile": [ - "https://fhir.nhs.uk/StructureDefinition/NHSEngland-Patient-Genomics", "http://hl7.org/fhir/StructureDefinition/Patient", "http://hl7.org/fhir/StructureDefinition/Group", "http://hl7.org/fhir/StructureDefinition/Device", @@ -270,7 +268,6 @@ { "code": "Reference", "targetProfile": [ - "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Organization", "http://hl7.org/fhir/StructureDefinition/Practitioner", "http://hl7.org/fhir/StructureDefinition/PractitionerRole", "http://hl7.org/fhir/StructureDefinition/Organization", @@ -306,7 +303,6 @@ { "code": "Reference", "targetProfile": [ - "https://fhir.nhs.uk/StructureDefinition/NHSEngland-PractitionerRole-Genomics", "http://hl7.org/fhir/StructureDefinition/Practitioner", "http://hl7.org/fhir/StructureDefinition/PractitionerRole", "http://hl7.org/fhir/StructureDefinition/Organization", @@ -328,7 +324,6 @@ { "code": "Reference", "targetProfile": [ - "https://fhir.nhs.uk/StructureDefinition/NHSEngland-Specimen-Genomics", "http://hl7.org/fhir/StructureDefinition/Specimen" ], "aggregation": [ @@ -373,7 +368,6 @@ { "code": "Reference", "targetProfile": [ - "https://fhir.nhs.uk/StructureDefinition/NHSEngland-DocumentReference-Genomics", "http://hl7.org/fhir/StructureDefinition/Resource" ], "aggregation": [ diff --git a/StructureDefinition/NHSEngland-Patient-Genomics.json b/StructureDefinition/NHSEngland-Patient-Genomics.json index 5bee313..5d2c471 100644 --- a/StructureDefinition/NHSEngland-Patient-Genomics.json +++ b/StructureDefinition/NHSEngland-Patient-Genomics.json @@ -2,11 +2,11 @@ "resourceType": "StructureDefinition", "id": "NHSEngland-Patient-Genomics", "url": "https://fhir.nhs.uk/StructureDefinition/NHSEngland-Patient-Genomics", - "version": "0.3.0", + "version": "0.4.0", "name": "NHSEngland_Patient_Genomics", "title": "NHSEngland Patient Genomics", "status": "active", - "date": "2026-04-16", + "date": "2026-06-03", "publisher": "NHS England", "contact": [ { @@ -107,9 +107,6 @@ { "id": "Patient.identifier", "path": "Patient.identifier", - "slicing": { - "rules": "open" - }, "definition": "SHALL be present for Patients within the Genomic Order Management ecosystem. It is preferred that all patients with an NHS number have this included within the Patient resource upon submission of a test order. Patient who do not have an NHS number SHOULD have a temporary one registered/assigned with PDS.\r\nFor patient records where the NHS number has been traced from PDS, the trace status SHOULD be provided within the NHS Number identifier slice.\r\n\r\nAdditional identifiers SHOULD include an appropriate naming system scheme which clearly identifies the assigner (to disambiguate the identifier from other resources where these are not nationally unique). Alternatively, the OID for local identifier MAY be used, with the 'assigner' organization explicitly referenced.", "min": 1 }, diff --git a/StructureDefinition/NHSEngland-ServiceRequest-Genomics.json b/StructureDefinition/NHSEngland-ServiceRequest-Genomics.json index 30c3dfe..2fe0b8f 100644 --- a/StructureDefinition/NHSEngland-ServiceRequest-Genomics.json +++ b/StructureDefinition/NHSEngland-ServiceRequest-Genomics.json @@ -2,11 +2,11 @@ "resourceType": "StructureDefinition", "id": "NHSEngland-ServiceRequest-Genomics", "url": "https://fhir.nhs.uk/StructureDefinition/NHSEngland-ServiceRequest-Genomics", - "version": "0.3.0", + "version": "0.4.0", "name": "NHSEngland_ServiceRequest_Genomics", "title": "NHSEngland ServiceRequest Genomics", "status": "active", - "date": "2026-04-16", + "date": "2026-06-03", "publisher": "NHS England", "contact": [ { @@ -222,9 +222,6 @@ { "id": "ServiceRequest.category", "path": "ServiceRequest.category", - "slicing": { - "rules": "open" - }, "definition": "Category SHALL be populated with the reason for the request being ordered e.g. Diagnostic, Carrier, Predictive, Stored DNA etc. The final list of applicable codes which can be selected is still under review, the Genomic-ReasonforTesting ValueSet SHOULD be used for this categorisation.", "min": 1 }, diff --git a/StructureDefinition/NHSEngland-Specimen-Genomics.json b/StructureDefinition/NHSEngland-Specimen-Genomics.json index 9aadddf..99a6afb 100644 --- a/StructureDefinition/NHSEngland-Specimen-Genomics.json +++ b/StructureDefinition/NHSEngland-Specimen-Genomics.json @@ -2,11 +2,11 @@ "resourceType": "StructureDefinition", "id": "NHSEngland-Specimen-Genomics", "url": "https://fhir.nhs.uk/StructureDefinition/NHSEngland-Specimen-Genomics", - "version": "0.3.0", + "version": "0.4.0", "name": "NHSEngland_Specimen_Genomics", "title": "NHSEngland Specimen Genomics", "status": "active", - "date": "2026-04-16", + "date": "2026-06-03", "publisher": "NHS England", "contact": [ { @@ -302,19 +302,6 @@ "definition": "The UK Core STU3 version of Specimen backports the R5 changes to the container BackboneElement to support capturing of storage location for a sample (through `container.location`) and recursive capture of device identifiers (e.g. tube, well, rack, freezer through `container.device`).\r\nThe container.identifier should match the identifier associated with the barcode for the tube/collection device. This can be searched using the container-id SearchParameter.\r\n\r\nAdditional examples/guidance will be provided within this IG once use of the fields has been appropriately tested.\r\n\r\nSample tracking information SHOULD be added to Tasks acting on Specimen resources, e.g. Tasks marked SamplePreparation or SampleProcessing, on either the output or input elements. This information MAY include consignment number, destination, date sent etc.\r\n\r\nIf known, the container type SHOULD be populated, using the example bound ValueSet, in SNOMED CT. If an appropraite code cannot be found, the specimen container type should be populated using free text, in Specimen.container.type.text. Additional container elements, such as capacity or specimenQuantity MAY be populated if known.", "max": "1" }, - { - "id": "Specimen.container.extension:specimenContainerLocationR5", - "path": "Specimen.container.extension", - "sliceName": "specimenContainerLocationR5", - "type": [ - { - "code": "Extension", - "profile": [ - "http://hl7.org/fhir/5.0/StructureDefinition/extension-Specimen.container.location" - ] - } - ] - }, { "id": "Specimen.condition", "path": "Specimen.condition", diff --git a/fhirpkg.lock.json b/fhirpkg.lock.json index c2dfd50..b06f07f 100644 --- a/fhirpkg.lock.json +++ b/fhirpkg.lock.json @@ -5,7 +5,7 @@ "hl7.fhir.uv.xver-r5.r4": "0.1.0", "fhir.r4.ukcore.stu3.currentbuild": "0.28.0-pre-release", "hl7.fhir.uv.genomics-reporting": "3.0.0", - "hl7.fhir.eu.laboratory": "2.0.0" + "hl7.fhir.eu.laboratory": "0.1.1" }, "missing": {} } \ No newline at end of file diff --git a/package.json b/package.json index 0cbe611..a40f0b3 100644 --- a/package.json +++ b/package.json @@ -7,7 +7,7 @@ "hl7.fhir.uv.xver-r5.r4": "0.1.0", "fhir.r4.ukcore.stu3.currentbuild": "0.28.0-pre-release", "hl7.fhir.uv.genomics-reporting": "3.0.0", - "hl7.fhir.eu.laboratory": "2.0.0" + "hl7.fhir.eu.laboratory": "0.1.1" }, "fhirVersions": [ "4.0.1" From 0c7d7dbec8c0a3b6a912af573abf1c20afff53c9 Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Wed, 3 Jun 2026 17:35:17 +0100 Subject: [PATCH 09/80] Update EU-Lab to 2..0.0 Update EU-Lab to 2..0.0 --- 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 b06f07f..c2dfd50 100644 --- a/fhirpkg.lock.json +++ b/fhirpkg.lock.json @@ -5,7 +5,7 @@ "hl7.fhir.uv.xver-r5.r4": "0.1.0", "fhir.r4.ukcore.stu3.currentbuild": "0.28.0-pre-release", "hl7.fhir.uv.genomics-reporting": "3.0.0", - "hl7.fhir.eu.laboratory": "0.1.1" + "hl7.fhir.eu.laboratory": "2.0.0" }, "missing": {} } \ No newline at end of file diff --git a/package.json b/package.json index a40f0b3..0cbe611 100644 --- a/package.json +++ b/package.json @@ -7,7 +7,7 @@ "hl7.fhir.uv.xver-r5.r4": "0.1.0", "fhir.r4.ukcore.stu3.currentbuild": "0.28.0-pre-release", "hl7.fhir.uv.genomics-reporting": "3.0.0", - "hl7.fhir.eu.laboratory": "0.1.1" + "hl7.fhir.eu.laboratory": "2.0.0" }, "fhirVersions": [ "4.0.1" From fa10dd24a1499c1abfb4ab3a37db8de3a750b447 Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Wed, 3 Jun 2026 18:02:45 +0100 Subject: [PATCH 10/80] Remove R5 Extension and References Remove R5 Extension and References --- ...HSEngland-Composition-GenomicsEULabReport.json | 4 ++-- ...NHSEngland-DiagnosticReport-GenomicReport.json | 15 --------------- ...England-DocumentReference-GenomicDataFile.json | 3 --- 3 files changed, 2 insertions(+), 20 deletions(-) diff --git a/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json b/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json index ffd9207..f14c3aa 100644 --- a/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json +++ b/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json @@ -176,7 +176,7 @@ "slicing": { "discriminator": [ { - "type": "pattern", + "type": "value", "path": "$this" }], "rules": "open" @@ -239,7 +239,7 @@ { "code": "Reference", "targetProfile": [ - "http://hl7.eu/fhir/laboratory/StructureDefinition/Patient-eu-lab", + "http://hl7.eu/fhir/base/StructureDefinition/patient-eu-core", "http://hl7.eu/fhir/laboratory/StructureDefinition/Patient-animal-eu-lab", "http://hl7.org/fhir/StructureDefinition/Group", "http://hl7.org/fhir/StructureDefinition/Location", diff --git a/StructureDefinition/NHSEngland-DiagnosticReport-GenomicReport.json b/StructureDefinition/NHSEngland-DiagnosticReport-GenomicReport.json index 57f184f..08da2eb 100644 --- a/StructureDefinition/NHSEngland-DiagnosticReport-GenomicReport.json +++ b/StructureDefinition/NHSEngland-DiagnosticReport-GenomicReport.json @@ -61,21 +61,6 @@ "path": "DiagnosticReport.extension.value[x].type", "fixedCode": "citation" }, - { - "id": "DiagnosticReport.extension:diagnosticReportCompositionR5", - "path": "DiagnosticReport.extension", - "sliceName": "diagnosticReportCompositionR5", - "definition": "TBC. Only relevant for EU Lab aligned reports (included in HL7 EU Laboratory Report: DiagnosticReport Profile). A reference to the Composition which wraps this report for data sharing.", - "type": [ - { - "code": "Extension", - "profile": [ - "http://hl7.org/fhir/5.0/StructureDefinition/extension-DiagnosticReport.composition" - ] - } - ], - "isModifier": false - }, { "id": "DiagnosticReport.identifier", "path": "DiagnosticReport.identifier", diff --git a/StructureDefinition/NHSEngland-DocumentReference-GenomicDataFile.json b/StructureDefinition/NHSEngland-DocumentReference-GenomicDataFile.json index ba1c44d..80aad78 100644 --- a/StructureDefinition/NHSEngland-DocumentReference-GenomicDataFile.json +++ b/StructureDefinition/NHSEngland-DocumentReference-GenomicDataFile.json @@ -118,9 +118,6 @@ { "code": "Reference", "targetProfile": [ - "https://fhir.nhs.uk/StructureDefinition/NHSEngland-Specimen-Genomics", - "https://fhir.nhs.uk/StructureDefinition/NHSEngland-DiagnosticReport-GenomicReport", - "https://fhir.nhs.uk/StructureDefinition/NHSEngland-ServiceRequest-Genomics", "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report" ], "aggregation": [ From d657bcde558fee2fdcda5999b73f8e328e3b0825 Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Wed, 3 Jun 2026 19:11:29 +0100 Subject: [PATCH 11/80] EU Lab 2.0.0 - ci-build 150 Cardinality issues: https://hl7.eu/fhir/laboratory/StructureDefinition-Composition-eu-lab.html --- ...omposition-EULabGenomicReport-Example.json | 196 +++--- ...gland-Composition-GenomicsEULabReport.json | 629 +++++++++--------- ...ngland-DiagnosticReport-GenomicReport.json | 3 - custom.rules.yaml | 2 + 4 files changed, 430 insertions(+), 400 deletions(-) diff --git a/Composition/Composition-EULabGenomicReport-Example.json b/Composition/Composition-EULabGenomicReport-Example.json index 4455a29..75ffbd6 100644 --- a/Composition/Composition-EULabGenomicReport-Example.json +++ b/Composition/Composition-EULabGenomicReport-Example.json @@ -1,98 +1,128 @@ { - "resourceType": "Composition", - "id": "Composition-EULabGenomicReport-Example", - "meta": { - "profile": [ - "http://hl7.eu/fhir/laboratory/StructureDefinition/Composition-eu-lab" - ] + "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" + } }, - "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" + } + } + ], + "identifier": { + "system": "https://fhir.nhs.uk/Id/genomic-report", + "value": "GR-12345" + }, + "status": "final", + "type": { + "coding": [ + { + "system": "http://loinc.org", + "code": "51969-4", + "display": "Genetic analysis report" + } + ] + }, + "category": [ + { + "coding": [ { - "url": "http://hl7.eu/fhir/StructureDefinition/information-recipient", - "valueReference": { - "reference": "PractitionerRole/PractitionerRole-EugeneSmith-Example" - } - }, + "system": "http://loinc.org", + "code": "26436-6", + "display": "Laboratory studies (set)" + } + ] + }, + { + "coding": [ { - "url": "http://hl7.eu/fhir/laboratory/StructureDefinition/composition-diagnosticReportReference", - "valueReference": { - "reference": "DiagnosticReport/DiagnosticReport-GenomicVariantAssessment-Example" - } + "system": "http://snomed.info/sct", + "code": "1236877003", + "display": "Genetic pathology" } - ], - "status": "final", - "type": { + ] + } + ], + "subject": { + "reference": "Patient/Patient-PheobeSmitham-Example", + "identifier": { + "system": "https://fhir.nhs.uk/Id/nhs-number", + "value": "9449307539" + } + }, + "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": "51969-4", - "display": "Genetic analysis report" - } + { + "system": "http://loinc.org", + "code": "26436-6", + "display": "Laboratory studies (set)" + } ] - }, - "category": [ + }, + "section": [ { + "title": "Results", + "text": { + "status": "generated", + "div": "
Genomic findings.
" + }, + "code": { "coding": [ - { - "system": "http://loinc.org", - "code": "26436-6", - "display": "Laboratory studies (set)" - } - ] - }, - { - "coding": [ - { - "system": "http://snomed.info/sct", - "code": "1236877003", - "display": "Genetic pathology" - } + { + "system": "http://loinc.org", + "code": "26436-6", + "display": "Laboratory studies (set)" + } ] - } - ], - "subject": { - "reference": "Patient/Patient-PheobeSmitham-Example", - "identifier": { - "system": "https://fhir.nhs.uk/Id/nhs-number", - "value": "9449307539" - } - }, - "date": "2023-10-16T00:00:00-05:00", - "author": [ - { - "identifier": { - "system": "https://fhir.nhs.uk/Id/ods-organization-code", - "value": "R0A" + }, + "entry": [ + { + "reference": "Observation/Observation-GenomicTherapeuticImplication-Example" + }, + { + "reference": "Observation/Observation-GenomicsVariantSLC52A2-Example" } + ] } - ], - "title": "Example Genomic Laboratory (Single) Report", - "section": [ + ], + "entry": [ { - "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" - } - ] + "reference": "Observation/Observation-GenomicTherapeuticImplication-Example" + }, + { + "reference": "Observation/Observation-GenomicsVariantSLC52A2-Example" } - ] + ] + } + ] } \ No newline at end of file diff --git a/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json b/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json index f14c3aa..0b2f06d 100644 --- a/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json +++ b/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json @@ -1,321 +1,322 @@ { - "resourceType": "StructureDefinition", - "id": "NHSEngland-Composition-GenomicsEULabReport", - "url": "https://fhir.nhs.uk/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport", - "version": "0.4.0", - "name": "NHSEngland_Composition_GenomicsEULabReport", - "title": "NHSEngland Composition GenomicsEULabReport", - "status": "active", - "date": "2026-06-03", - "publisher": "NHS England", - "contact": [ + "resourceType": "StructureDefinition", + "id": "NHSEngland-Composition-GenomicsEULabReport", + "url": "https://fhir.nhs.uk/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport", + "version": "0.4.0", + "name": "NHSEngland_Composition_GenomicsEULabReport", + "title": "NHSEngland Composition GenomicsEULabReport", + "status": "active", + "date": "2026-06-03", + "publisher": "NHS England", + "contact": [ + { + "name": "NHS England", + "telecom": [ { - "name": "NHS England", - "telecom": [ - { - "system": "email", - "value": "interoperabilityteam@nhs.net", - "use": "work", - "rank": 1 - } + "system": "email", + "value": "interoperabilityteam@nhs.net", + "use": "work", + "rank": 1 + } + ] + } + ], + "description": "This profile defines the Genomics constraints and extensions on the EU Lab FHIR resource [EU Lab Composition](http://hl7.eu/fhir/laboratory/StructureDefinition/Composition-eu-lab).", + "purpose": "There are two use cases for Compositions within Genomics.\r\n\r\nFor Order Management, Compositions will be limited to documents generated by the central broker for capturing snapshots of Test orders and results in order to maintain historical accuracy, as per the DocumentReference generate OperationDefinition. These will typically form the first entry of a Document Bundle and as such will not be exposed via their own endpoint, nor allow creates, reads or updates from client systems on the resource itself.\r\n\r\nTo support cross border data sharing Compositions MAY be aligned to the HL7 EU Lab Composition profile as a wrap around structured reports.\r\n\r\nFor the Unified Genomic Record, Compositions will form the header or 'contents page' of the UGR itself. section elements will be used to emulate the UGR folders. ", + "copyright": "Copyright © 2026+ NHS England Licensed under the Apache License, Version 2.0 (the \\\\\\\"License\\\\\\\"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \\\\\\\"AS IS\\\\\\\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. HL7® FHIR® standard Copyright © 2011+ HL7 The HL7® FHIR® standard is used under the FHIR license. You may obtain a copy of the FHIR license at https://www.hl7.org/fhir/license.html.", + "fhirVersion": "4.0.1", + "kind": "resource", + "abstract": false, + "type": "Composition", + "baseDefinition": "http://hl7.eu/fhir/laboratory/StructureDefinition/Composition-eu-lab", + "derivation": "constraint", + "differential": { + "element": [ + { + "id": "Composition.extension:basedOn-order-or-requisition", + "path": "Composition.extension", + "sliceName": "basedOn-order-or-requisition", + "definition": "TBC. Only relevant for EU Lab aligned reports (included in HL7 EU Laboratory Report: Composition Profile). A reference to the ServiceRequest which this report is in response to." + }, + { + "id": "Composition.extension:basedOn-order-or-requisition.value[x]:valueReference", + "path": "Composition.extension.value[x]", + "sliceName": "valueReference", + "type": [ + { + "code": "Reference", + "targetProfile": [ + "http://hl7.eu/fhir/laboratory/StructureDefinition/ServiceRequest-eu-lab" + ], + "aggregation": [ + "referenced", + "bundled" + ] + } + ] + }, + { + "id": "Composition.extension:information-recipient", + "path": "Composition.extension", + "sliceName": "information-recipient", + "definition": "TBC. Only relevant for EU Lab aligned reports (included in HL7 EU Laboratory Report: Composition Profile). A reference to the recipient for a report, could potentially be used to reference additional recipients over the subject and original requester for the request." + }, + { + "id": "Composition.extension:information-recipient.value[x]", + "path": "Composition.extension.value[x]", + "type": [ + { + "code": "Reference", + "targetProfile": [ + "https://fhir.nhs.uk/StructureDefinition/NHSEngland-PractitionerRole-Genomics", + "http://hl7.eu/fhir/laboratory/StructureDefinition/Practitioner-eu-lab", + "http://hl7.org/fhir/StructureDefinition/Device", + "http://hl7.eu/fhir/laboratory/StructureDefinition/Patient-eu-lab", + "http://hl7.org/fhir/StructureDefinition/RelatedPerson", + "http://hl7.eu/fhir/laboratory/StructureDefinition/PractitionerRole-eu-lab", + "http://hl7.org/fhir/StructureDefinition/Organization" + ], + "aggregation": [ + "referenced", + "bundled" ] + } + ] + }, + { + "id": "Composition.extension:diagnosticReport-reference", + "path": "Composition.extension", + "sliceName": "diagnosticReport-reference", + "definition": "TBC. Only relevant for EU Lab aligned reports (included in HL7 EU Laboratory Report: Composition Profile). A reference to the focal DiagnosticReport this Composition is for." + }, + { + "id": "Composition.extension:diagnosticReport-reference.value[x]", + "path": "Composition.extension.value[x]", + "type": [ + { + "code": "Reference", + "targetProfile": [ + "https://fhir.nhs.uk/StructureDefinition/NHSEngland-DiagnosticReport-GenomicReport", + "http://hl7.eu/fhir/laboratory/StructureDefinition/DiagnosticReport-eu-lab" + ], + "aggregation": [ + "referenced", + "bundled" + ] + } + ] + }, + { + "id": "Composition.status", + "path": "Composition.status", + "definition": "Fixed value of 'final'", + "fixedCode": "final" + }, + { + "id": "Composition.type", + "path": "Composition.type", + "definition": "SNOMED CT code for either a Laboratory Request (24691000000102) or Genetic report (1054161000000101)" + }, + { + "id": "Composition.type.coding", + "path": "Composition.type.coding", + "slicing": { + "discriminator": [ + { + "type": "pattern", + "path": "$this" + } + ], + "rules": "open" } - ], - "description": "This profile defines the Genomics constraints and extensions on the EU Lab FHIR resource [EU Lab Composition](http://hl7.eu/fhir/laboratory/StructureDefinition/Composition-eu-lab).", - "purpose": "There are two use cases for Compositions within Genomics.\r\n\r\nFor Order Management, Compositions will be limited to documents generated by the central broker for capturing snapshots of Test orders and results in order to maintain historical accuracy, as per the DocumentReference generate OperationDefinition. These will typically form the first entry of a Document Bundle and as such will not be exposed via their own endpoint, nor allow creates, reads or updates from client systems on the resource itself.\r\n\r\nTo support cross border data sharing Compositions MAY be aligned to the HL7 EU Lab Composition profile as a wrap around structured reports.\r\n\r\nFor the Unified Genomic Record, Compositions will form the header or 'contents page' of the UGR itself. section elements will be used to emulate the UGR folders. ", - "copyright": "Copyright © 2026+ NHS England Licensed under the Apache License, Version 2.0 (the \\\\\\\"License\\\\\\\"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \\\\\\\"AS IS\\\\\\\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. HL7® FHIR® standard Copyright © 2011+ HL7 The HL7® FHIR® standard is used under the FHIR license. You may obtain a copy of the FHIR license at https://www.hl7.org/fhir/license.html.", - "fhirVersion": "4.0.1", - "kind": "resource", - "abstract": false, - "type": "Composition", - "baseDefinition": "http://hl7.eu/fhir/laboratory/StructureDefinition/Composition-eu-lab", - "derivation": "constraint", - "differential": { - "element": [ - { - "id": "Composition.extension:basedOn-order-or-requisition", - "path": "Composition.extension", - "sliceName": "basedOn-order-or-requisition", - "definition": "TBC. Only relevant for EU Lab aligned reports (included in HL7 EU Laboratory Report: Composition Profile). A reference to the ServiceRequest which this report is in response to." - }, - { - "id": "Composition.extension:basedOn-order-or-requisition.value[x]:valueReference", - "path": "Composition.extension.value[x]", - "sliceName": "valueReference", - "type": [ - { - "code": "Reference", - "targetProfile": [ - "http://hl7.eu/fhir/laboratory/StructureDefinition/ServiceRequest-eu-lab" - ], - "aggregation": [ - "referenced", - "bundled" - ] - } - ] - }, - { - "id": "Composition.extension:information-recipient", - "path": "Composition.extension", - "sliceName": "information-recipient", - "definition": "TBC. Only relevant for EU Lab aligned reports (included in HL7 EU Laboratory Report: Composition Profile). A reference to the recipient for a report, could potentially be used to reference additional recipients over the subject and original requester for the request." - }, - { - "id": "Composition.extension:information-recipient.value[x]", - "path": "Composition.extension.value[x]", - "type": [ - { - "code": "Reference", - "targetProfile": [ - "https://fhir.nhs.uk/StructureDefinition/NHSEngland-PractitionerRole-Genomics", - "http://hl7.eu/fhir/laboratory/StructureDefinition/Practitioner-eu-lab", - "http://hl7.org/fhir/StructureDefinition/Device", - "http://hl7.eu/fhir/laboratory/StructureDefinition/Patient-eu-lab", - "http://hl7.org/fhir/StructureDefinition/RelatedPerson", - "http://hl7.eu/fhir/laboratory/StructureDefinition/PractitionerRole-eu-lab", - "http://hl7.org/fhir/StructureDefinition/Organization" - ], - "aggregation": [ - "referenced", - "bundled" - ] - } - ] - }, - { - "id": "Composition.extension:diagnosticReport-reference", - "path": "Composition.extension", - "sliceName": "diagnosticReport-reference", - "definition": "TBC. Only relevant for EU Lab aligned reports (included in HL7 EU Laboratory Report: Composition Profile). A reference to the focal DiagnosticReport this Composition is for." - }, - { - "id": "Composition.extension:diagnosticReport-reference.value[x]", - "path": "Composition.extension.value[x]", - "type": [ - { - "code": "Reference", - "targetProfile": [ - "https://fhir.nhs.uk/StructureDefinition/NHSEngland-DiagnosticReport-GenomicReport", - "http://hl7.eu/fhir/laboratory/StructureDefinition/DiagnosticReport-eu-lab" - ], - "aggregation": [ - "referenced", - "bundled" - ] - } - ] - }, - { - "id": "Composition.status", - "path": "Composition.status", - "definition": "Fixed value of 'final'", - "fixedCode": "final" - }, - { - "id": "Composition.type", - "path": "Composition.type", - "definition": "SNOMED CT code for either a Laboratory Request (24691000000102) or Genetic report (1054161000000101)" - }, - { - "id": "Composition.type.coding", - "path": "Composition.type.coding", - "slicing": { - "discriminator": [ - { - "type": "pattern", - "path": "$this" - } - ], - "rules": "open" - } - }, - { - "id": "Composition.type.coding.display.extension:translation", - "path": "Composition.type.coding.display.extension", - "sliceName": "translation" - }, - { - "id": "Composition.type.coding.display.extension:translation.extension", - "path": "Composition.type.coding.display.extension.extension", - "min": 2 - }, - { - "id": "Composition.type.coding:codingGenomics", - "path": "Composition.type.coding", - "sliceName": "codingGenomics", - "fixedCoding": { - "system": "http://snomed.info/sct", - "code": "1054161000000101", - "display": "Genetic report" - } - }, - { - "id": "Composition.type.coding:codingGenomics.display.extension:translation", - "path": "Composition.type.coding.display.extension", - "sliceName": "translation" - }, - { - "id": "Composition.type.coding:codingGenomics.display.extension:translation.extension", - "path": "Composition.type.coding.display.extension.extension", - "min": 2 - }, - { - "id": "Composition.type.text.extension:translation", - "path": "Composition.type.text.extension", - "sliceName": "translation" - }, - { - "id": "Composition.type.text.extension:translation.extension", - "path": "Composition.type.text.extension.extension", - "min": 2 - }, - { - "id": "Composition.category", - "path": "Composition.category", - "slicing": { - "discriminator": [ - { - "type": "value", - "path": "$this" - }], - "rules": "open" - }, - "definition": "Fixed codes for conformance to the EU Lab Composition profile (for cross border sharing of lab reports)." - }, - { - "id": "Composition.category.coding.display.extension:translation", - "path": "Composition.category.coding.display.extension", - "sliceName": "translation" - }, - { - "id": "Composition.category.coding.display.extension:translation.extension", - "path": "Composition.category.coding.display.extension.extension", - "min": 2 - }, - { - "id": "Composition.category.text.extension:translation", - "path": "Composition.category.text.extension", - "sliceName": "translation" - }, - { - "id": "Composition.category.text.extension:translation.extension", - "path": "Composition.category.text.extension.extension", - "min": 2 - }, - { - "id": "Composition.category:studyType", - "path": "Composition.category", - "sliceName": "studyType", - "fixedCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "26436-6", - "display": "Laboratory studies (set)" - } - ] - } - }, - { - "id": "Composition.category:specialty", - "path": "Composition.category", - "sliceName": "specialty", - "fixedCodeableConcept": { - "coding": [ - { - "system": "http://snomed.info/sct", - "code": "1236877003", - "display": "Genetic pathology" - } - ] - } - }, - { - "id": "Composition.subject", - "path": "Composition.subject", - "definition": "Matches subject reference included in either the DiagnosticReport or ServiceRequest", - "type": [ - { - "code": "Reference", - "targetProfile": [ - "http://hl7.eu/fhir/base/StructureDefinition/patient-eu-core", - "http://hl7.eu/fhir/laboratory/StructureDefinition/Patient-animal-eu-lab", - "http://hl7.org/fhir/StructureDefinition/Group", - "http://hl7.org/fhir/StructureDefinition/Location", - "http://hl7.org/fhir/StructureDefinition/Device" - ], - "aggregation": [ - "referenced", - "bundled" - ] - } - ] - }, - { - "id": "Composition.date", - "path": "Composition.date", - "definition": "SHALL be the dateTime the Composition was generated by the central broker" - }, - { - "id": "Composition.author", - "path": "Composition.author", - "definition": "Fixed to an identifier for the central broker (TBC). The author for the underlying ServiceRequest or DiagnosticReport can be retrieved by interrogating the appropriate resources." - }, - { - "id": "Composition.title", - "path": "Composition.title", - "definition": "SHALL match the SNOMED CT display used within Composition.type", - "fixedString": "Genetic report" - }, - { - "id": "Composition.section", - "path": "Composition.section", - "slicing": { - "discriminator": [ - { - "type": "pattern", - "path": "$this" - }], - "rules": "open" - }, - "definition": "To conform to EU Lab, SHOULD include references to the results that form part of the genomic report. For the UGR, will include sections that conform to the UGR folders, this work is currently in development." - }, - { - "id": "Composition.section.code.coding.display.extension:translation", - "path": "Composition.section.code.coding.display.extension", - "sliceName": "translation" - }, - { - "id": "Composition.section.code.coding.display.extension:translation.extension", - "path": "Composition.section.code.coding.display.extension.extension", - "min": 2 - }, - { - "id": "Composition.section.code.text.extension:translation", - "path": "Composition.section.code.text.extension", - "sliceName": "translation" - }, - { - "id": "Composition.section.code.text.extension:translation.extension", - "path": "Composition.section.code.text.extension.extension", - "min": 2 - }, - { - "id": "Composition.section:sectionUGR", - "path": "Composition.section", - "sliceName": "sectionUGR", - "definition": "Sections included within the UGR: patient-demographics | investigations-and-procedures-requested | investigation-results | consent-for-information-sharing | family-history " - }, - { - "id": "Composition.section:sectionUGR.code", - "path": "Composition.section.code", - "binding": { - "strength": "extensible", - "description": "UK Core Composition Section Codes", - "valueSet": "https://fhir.hl7.org.uk/ValueSet/UKCore-CompositionSectionCode" - } + }, + { + "id": "Composition.type.coding.display.extension:translation", + "path": "Composition.type.coding.display.extension", + "sliceName": "translation" + }, + { + "id": "Composition.type.coding.display.extension:translation.extension", + "path": "Composition.type.coding.display.extension.extension", + "min": 2 + }, + { + "id": "Composition.type.coding:codingGenomics", + "path": "Composition.type.coding", + "sliceName": "codingGenomics", + "fixedCoding": { + "system": "http://snomed.info/sct", + "code": "1054161000000101", + "display": "Genetic report" + } + }, + { + "id": "Composition.type.coding:codingGenomics.display.extension:translation", + "path": "Composition.type.coding.display.extension", + "sliceName": "translation" + }, + { + "id": "Composition.type.coding:codingGenomics.display.extension:translation.extension", + "path": "Composition.type.coding.display.extension.extension", + "min": 2 + }, + { + "id": "Composition.type.text.extension:translation", + "path": "Composition.type.text.extension", + "sliceName": "translation" + }, + { + "id": "Composition.type.text.extension:translation.extension", + "path": "Composition.type.text.extension.extension", + "min": 2 + }, + { + "id": "Composition.category", + "path": "Composition.category", + "slicing": { + "discriminator": [ + { + "type": "value", + "path": "$this" + } + ], + "rules": "open" + }, + "definition": "Fixed codes for conformance to the EU Lab Composition profile (for cross border sharing of lab reports)." + }, + { + "id": "Composition.category.coding.display.extension:translation", + "path": "Composition.category.coding.display.extension", + "sliceName": "translation" + }, + { + "id": "Composition.category.coding.display.extension:translation.extension", + "path": "Composition.category.coding.display.extension.extension", + "min": 2 + }, + { + "id": "Composition.category.text.extension:translation", + "path": "Composition.category.text.extension", + "sliceName": "translation" + }, + { + "id": "Composition.category.text.extension:translation.extension", + "path": "Composition.category.text.extension.extension", + "min": 2 + }, + { + "id": "Composition.category:studyType", + "path": "Composition.category", + "sliceName": "studyType", + "fixedCodeableConcept": { + "coding": [ + { + "system": "http://loinc.org", + "code": "26436-6", + "display": "Laboratory studies (set)" } + ] + } + }, + { + "id": "Composition.category:specialty", + "path": "Composition.category", + "sliceName": "specialty", + "fixedCodeableConcept": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "1236877003", + "display": "Genetic pathology" + } + ] + } + }, + { + "id": "Composition.subject", + "path": "Composition.subject", + "definition": "Matches subject reference included in either the DiagnosticReport or ServiceRequest", + "type": [ + { + "code": "Reference", + "targetProfile": [ + "http://hl7.eu/fhir/laboratory/StructureDefinition/Patient-animal-eu-lab", + "http://hl7.org/fhir/StructureDefinition/Group", + "http://hl7.org/fhir/StructureDefinition/Location", + "http://hl7.org/fhir/StructureDefinition/Device" + ], + "aggregation": [ + "referenced", + "bundled" + ] + } ] - } + }, + { + "id": "Composition.date", + "path": "Composition.date", + "definition": "SHALL be the dateTime the Composition was generated by the central broker" + }, + { + "id": "Composition.author", + "path": "Composition.author", + "definition": "Fixed to an identifier for the central broker (TBC). The author for the underlying ServiceRequest or DiagnosticReport can be retrieved by interrogating the appropriate resources." + }, + { + "id": "Composition.title", + "path": "Composition.title", + "definition": "SHALL match the SNOMED CT display used within Composition.type", + "fixedString": "Genetic report" + }, + { + "id": "Composition.section", + "path": "Composition.section", + "slicing": { + "discriminator": [ + { + "type": "value", + "path": "$this" + } + ], + "rules": "open" + }, + "definition": "To conform to EU Lab, SHOULD include references to the results that form part of the genomic report. For the UGR, will include sections that conform to the UGR folders, this work is currently in development." + }, + { + "id": "Composition.section.code.coding.display.extension:translation", + "path": "Composition.section.code.coding.display.extension", + "sliceName": "translation" + }, + { + "id": "Composition.section.code.coding.display.extension:translation.extension", + "path": "Composition.section.code.coding.display.extension.extension", + "min": 2 + }, + { + "id": "Composition.section.code.text.extension:translation", + "path": "Composition.section.code.text.extension", + "sliceName": "translation" + }, + { + "id": "Composition.section.code.text.extension:translation.extension", + "path": "Composition.section.code.text.extension.extension", + "min": 2 + }, + { + "id": "Composition.section:sectionUGR", + "path": "Composition.section", + "sliceName": "sectionUGR", + "definition": "Sections included within the UGR: patient-demographics | investigations-and-procedures-requested | investigation-results | consent-for-information-sharing | family-history " + }, + { + "id": "Composition.section:sectionUGR.code", + "path": "Composition.section.code", + "binding": { + "strength": "extensible", + "description": "UK Core Composition Section Codes", + "valueSet": "https://fhir.hl7.org.uk/ValueSet/UKCore-CompositionSectionCode" + } + } + ] + } } \ No newline at end of file diff --git a/StructureDefinition/NHSEngland-DiagnosticReport-GenomicReport.json b/StructureDefinition/NHSEngland-DiagnosticReport-GenomicReport.json index 08da2eb..ba36c88 100644 --- a/StructureDefinition/NHSEngland-DiagnosticReport-GenomicReport.json +++ b/StructureDefinition/NHSEngland-DiagnosticReport-GenomicReport.json @@ -174,9 +174,6 @@ { "id": "DiagnosticReport.category", "path": "DiagnosticReport.category", - "slicing": { - "rules": "open" - }, "definition": "Potentially multiple categories to specify the specialty the report is relevant for. Different codings are expected by the Genomic Report and EU Lab profiles." }, { diff --git a/custom.rules.yaml b/custom.rules.yaml index 4fe6926..3a4a92a 100644 --- a/custom.rules.yaml +++ b/custom.rules.yaml @@ -23,6 +23,8 @@ - CONFIG #errors in dependencies e.g. loops, outdated, pre-release - 6006 #failure to contact term service - 1030 #reference loop + - 4000 # Eu-Lab issues + - 4009 ~ Extension-reference - action: unique name: unique-canonicals From 746f333b09344d7693224653aebb58adfcf61cb4 Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Wed, 3 Jun 2026 19:29:37 +0100 Subject: [PATCH 12/80] Re-arrange text in Component.section Re-arrange text in Component.section --- ...omposition-EULabGenomicReport-Example.json | 30 +-- Patient/Patient-PheobeSmitham-Example.json | 207 +++++++++--------- ...gland-Composition-GenomicsEULabReport.json | 9 - 3 files changed, 107 insertions(+), 139 deletions(-) diff --git a/Composition/Composition-EULabGenomicReport-Example.json b/Composition/Composition-EULabGenomicReport-Example.json index 75ffbd6..fccff7a 100644 --- a/Composition/Composition-EULabGenomicReport-Example.json +++ b/Composition/Composition-EULabGenomicReport-Example.json @@ -80,6 +80,10 @@ "section": [ { "title": "Results", + "text": { + "status": "generated", + "div": "
Genomic findings.
" + }, "code": { "coding": [ { @@ -89,32 +93,6 @@ } ] }, - "section": [ - { - "title": "Results", - "text": { - "status": "generated", - "div": "
Genomic findings.
" - }, - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "26436-6", - "display": "Laboratory studies (set)" - } - ] - }, - "entry": [ - { - "reference": "Observation/Observation-GenomicTherapeuticImplication-Example" - }, - { - "reference": "Observation/Observation-GenomicsVariantSLC52A2-Example" - } - ] - } - ], "entry": [ { "reference": "Observation/Observation-GenomicTherapeuticImplication-Example" diff --git a/Patient/Patient-PheobeSmitham-Example.json b/Patient/Patient-PheobeSmitham-Example.json index 94281a7..d5978d7 100644 --- a/Patient/Patient-PheobeSmitham-Example.json +++ b/Patient/Patient-PheobeSmitham-Example.json @@ -1,111 +1,110 @@ { - "resourceType": "Patient", - "id": "Patient-PheobeSmitham-Example", - "meta": { - "profile": [ - "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Patient", - "http://hl7.eu/fhir/laboratory/StructureDefinition/Patient-animal-eu-lab" + "resourceType": "Patient", + "id": "Patient-PheobeSmitham-Example", + "meta": { + "profile": [ + "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Patient" + ] + }, + "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" + } ] + } }, - "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": [ + { + "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": [ { - "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": "1.1.1", - "code": "01", - "display": "Number present and verified" - } - ] - } - } + "url": "https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-NHSNumberVerificationStatus", + "valueCodeableConcept": { + "coding": [ + { + "system": "https://fhir.hl7.org.uk/CodeSystem/UKCore-NHSNumberVerificationStatusEngland", + "version": "1.1.1", + "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" + ] + }, + { + "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" + } + ] +} \ No newline at end of file diff --git a/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json b/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json index 0b2f06d..039c015 100644 --- a/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json +++ b/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json @@ -271,15 +271,6 @@ { "id": "Composition.section", "path": "Composition.section", - "slicing": { - "discriminator": [ - { - "type": "value", - "path": "$this" - } - ], - "rules": "open" - }, "definition": "To conform to EU Lab, SHOULD include references to the results that form part of the genomic report. For the UGR, will include sections that conform to the UGR folders, this work is currently in development." }, { From d292e79fe80be1ce48da0b1032d7bdaded053cb0 Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Wed, 3 Jun 2026 20:04:57 +0100 Subject: [PATCH 13/80] Added EU Core Added EU Core --- Composition/Composition-EULabGenomicReport-Example.json | 2 +- Patient/Patient-PheobeSmitham-Example.json | 3 ++- .../NHSEngland-Composition-GenomicsEULabReport.json | 4 ++-- fhirpkg.lock.json | 6 ++++-- package.json | 4 +++- 5 files changed, 12 insertions(+), 7 deletions(-) diff --git a/Composition/Composition-EULabGenomicReport-Example.json b/Composition/Composition-EULabGenomicReport-Example.json index fccff7a..65db5ad 100644 --- a/Composition/Composition-EULabGenomicReport-Example.json +++ b/Composition/Composition-EULabGenomicReport-Example.json @@ -20,7 +20,7 @@ } }, { - "url": "http://hl7.eu/fhir/laboratory/StructureDefinition/composition-diagnosticReportReference", + "url": "http://hl7.eu/fhir/extensions/StructureDefinition/composition-diagnosticReportReference", "valueReference": { "reference": "DiagnosticReport/DiagnosticReport-GenomicVariantAssessment-Example" } diff --git a/Patient/Patient-PheobeSmitham-Example.json b/Patient/Patient-PheobeSmitham-Example.json index d5978d7..ec1870e 100644 --- a/Patient/Patient-PheobeSmitham-Example.json +++ b/Patient/Patient-PheobeSmitham-Example.json @@ -3,7 +3,8 @@ "id": "Patient-PheobeSmitham-Example", "meta": { "profile": [ - "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Patient" + "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Patient", + "http://hl7.eu/fhir/base/StructureDefinition/patient-eu" ] }, "extension": [ diff --git a/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json b/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json index 039c015..f831019 100644 --- a/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json +++ b/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json @@ -240,9 +240,9 @@ { "code": "Reference", "targetProfile": [ - "http://hl7.eu/fhir/laboratory/StructureDefinition/Patient-animal-eu-lab", + " http://hl7.eu/fhir/base/StructureDefinition/patient-eu-core", "http://hl7.org/fhir/StructureDefinition/Group", - "http://hl7.org/fhir/StructureDefinition/Location", + "http://hl7.eu/fhir/base/StructureDefinition/location-eu-core", "http://hl7.org/fhir/StructureDefinition/Device" ], "aggregation": [ diff --git a/fhirpkg.lock.json b/fhirpkg.lock.json index c2dfd50..47650c2 100644 --- a/fhirpkg.lock.json +++ b/fhirpkg.lock.json @@ -1,11 +1,13 @@ { "updated": "2026-05-06T10:21:55.9845039+01:00", "dependencies": { - "hl7.fhir.r4.core": "4.0.1", +"hl7.fhir.r4.core": "4.0.1", "hl7.fhir.uv.xver-r5.r4": "0.1.0", "fhir.r4.ukcore.stu3.currentbuild": "0.28.0-pre-release", "hl7.fhir.uv.genomics-reporting": "3.0.0", - "hl7.fhir.eu.laboratory": "2.0.0" + "hl7.fhir.uv.tools.r4": "1.1.2", + "hl7.fhir.eu.laboratory": "2.0.0", + " hl7.fhir.eu.base-r5": "2.0.0" }, "missing": {} } \ No newline at end of file diff --git a/package.json b/package.json index 0cbe611..f725375 100644 --- a/package.json +++ b/package.json @@ -7,7 +7,9 @@ "hl7.fhir.uv.xver-r5.r4": "0.1.0", "fhir.r4.ukcore.stu3.currentbuild": "0.28.0-pre-release", "hl7.fhir.uv.genomics-reporting": "3.0.0", - "hl7.fhir.eu.laboratory": "2.0.0" + "hl7.fhir.uv.tools.r4": "1.1.2", + "hl7.fhir.eu.laboratory": "2.0.0", + " hl7.fhir.eu.base-r5": "2.0.0" }, "fhirVersions": [ "4.0.1" From 2efa4326d3d3dae32c08ec603adc56815162962b Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Wed, 3 Jun 2026 20:09:31 +0100 Subject: [PATCH 14/80] Remove White space Remove White space --- .../NHSEngland-Composition-GenomicsEULabReport.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json b/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json index f831019..03fa987 100644 --- a/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json +++ b/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json @@ -240,7 +240,7 @@ { "code": "Reference", "targetProfile": [ - " http://hl7.eu/fhir/base/StructureDefinition/patient-eu-core", + "http://hl7.eu/fhir/base/StructureDefinition/patient-eu-core", "http://hl7.org/fhir/StructureDefinition/Group", "http://hl7.eu/fhir/base/StructureDefinition/location-eu-core", "http://hl7.org/fhir/StructureDefinition/Device" From 56fc0c9aee2621379d45fafc77dde314c83f5e08 Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Wed, 3 Jun 2026 20:15:37 +0100 Subject: [PATCH 15/80] Remove Eu Core Remove Eu Core --- 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 47650c2..27a0d24 100644 --- a/fhirpkg.lock.json +++ b/fhirpkg.lock.json @@ -6,8 +6,7 @@ "fhir.r4.ukcore.stu3.currentbuild": "0.28.0-pre-release", "hl7.fhir.uv.genomics-reporting": "3.0.0", "hl7.fhir.uv.tools.r4": "1.1.2", - "hl7.fhir.eu.laboratory": "2.0.0", - " hl7.fhir.eu.base-r5": "2.0.0" + "hl7.fhir.eu.laboratory": "2.0.0" }, "missing": {} } \ No newline at end of file diff --git a/package.json b/package.json index f725375..f2034a1 100644 --- a/package.json +++ b/package.json @@ -8,8 +8,7 @@ "fhir.r4.ukcore.stu3.currentbuild": "0.28.0-pre-release", "hl7.fhir.uv.genomics-reporting": "3.0.0", "hl7.fhir.uv.tools.r4": "1.1.2", - "hl7.fhir.eu.laboratory": "2.0.0", - " hl7.fhir.eu.base-r5": "2.0.0" + "hl7.fhir.eu.laboratory": "2.0.0" }, "fhirVersions": [ "4.0.1" From 23b371e9ebcfd1939a54c1fddcd3fe8a7932a0b0 Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Wed, 3 Jun 2026 20:21:02 +0100 Subject: [PATCH 16/80] Added R4 hl7.fhir.eu.base 2.0.0 Added R4 hl7.fhir.eu.base 2.0.0 --- fhirpkg.lock.json | 3 ++- package.json | 6 +++--- 2 files changed, 5 insertions(+), 4 deletions(-) diff --git a/fhirpkg.lock.json b/fhirpkg.lock.json index 27a0d24..366cf0d 100644 --- a/fhirpkg.lock.json +++ b/fhirpkg.lock.json @@ -6,7 +6,8 @@ "fhir.r4.ukcore.stu3.currentbuild": "0.28.0-pre-release", "hl7.fhir.uv.genomics-reporting": "3.0.0", "hl7.fhir.uv.tools.r4": "1.1.2", - "hl7.fhir.eu.laboratory": "2.0.0" + "hl7.fhir.eu.laboratory": "2.0.0", + "hl7.fhir.eu.base": "2.0.0" }, "missing": {} } \ No newline at end of file diff --git a/package.json b/package.json index f2034a1..70651d4 100644 --- a/package.json +++ b/package.json @@ -3,12 +3,12 @@ "description": "FHIR Genomics Implementation Guide", "author": "nhsdigital", "dependencies": { - "hl7.fhir.r4.core": "4.0.1", - "hl7.fhir.uv.xver-r5.r4": "0.1.0", + "hl7.fhir.uv.xver-r5.r4": "0.1.0", "fhir.r4.ukcore.stu3.currentbuild": "0.28.0-pre-release", "hl7.fhir.uv.genomics-reporting": "3.0.0", "hl7.fhir.uv.tools.r4": "1.1.2", - "hl7.fhir.eu.laboratory": "2.0.0" + "hl7.fhir.eu.laboratory": "2.0.0", + "hl7.fhir.eu.base": "2.0.0" }, "fhirVersions": [ "4.0.1" From 632aec3daf94301a2498ce3a877f2fd73d26d49c Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Wed, 3 Jun 2026 20:28:32 +0100 Subject: [PATCH 17/80] Remove EU Base R4 Remove EU Base R4 --- fhirpkg.lock.json | 4 +--- package.json | 5 ++--- 2 files changed, 3 insertions(+), 6 deletions(-) diff --git a/fhirpkg.lock.json b/fhirpkg.lock.json index 366cf0d..635fce2 100644 --- a/fhirpkg.lock.json +++ b/fhirpkg.lock.json @@ -1,13 +1,11 @@ { "updated": "2026-05-06T10:21:55.9845039+01:00", "dependencies": { -"hl7.fhir.r4.core": "4.0.1", "hl7.fhir.uv.xver-r5.r4": "0.1.0", "fhir.r4.ukcore.stu3.currentbuild": "0.28.0-pre-release", "hl7.fhir.uv.genomics-reporting": "3.0.0", "hl7.fhir.uv.tools.r4": "1.1.2", - "hl7.fhir.eu.laboratory": "2.0.0", - "hl7.fhir.eu.base": "2.0.0" + "hl7.fhir.eu.laboratory": "2.0.0" }, "missing": {} } \ No newline at end of file diff --git a/package.json b/package.json index 70651d4..10f7ca9 100644 --- a/package.json +++ b/package.json @@ -3,12 +3,11 @@ "description": "FHIR Genomics Implementation Guide", "author": "nhsdigital", "dependencies": { - "hl7.fhir.uv.xver-r5.r4": "0.1.0", + "hl7.fhir.uv.xver-r5.r4": "0.1.0", "fhir.r4.ukcore.stu3.currentbuild": "0.28.0-pre-release", "hl7.fhir.uv.genomics-reporting": "3.0.0", "hl7.fhir.uv.tools.r4": "1.1.2", - "hl7.fhir.eu.laboratory": "2.0.0", - "hl7.fhir.eu.base": "2.0.0" + "hl7.fhir.eu.laboratory": "2.0.0" }, "fhirVersions": [ "4.0.1" From 26ef76c3e0ab3365b7ccbae5f30e245274ce0c31 Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Wed, 3 Jun 2026 20:36:26 +0100 Subject: [PATCH 18/80] Re-instate R4 Re-instate R4 --- fhirpkg.lock.json | 1 + package.json | 1 + 2 files changed, 2 insertions(+) diff --git a/fhirpkg.lock.json b/fhirpkg.lock.json index 635fce2..4a86328 100644 --- a/fhirpkg.lock.json +++ b/fhirpkg.lock.json @@ -1,6 +1,7 @@ { "updated": "2026-05-06T10:21:55.9845039+01:00", "dependencies": { + "hl7.fhir.r4.core": "4.0.1", "hl7.fhir.uv.xver-r5.r4": "0.1.0", "fhir.r4.ukcore.stu3.currentbuild": "0.28.0-pre-release", "hl7.fhir.uv.genomics-reporting": "3.0.0", diff --git a/package.json b/package.json index 10f7ca9..f2034a1 100644 --- a/package.json +++ b/package.json @@ -3,6 +3,7 @@ "description": "FHIR Genomics Implementation Guide", "author": "nhsdigital", "dependencies": { + "hl7.fhir.r4.core": "4.0.1", "hl7.fhir.uv.xver-r5.r4": "0.1.0", "fhir.r4.ukcore.stu3.currentbuild": "0.28.0-pre-release", "hl7.fhir.uv.genomics-reporting": "3.0.0", From 8f70af6078575bebd9e93d608702c92a72273ae0 Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Thu, 4 Jun 2026 16:01:23 +0100 Subject: [PATCH 19/80] Testing --- 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 df3c15f..fc05787 100644 --- a/fhirpkg.lock.json +++ b/fhirpkg.lock.json @@ -15,4 +15,4 @@ "fhir.r4.ukcore.stu3.currentbuild": "0.28.0-pre-release" }, "missing": {} -} +} \ No newline at end of file diff --git a/package.json b/package.json index b104930..77a54a5 100644 --- a/package.json +++ b/package.json @@ -20,4 +20,4 @@ "4.0.1" ], "jurisdiction": "urn:iso:std:iso:3166:-2#GB" -} +} \ No newline at end of file From 9145ae7d3258fd477a7eb62150e7e769cf2e3eb2 Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Thu, 4 Jun 2026 16:25:45 +0100 Subject: [PATCH 20/80] Reverse Eu-Lab Reverse Eu-Lab --- 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 fc05787..a739a4d 100644 --- a/fhirpkg.lock.json +++ b/fhirpkg.lock.json @@ -6,7 +6,7 @@ "hl7.fhir.uv.xver-r5.r4": "0.1.0", "hl7.fhir.uv.genomics-reporting": "3.0.0", "hl7.fhir.uv.ips": "2.0.0", - "hl7.fhir.eu.laboratory": "0.1.1", + "hl7.fhir.eu.laboratory": "0.1.0-ballot", "ihe.iti.pcf": "1.1.0", "hl7.fhir.us.mcode": "4.0.0", "fhir.r4.nhsengland.pathology": "0.1.4-alpha", diff --git a/package.json b/package.json index 77a54a5..4c2ff6b 100644 --- a/package.json +++ b/package.json @@ -8,7 +8,7 @@ "hl7.fhir.uv.xver-r5.r4": "0.1.0", "hl7.fhir.uv.genomics-reporting": "3.0.0", "hl7.fhir.uv.ips": "2.0.0", - "hl7.fhir.eu.laboratory": "0.1.1", + "hl7.fhir.eu.laboratory": "0.1.0-ballot", "ihe.iti.pcf": "1.1.0", "hl7.fhir.us.mcode": "4.0.0", "fhir.r4.nhsengland.pathology": "0.1.4-alpha", From 61eabb06bbd59edc89632fc23b283f9d89970039 Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Thu, 4 Jun 2026 17:24:05 +0100 Subject: [PATCH 21/80] Testing with Eu-Lab 2,0,0 Testing with Eu-Lab 2,0,0 --- 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 a739a4d..1415c84 100644 --- a/fhirpkg.lock.json +++ b/fhirpkg.lock.json @@ -6,7 +6,7 @@ "hl7.fhir.uv.xver-r5.r4": "0.1.0", "hl7.fhir.uv.genomics-reporting": "3.0.0", "hl7.fhir.uv.ips": "2.0.0", - "hl7.fhir.eu.laboratory": "0.1.0-ballot", + "hl7.fhir.eu.laboratory": "2.0.0", "ihe.iti.pcf": "1.1.0", "hl7.fhir.us.mcode": "4.0.0", "fhir.r4.nhsengland.pathology": "0.1.4-alpha", diff --git a/package.json b/package.json index 4c2ff6b..26ff029 100644 --- a/package.json +++ b/package.json @@ -8,7 +8,7 @@ "hl7.fhir.uv.xver-r5.r4": "0.1.0", "hl7.fhir.uv.genomics-reporting": "3.0.0", "hl7.fhir.uv.ips": "2.0.0", - "hl7.fhir.eu.laboratory": "0.1.0-ballot", + "hl7.fhir.eu.laboratory": "2.0.0", "ihe.iti.pcf": "1.1.0", "hl7.fhir.us.mcode": "4.0.0", "fhir.r4.nhsengland.pathology": "0.1.4-alpha", From c7c8edceabe863b06799adcf3001e5162b616d82 Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Thu, 4 Jun 2026 18:06:18 +0100 Subject: [PATCH 22/80] Added IHE & Pathology Added IHE & Pathology --- fhirpkg.lock.json | 11 ++++++++--- package.json | 9 +++++++-- 2 files changed, 15 insertions(+), 5 deletions(-) diff --git a/fhirpkg.lock.json b/fhirpkg.lock.json index 4a86328..6bf2af1 100644 --- a/fhirpkg.lock.json +++ b/fhirpkg.lock.json @@ -1,12 +1,17 @@ { "updated": "2026-05-06T10:21:55.9845039+01:00", "dependencies": { - "hl7.fhir.r4.core": "4.0.1", + "hl7.fhir.r4.core": "4.0.1", + "hl7.fhir.uv.extensions.r4": "5.3.0-ballot-tc1", + "hl7.fhir.uv.ips": "2.0.0", "hl7.fhir.uv.xver-r5.r4": "0.1.0", - "fhir.r4.ukcore.stu3.currentbuild": "0.28.0-pre-release", "hl7.fhir.uv.genomics-reporting": "3.0.0", + "fhir.r4.nhsengland.pathology": "0.1.4-alpha", "hl7.fhir.uv.tools.r4": "1.1.2", - "hl7.fhir.eu.laboratory": "2.0.0" + "hl7.fhir.eu.laboratory": "2.0.0", + "ihe.iti.pcf": "1.1.0", + "hl7.fhir.us.mcode": "4.0.0", + "fhir.r4.ukcore.stu3.currentbuild": "0.28.0-pre-release" }, "missing": {} } \ No newline at end of file diff --git a/package.json b/package.json index f2034a1..3b444b0 100644 --- a/package.json +++ b/package.json @@ -4,11 +4,16 @@ "author": "nhsdigital", "dependencies": { "hl7.fhir.r4.core": "4.0.1", + "hl7.fhir.uv.extensions.r4": "5.3.0-ballot-tc1", + "hl7.fhir.uv.ips": "2.0.0", "hl7.fhir.uv.xver-r5.r4": "0.1.0", - "fhir.r4.ukcore.stu3.currentbuild": "0.28.0-pre-release", "hl7.fhir.uv.genomics-reporting": "3.0.0", + "fhir.r4.nhsengland.pathology": "0.1.4-alpha", "hl7.fhir.uv.tools.r4": "1.1.2", - "hl7.fhir.eu.laboratory": "2.0.0" + "hl7.fhir.eu.laboratory": "2.0.0", + "ihe.iti.pcf": "1.1.0", + "hl7.fhir.us.mcode": "4.0.0", + "fhir.r4.ukcore.stu3.currentbuild": "0.28.0-pre-release" }, "fhirVersions": [ "4.0.1" From 83cd276534fd8d85a8d0057408c3f4a96785ff25 Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Fri, 5 Jun 2026 06:46:00 +0100 Subject: [PATCH 23/80] Testing ihe.iti.pcf": "1.0.0-comment" Testing ihe.iti.pcf": "1.0.0-comment" --- .../NHSEngland-Composition-GenomicsEULabReport.json | 3 +-- fhirpkg.lock.json | 2 +- package.json | 2 +- 3 files changed, 3 insertions(+), 4 deletions(-) diff --git a/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json b/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json index 03fa987..2cd6f49 100644 --- a/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json +++ b/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json @@ -96,8 +96,7 @@ { "code": "Reference", "targetProfile": [ - "https://fhir.nhs.uk/StructureDefinition/NHSEngland-DiagnosticReport-GenomicReport", - "http://hl7.eu/fhir/laboratory/StructureDefinition/DiagnosticReport-eu-lab" + "https://fhir.nhs.uk/StructureDefinition/NHSEngland-DiagnosticReport-GenomicReport" ], "aggregation": [ "referenced", diff --git a/fhirpkg.lock.json b/fhirpkg.lock.json index 6bf2af1..14fb1fb 100644 --- a/fhirpkg.lock.json +++ b/fhirpkg.lock.json @@ -9,7 +9,7 @@ "fhir.r4.nhsengland.pathology": "0.1.4-alpha", "hl7.fhir.uv.tools.r4": "1.1.2", "hl7.fhir.eu.laboratory": "2.0.0", - "ihe.iti.pcf": "1.1.0", + "ihe.iti.pcf": "1.0.0-comment", "hl7.fhir.us.mcode": "4.0.0", "fhir.r4.ukcore.stu3.currentbuild": "0.28.0-pre-release" }, diff --git a/package.json b/package.json index 3b444b0..6219ed1 100644 --- a/package.json +++ b/package.json @@ -11,7 +11,7 @@ "fhir.r4.nhsengland.pathology": "0.1.4-alpha", "hl7.fhir.uv.tools.r4": "1.1.2", "hl7.fhir.eu.laboratory": "2.0.0", - "ihe.iti.pcf": "1.1.0", + "ihe.iti.pcf": "1.0.0-comment", "hl7.fhir.us.mcode": "4.0.0", "fhir.r4.ukcore.stu3.currentbuild": "0.28.0-pre-release" }, From 252046d77ee9542dc8252a915570187255c2c8c5 Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Fri, 5 Jun 2026 06:52:35 +0100 Subject: [PATCH 24/80] Update Update --- Composition/Composition-EULabGenomicReport-Example.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Composition/Composition-EULabGenomicReport-Example.json b/Composition/Composition-EULabGenomicReport-Example.json index 65db5ad..fccff7a 100644 --- a/Composition/Composition-EULabGenomicReport-Example.json +++ b/Composition/Composition-EULabGenomicReport-Example.json @@ -20,7 +20,7 @@ } }, { - "url": "http://hl7.eu/fhir/extensions/StructureDefinition/composition-diagnosticReportReference", + "url": "http://hl7.eu/fhir/laboratory/StructureDefinition/composition-diagnosticReportReference", "valueReference": { "reference": "DiagnosticReport/DiagnosticReport-GenomicVariantAssessment-Example" } From 677dccc17d9a96571055c2808a204d0435bea66b Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Fri, 5 Jun 2026 07:10:57 +0100 Subject: [PATCH 25/80] Testing 0.1.0-ballot Testing 0.1.0-ballot --- 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 1415c84..a739a4d 100644 --- a/fhirpkg.lock.json +++ b/fhirpkg.lock.json @@ -6,7 +6,7 @@ "hl7.fhir.uv.xver-r5.r4": "0.1.0", "hl7.fhir.uv.genomics-reporting": "3.0.0", "hl7.fhir.uv.ips": "2.0.0", - "hl7.fhir.eu.laboratory": "2.0.0", + "hl7.fhir.eu.laboratory": "0.1.0-ballot", "ihe.iti.pcf": "1.1.0", "hl7.fhir.us.mcode": "4.0.0", "fhir.r4.nhsengland.pathology": "0.1.4-alpha", diff --git a/package.json b/package.json index 26ff029..4c2ff6b 100644 --- a/package.json +++ b/package.json @@ -8,7 +8,7 @@ "hl7.fhir.uv.xver-r5.r4": "0.1.0", "hl7.fhir.uv.genomics-reporting": "3.0.0", "hl7.fhir.uv.ips": "2.0.0", - "hl7.fhir.eu.laboratory": "2.0.0", + "hl7.fhir.eu.laboratory": "0.1.0-ballot", "ihe.iti.pcf": "1.1.0", "hl7.fhir.us.mcode": "4.0.0", "fhir.r4.nhsengland.pathology": "0.1.4-alpha", From f15749f722d04865e60018be03b840cb00c1fede Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Fri, 5 Jun 2026 07:13:54 +0100 Subject: [PATCH 26/80] Testing "hl7.fhir.eu.laboratory": "0.1.0-ballot", Testing "hl7.fhir.eu.laboratory": "0.1.0-ballot", --- 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 14fb1fb..ff22b84 100644 --- a/fhirpkg.lock.json +++ b/fhirpkg.lock.json @@ -8,7 +8,7 @@ "hl7.fhir.uv.genomics-reporting": "3.0.0", "fhir.r4.nhsengland.pathology": "0.1.4-alpha", "hl7.fhir.uv.tools.r4": "1.1.2", - "hl7.fhir.eu.laboratory": "2.0.0", + "hl7.fhir.eu.laboratory": "0.1.0-ballot", "ihe.iti.pcf": "1.0.0-comment", "hl7.fhir.us.mcode": "4.0.0", "fhir.r4.ukcore.stu3.currentbuild": "0.28.0-pre-release" diff --git a/package.json b/package.json index 6219ed1..27936f5 100644 --- a/package.json +++ b/package.json @@ -10,7 +10,7 @@ "hl7.fhir.uv.genomics-reporting": "3.0.0", "fhir.r4.nhsengland.pathology": "0.1.4-alpha", "hl7.fhir.uv.tools.r4": "1.1.2", - "hl7.fhir.eu.laboratory": "2.0.0", + "hl7.fhir.eu.laboratory": "0.1.0-ballot", "ihe.iti.pcf": "1.0.0-comment", "hl7.fhir.us.mcode": "4.0.0", "fhir.r4.ukcore.stu3.currentbuild": "0.28.0-pre-release" From 4c6eb88ae49f4637bac6daa1aa552d76179000d9 Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Fri, 5 Jun 2026 07:14:37 +0100 Subject: [PATCH 27/80] Update NHSEngland-Composition-GenomicsEULabReport.json --- .../NHSEngland-Composition-GenomicsEULabReport.json | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json b/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json index 2cd6f49..03fa987 100644 --- a/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json +++ b/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json @@ -96,7 +96,8 @@ { "code": "Reference", "targetProfile": [ - "https://fhir.nhs.uk/StructureDefinition/NHSEngland-DiagnosticReport-GenomicReport" + "https://fhir.nhs.uk/StructureDefinition/NHSEngland-DiagnosticReport-GenomicReport", + "http://hl7.eu/fhir/laboratory/StructureDefinition/DiagnosticReport-eu-lab" ], "aggregation": [ "referenced", From 409dc0f570d77d4dbda6aac85fb47042dc3fd58c Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Fri, 5 Jun 2026 07:25:09 +0100 Subject: [PATCH 28/80] Update Custom rule Update Custom rule --- custom.rules.yaml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/custom.rules.yaml b/custom.rules.yaml index 3a4a92a..5effac8 100644 --- a/custom.rules.yaml +++ b/custom.rules.yaml @@ -23,8 +23,7 @@ - CONFIG #errors in dependencies e.g. loops, outdated, pre-release - 6006 #failure to contact term service - 1030 #reference loop - - 4000 # Eu-Lab issues - - 4009 ~ Extension-reference + - action: unique name: unique-canonicals From beb3e09fc595da5aa13ee48066dcd9e1401f0199 Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Fri, 5 Jun 2026 07:34:30 +0100 Subject: [PATCH 29/80] Remove Mcode & UVtools Remove Mcode & UVtools --- fhirpkg.lock.json | 2 -- package.json | 2 -- 2 files changed, 4 deletions(-) diff --git a/fhirpkg.lock.json b/fhirpkg.lock.json index a739a4d..077222a 100644 --- a/fhirpkg.lock.json +++ b/fhirpkg.lock.json @@ -8,9 +8,7 @@ "hl7.fhir.uv.ips": "2.0.0", "hl7.fhir.eu.laboratory": "0.1.0-ballot", "ihe.iti.pcf": "1.1.0", - "hl7.fhir.us.mcode": "4.0.0", "fhir.r4.nhsengland.pathology": "0.1.4-alpha", - "hl7.fhir.uv.tools.r4": "1.1.2", "fhir.r4.nhsengland.nhse-identifiers": "0.1.1-alpha", "fhir.r4.ukcore.stu3.currentbuild": "0.28.0-pre-release" }, diff --git a/package.json b/package.json index 4c2ff6b..77d71c4 100644 --- a/package.json +++ b/package.json @@ -10,9 +10,7 @@ "hl7.fhir.uv.ips": "2.0.0", "hl7.fhir.eu.laboratory": "0.1.0-ballot", "ihe.iti.pcf": "1.1.0", - "hl7.fhir.us.mcode": "4.0.0", "fhir.r4.nhsengland.pathology": "0.1.4-alpha", - "hl7.fhir.uv.tools.r4": "1.1.2", "fhir.r4.nhsengland.nhse-identifiers": "0.1.1-alpha", "fhir.r4.ukcore.stu3.currentbuild": "0.28.0-pre-release" }, From b10406249ead8a248544c4a073641760c4346c1e Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Fri, 5 Jun 2026 08:13:02 +0100 Subject: [PATCH 30/80] Remove MCode & UVtools Remove MCode & UVtools --- fhirpkg.lock.json | 2 -- package.json | 5 +---- 2 files changed, 1 insertion(+), 6 deletions(-) diff --git a/fhirpkg.lock.json b/fhirpkg.lock.json index ff22b84..73120cf 100644 --- a/fhirpkg.lock.json +++ b/fhirpkg.lock.json @@ -7,10 +7,8 @@ "hl7.fhir.uv.xver-r5.r4": "0.1.0", "hl7.fhir.uv.genomics-reporting": "3.0.0", "fhir.r4.nhsengland.pathology": "0.1.4-alpha", - "hl7.fhir.uv.tools.r4": "1.1.2", "hl7.fhir.eu.laboratory": "0.1.0-ballot", "ihe.iti.pcf": "1.0.0-comment", - "hl7.fhir.us.mcode": "4.0.0", "fhir.r4.ukcore.stu3.currentbuild": "0.28.0-pre-release" }, "missing": {} diff --git a/package.json b/package.json index 27936f5..e44890a 100644 --- a/package.json +++ b/package.json @@ -3,16 +3,13 @@ "description": "FHIR Genomics Implementation Guide", "author": "nhsdigital", "dependencies": { - "hl7.fhir.r4.core": "4.0.1", - "hl7.fhir.uv.extensions.r4": "5.3.0-ballot-tc1", + "hl7.fhir.uv.extensions.r4": "5.3.0-ballot-tc1", "hl7.fhir.uv.ips": "2.0.0", "hl7.fhir.uv.xver-r5.r4": "0.1.0", "hl7.fhir.uv.genomics-reporting": "3.0.0", "fhir.r4.nhsengland.pathology": "0.1.4-alpha", - "hl7.fhir.uv.tools.r4": "1.1.2", "hl7.fhir.eu.laboratory": "0.1.0-ballot", "ihe.iti.pcf": "1.0.0-comment", - "hl7.fhir.us.mcode": "4.0.0", "fhir.r4.ukcore.stu3.currentbuild": "0.28.0-pre-release" }, "fhirVersions": [ From 255da13c3c854057bfd2dae15c0e40f03cff5450 Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Fri, 5 Jun 2026 09:01:51 +0100 Subject: [PATCH 31/80] Testing "ihe.iti.pcf": "1.1.0" Testing "ihe.iti.pcf": "1.1.0" --- 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 73120cf..036e664 100644 --- a/fhirpkg.lock.json +++ b/fhirpkg.lock.json @@ -8,7 +8,7 @@ "hl7.fhir.uv.genomics-reporting": "3.0.0", "fhir.r4.nhsengland.pathology": "0.1.4-alpha", "hl7.fhir.eu.laboratory": "0.1.0-ballot", - "ihe.iti.pcf": "1.0.0-comment", + "ihe.iti.pcf": "1.1.0", "fhir.r4.ukcore.stu3.currentbuild": "0.28.0-pre-release" }, "missing": {} diff --git a/package.json b/package.json index e44890a..dd5210b 100644 --- a/package.json +++ b/package.json @@ -9,7 +9,7 @@ "hl7.fhir.uv.genomics-reporting": "3.0.0", "fhir.r4.nhsengland.pathology": "0.1.4-alpha", "hl7.fhir.eu.laboratory": "0.1.0-ballot", - "ihe.iti.pcf": "1.0.0-comment", + "ihe.iti.pcf": "1.1.0", "fhir.r4.ukcore.stu3.currentbuild": "0.28.0-pre-release" }, "fhirVersions": [ From 6a9c81c45db13ce1d626996e7e9d1b4243cd68f3 Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Fri, 5 Jun 2026 09:31:30 +0100 Subject: [PATCH 32/80] Testing "hl7.fhir.eu.laboratory": "0.1.1", Testing "hl7.fhir.eu.laboratory": "0.1.1", --- 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 036e664..7bcd966 100644 --- a/fhirpkg.lock.json +++ b/fhirpkg.lock.json @@ -7,7 +7,7 @@ "hl7.fhir.uv.xver-r5.r4": "0.1.0", "hl7.fhir.uv.genomics-reporting": "3.0.0", "fhir.r4.nhsengland.pathology": "0.1.4-alpha", - "hl7.fhir.eu.laboratory": "0.1.0-ballot", + "hl7.fhir.eu.laboratory": "0.1.1", "ihe.iti.pcf": "1.1.0", "fhir.r4.ukcore.stu3.currentbuild": "0.28.0-pre-release" }, diff --git a/package.json b/package.json index dd5210b..d9942bd 100644 --- a/package.json +++ b/package.json @@ -8,7 +8,7 @@ "hl7.fhir.uv.xver-r5.r4": "0.1.0", "hl7.fhir.uv.genomics-reporting": "3.0.0", "fhir.r4.nhsengland.pathology": "0.1.4-alpha", - "hl7.fhir.eu.laboratory": "0.1.0-ballot", + "hl7.fhir.eu.laboratory": "0.1.1", "ihe.iti.pcf": "1.1.0", "fhir.r4.ukcore.stu3.currentbuild": "0.28.0-pre-release" }, From d62bafb71f154dd0115e5c3b7f41684eb0e7320a Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Fri, 5 Jun 2026 09:32:53 +0100 Subject: [PATCH 33/80] Testing "hl7.fhir.eu.laboratory": "0.1.1", Testing "hl7.fhir.eu.laboratory": "0.1.1", --- 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 077222a..ce08e13 100644 --- a/fhirpkg.lock.json +++ b/fhirpkg.lock.json @@ -6,7 +6,7 @@ "hl7.fhir.uv.xver-r5.r4": "0.1.0", "hl7.fhir.uv.genomics-reporting": "3.0.0", "hl7.fhir.uv.ips": "2.0.0", - "hl7.fhir.eu.laboratory": "0.1.0-ballot", + "hl7.fhir.eu.laboratory": "0.1.1", "ihe.iti.pcf": "1.1.0", "fhir.r4.nhsengland.pathology": "0.1.4-alpha", "fhir.r4.nhsengland.nhse-identifiers": "0.1.1-alpha", diff --git a/package.json b/package.json index 77d71c4..e0bbdcc 100644 --- a/package.json +++ b/package.json @@ -8,7 +8,7 @@ "hl7.fhir.uv.xver-r5.r4": "0.1.0", "hl7.fhir.uv.genomics-reporting": "3.0.0", "hl7.fhir.uv.ips": "2.0.0", - "hl7.fhir.eu.laboratory": "0.1.0-ballot", + "hl7.fhir.eu.laboratory": "0.1.1", "ihe.iti.pcf": "1.1.0", "fhir.r4.nhsengland.pathology": "0.1.4-alpha", "fhir.r4.nhsengland.nhse-identifiers": "0.1.1-alpha", From 226bd1cf6d26ece241193dbd27f21d7be0f0e372 Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Fri, 5 Jun 2026 09:41:35 +0100 Subject: [PATCH 34/80] Add mcode Add mcode --- fhirpkg.lock.json | 1 + package.json | 1 + 2 files changed, 2 insertions(+) diff --git a/fhirpkg.lock.json b/fhirpkg.lock.json index ce08e13..6efab8e 100644 --- a/fhirpkg.lock.json +++ b/fhirpkg.lock.json @@ -8,6 +8,7 @@ "hl7.fhir.uv.ips": "2.0.0", "hl7.fhir.eu.laboratory": "0.1.1", "ihe.iti.pcf": "1.1.0", + "hl7.fhir.us.mcode": "4.0.0", "fhir.r4.nhsengland.pathology": "0.1.4-alpha", "fhir.r4.nhsengland.nhse-identifiers": "0.1.1-alpha", "fhir.r4.ukcore.stu3.currentbuild": "0.28.0-pre-release" diff --git a/package.json b/package.json index e0bbdcc..df876de 100644 --- a/package.json +++ b/package.json @@ -10,6 +10,7 @@ "hl7.fhir.uv.ips": "2.0.0", "hl7.fhir.eu.laboratory": "0.1.1", "ihe.iti.pcf": "1.1.0", + "hl7.fhir.us.mcode": "4.0.0", "fhir.r4.nhsengland.pathology": "0.1.4-alpha", "fhir.r4.nhsengland.nhse-identifiers": "0.1.1-alpha", "fhir.r4.ukcore.stu3.currentbuild": "0.28.0-pre-release" From 1671e2cbffba48f101aa69821b84b020829105cd Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Fri, 5 Jun 2026 09:47:55 +0100 Subject: [PATCH 35/80] Testing EU -lab 2..0.0 Testing EU -lab 2..0.0 --- 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 7bcd966..ccf0de6 100644 --- a/fhirpkg.lock.json +++ b/fhirpkg.lock.json @@ -7,7 +7,7 @@ "hl7.fhir.uv.xver-r5.r4": "0.1.0", "hl7.fhir.uv.genomics-reporting": "3.0.0", "fhir.r4.nhsengland.pathology": "0.1.4-alpha", - "hl7.fhir.eu.laboratory": "0.1.1", + "hl7.fhir.eu.laboratory": "2.0.0", "ihe.iti.pcf": "1.1.0", "fhir.r4.ukcore.stu3.currentbuild": "0.28.0-pre-release" }, diff --git a/package.json b/package.json index d9942bd..84b33a6 100644 --- a/package.json +++ b/package.json @@ -8,7 +8,7 @@ "hl7.fhir.uv.xver-r5.r4": "0.1.0", "hl7.fhir.uv.genomics-reporting": "3.0.0", "fhir.r4.nhsengland.pathology": "0.1.4-alpha", - "hl7.fhir.eu.laboratory": "0.1.1", + "hl7.fhir.eu.laboratory": "2.0.0", "ihe.iti.pcf": "1.1.0", "fhir.r4.ukcore.stu3.currentbuild": "0.28.0-pre-release" }, From 8d9ce8fae8b4433a5a36de136911e660103ff8e6 Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Fri, 5 Jun 2026 10:04:05 +0100 Subject: [PATCH 36/80] Testing 0.1.0-ballot Testing 0.1.0-ballot --- Patient/Patient-PheobeSmitham-Example.json | 2 +- fhirpkg.lock.json | 2 +- package.json | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/Patient/Patient-PheobeSmitham-Example.json b/Patient/Patient-PheobeSmitham-Example.json index ec1870e..82fc92c 100644 --- a/Patient/Patient-PheobeSmitham-Example.json +++ b/Patient/Patient-PheobeSmitham-Example.json @@ -4,7 +4,7 @@ "meta": { "profile": [ "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Patient", - "http://hl7.eu/fhir/base/StructureDefinition/patient-eu" + "http://hl7.eu/fhir/laboratory/StructureDefinition/Patient-eu-lab" ] }, "extension": [ diff --git a/fhirpkg.lock.json b/fhirpkg.lock.json index ccf0de6..7c03480 100644 --- a/fhirpkg.lock.json +++ b/fhirpkg.lock.json @@ -7,7 +7,7 @@ "hl7.fhir.uv.xver-r5.r4": "0.1.0", "hl7.fhir.uv.genomics-reporting": "3.0.0", "fhir.r4.nhsengland.pathology": "0.1.4-alpha", - "hl7.fhir.eu.laboratory": "2.0.0", + "hl7.fhir.eu.laboratory": "0.1.0-ballot", "ihe.iti.pcf": "1.1.0", "fhir.r4.ukcore.stu3.currentbuild": "0.28.0-pre-release" }, diff --git a/package.json b/package.json index 84b33a6..dd5210b 100644 --- a/package.json +++ b/package.json @@ -8,7 +8,7 @@ "hl7.fhir.uv.xver-r5.r4": "0.1.0", "hl7.fhir.uv.genomics-reporting": "3.0.0", "fhir.r4.nhsengland.pathology": "0.1.4-alpha", - "hl7.fhir.eu.laboratory": "2.0.0", + "hl7.fhir.eu.laboratory": "0.1.0-ballot", "ihe.iti.pcf": "1.1.0", "fhir.r4.ukcore.stu3.currentbuild": "0.28.0-pre-release" }, From 4d83f89f70ff607d6bdcc905a671e630344f9a2d Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Fri, 5 Jun 2026 11:30:53 +0100 Subject: [PATCH 37/80] Testing 0.1.0-ballot Testing 0.1.0-ballot --- 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 6efab8e..7ba1b4f 100644 --- a/fhirpkg.lock.json +++ b/fhirpkg.lock.json @@ -6,7 +6,7 @@ "hl7.fhir.uv.xver-r5.r4": "0.1.0", "hl7.fhir.uv.genomics-reporting": "3.0.0", "hl7.fhir.uv.ips": "2.0.0", - "hl7.fhir.eu.laboratory": "0.1.1", + "hl7.fhir.eu.laboratory": "0.1.0-ballot", "ihe.iti.pcf": "1.1.0", "hl7.fhir.us.mcode": "4.0.0", "fhir.r4.nhsengland.pathology": "0.1.4-alpha", diff --git a/package.json b/package.json index df876de..0e76c1c 100644 --- a/package.json +++ b/package.json @@ -8,7 +8,7 @@ "hl7.fhir.uv.xver-r5.r4": "0.1.0", "hl7.fhir.uv.genomics-reporting": "3.0.0", "hl7.fhir.uv.ips": "2.0.0", - "hl7.fhir.eu.laboratory": "0.1.1", + "hl7.fhir.eu.laboratory": "0.1.0-ballot", "ihe.iti.pcf": "1.1.0", "hl7.fhir.us.mcode": "4.0.0", "fhir.r4.nhsengland.pathology": "0.1.4-alpha", From 147a74a182d74e4330d236c5d77d6794a19354f7 Mon Sep 17 00:00:00 2001 From: Ryan May <112563297+ryma2fhir@users.noreply.github.com> Date: Fri, 5 Jun 2026 11:43:47 +0100 Subject: [PATCH 38/80] Add implementation guides to private.package.yaml --- private.package.yaml | 55 ++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 private.package.yaml diff --git a/private.package.yaml b/private.package.yaml new file mode 100644 index 0000000..5e6e0b7 --- /dev/null +++ b/private.package.yaml @@ -0,0 +1,55 @@ +implementationguides: + hl7-fhir-uv-extensions-r4: + name: hl7.fhir.uv.extensions.r4 + version: 5.3.0-ballot-tc1 + installMode: STORE_AND_INSTALL + fetchDependencies: false + hl7-fhir-uv-xver-r5-r4: + name: hl7.fhir.uv.xver-r5.r4 + version: 0.1.0 + installMode: STORE_AND_INSTALL + fetchDependencies: false + hl7-fhir-uv-genomics-reporting: + name: hl7.fhir.uv.genomics-reporting + version: 3.0.0 + installMode: STORE_AND_INSTALL + fetchDependencies: false + hl7-fhir-uv-ips: + name: hl7.fhir.uv.ips + version: 2.0.0 + installMode: STORE_AND_INSTALL + fetchDependencies: false + hl7-fhir-eu-laboratory: + name: hl7.fhir.eu.laboratory + version: 0.1.1 + installMode: STORE_AND_INSTALL + fetchDependencies: false + ihe-iti-pcf: + name: ihe.iti.pcf + version: 1.1.0 + installMode: STORE_AND_INSTALL + fetchDependencies: false + hl7-fhir-us-mcode: + name: hl7.fhir.us.mcode + version: 4.0.0 + installMode: STORE_AND_INSTALL + fetchDependencies: false + fhir-r4-nhsengland-pathology: + name: fhir.r4.nhsengland.pathology + version: 0.1.4-alpha + installMode: STORE_AND_INSTALL + fetchDependencies: false + hl7-fhir-uv-tools-r4: + name: hl7.fhir.uv.tools.r4 + version: 1.1.2 + installMode: STORE_AND_INSTALL + fhir-r4-nhsengland-nhse-identifiers: + name: fhir.r4.nhsengland.nhse-identifiers + version: 0.1.1-alpha + installMode: STORE_AND_INSTALL + fetchDependencies: false + fhir-r4-ukcore-stu3-currentbuild: + name: fhir.r4.ukcore.stu3.currentbuild + version: 0.28.0-pre-release + installMode: STORE_AND_INSTALL + fetchDependencies: false From 5b79259798154b09724bb9786dc77a3fe6f3063a Mon Sep 17 00:00:00 2001 From: Ryan May <112563297+ryma2fhir@users.noreply.github.com> Date: Fri, 5 Jun 2026 11:44:27 +0100 Subject: [PATCH 39/80] Remove outdated FHIR dependencies from package.json Removed several outdated dependencies related to FHIR. --- package.json | 12 +----------- 1 file changed, 1 insertion(+), 11 deletions(-) diff --git a/package.json b/package.json index 0e76c1c..80bf662 100644 --- a/package.json +++ b/package.json @@ -4,19 +4,9 @@ "author": "nhsdigital", "dependencies": { "hl7.fhir.r4.core": "4.0.1", - "hl7.fhir.uv.extensions.r4": "5.3.0-ballot-tc1", - "hl7.fhir.uv.xver-r5.r4": "0.1.0", - "hl7.fhir.uv.genomics-reporting": "3.0.0", - "hl7.fhir.uv.ips": "2.0.0", - "hl7.fhir.eu.laboratory": "0.1.0-ballot", - "ihe.iti.pcf": "1.1.0", - "hl7.fhir.us.mcode": "4.0.0", - "fhir.r4.nhsengland.pathology": "0.1.4-alpha", - "fhir.r4.nhsengland.nhse-identifiers": "0.1.1-alpha", - "fhir.r4.ukcore.stu3.currentbuild": "0.28.0-pre-release" }, "fhirVersions": [ "4.0.1" ], "jurisdiction": "urn:iso:std:iso:3166:-2#GB" -} \ No newline at end of file +} From 16b3b29512dbdaa76e448d99def39b33162c4bbf Mon Sep 17 00:00:00 2001 From: Ryan May <112563297+ryma2fhir@users.noreply.github.com> Date: Fri, 5 Jun 2026 11:49:57 +0100 Subject: [PATCH 40/80] Update package.json --- package.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package.json b/package.json index 80bf662..eabc112 100644 --- a/package.json +++ b/package.json @@ -3,7 +3,7 @@ "description": "FHIR Genomics Implementation Guide", "author": "nhsdigital", "dependencies": { - "hl7.fhir.r4.core": "4.0.1", + "hl7.fhir.r4.core": "4.0.1" }, "fhirVersions": [ "4.0.1" From 6e94845ee7c7a2a21c74e4170394cb2bbd65c04c Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Fri, 5 Jun 2026 12:35:52 +0100 Subject: [PATCH 41/80] Testing with Private Package Testing with Private Package --- fhirpkg.lock.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/fhirpkg.lock.json b/fhirpkg.lock.json index 7ba1b4f..6efab8e 100644 --- a/fhirpkg.lock.json +++ b/fhirpkg.lock.json @@ -6,7 +6,7 @@ "hl7.fhir.uv.xver-r5.r4": "0.1.0", "hl7.fhir.uv.genomics-reporting": "3.0.0", "hl7.fhir.uv.ips": "2.0.0", - "hl7.fhir.eu.laboratory": "0.1.0-ballot", + "hl7.fhir.eu.laboratory": "0.1.1", "ihe.iti.pcf": "1.1.0", "hl7.fhir.us.mcode": "4.0.0", "fhir.r4.nhsengland.pathology": "0.1.4-alpha", From 7c26fb957946b827f1eab368f3c79d5fc99b5a1b Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Fri, 5 Jun 2026 14:53:14 +0100 Subject: [PATCH 42/80] Update Update --- .../NHSEngland-Composition-GenomicsEULabReport.json | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json b/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json index 03fa987..a5df0b2 100644 --- a/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json +++ b/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json @@ -64,6 +64,7 @@ { "id": "Composition.extension:information-recipient.value[x]", "path": "Composition.extension.value[x]", + "sliceName": "valueReference", "type": [ { "code": "Reference", @@ -240,9 +241,9 @@ { "code": "Reference", "targetProfile": [ - "http://hl7.eu/fhir/base/StructureDefinition/patient-eu-core", + "http://hl7.eu/fhir/laboratory/StructureDefinition/Patient-eu-lab", "http://hl7.org/fhir/StructureDefinition/Group", - "http://hl7.eu/fhir/base/StructureDefinition/location-eu-core", + "http://hl7.org/fhir/StructureDefinition/Location", "http://hl7.org/fhir/StructureDefinition/Device" ], "aggregation": [ From 1d565a162a14ea79de2c1c5ec00fb498a2b9ac02 Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Fri, 5 Jun 2026 17:34:08 +0100 Subject: [PATCH 43/80] Testing IOPS Val Testing IOPS Val --- .github/workflows/firely-validation.yml | 10 +- .github/workflows/terminology.yml | 2 +- ...gland-Composition-GenomicsEULabReport.json | 621 +++++++++--------- 3 files changed, 320 insertions(+), 313 deletions(-) diff --git a/.github/workflows/firely-validation.yml b/.github/workflows/firely-validation.yml index bb8cbd9..2d31c30 100644 --- a/.github/workflows/firely-validation.yml +++ b/.github/workflows/firely-validation.yml @@ -5,11 +5,11 @@ name: Firely Validation # Controls when the action will run. on: # Triggers the workflow on push or pull request events but only for the master branch - push: - branches: - - '**' - pull_request: - branches: [ master, main ] + #push: + #branches: + #- '**' + #pull_request: + #branches: [ master, main ] # Allows you to run this workflow manually from the Actions tab workflow_dispatch: diff --git a/.github/workflows/terminology.yml b/.github/workflows/terminology.yml index 5174c15..a6f2ed8 100644 --- a/.github/workflows/terminology.yml +++ b/.github/workflows/terminology.yml @@ -5,7 +5,7 @@ on: # Triggers the workflow on push or pull request events but only for the master branch # Allows you to run this workflow manually from the Actions tab - #push: + push: # Allows you to run this workflow manually from the Actions tab diff --git a/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json b/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json index a5df0b2..f6ccc9a 100644 --- a/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json +++ b/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json @@ -1,314 +1,321 @@ { - "resourceType": "StructureDefinition", - "id": "NHSEngland-Composition-GenomicsEULabReport", - "url": "https://fhir.nhs.uk/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport", - "version": "0.4.0", - "name": "NHSEngland_Composition_GenomicsEULabReport", - "title": "NHSEngland Composition GenomicsEULabReport", - "status": "active", - "date": "2026-06-03", - "publisher": "NHS England", - "contact": [ - { - "name": "NHS England", - "telecom": [ + "resourceType": "StructureDefinition", + "id": "NHSEngland-Composition-GenomicsEULabReport", + "url": "https://fhir.nhs.uk/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport", + "version": "0.3.0", + "name": "NHSEngland_Composition_GenomicsEULabReport", + "title": "NHSEngland Composition GenomicsEULabReport", + "status": "active", + "date": "2026-04-16", + "publisher": "NHS England", + "contact": [ { - "system": "email", - "value": "interoperabilityteam@nhs.net", - "use": "work", - "rank": 1 - } - ] - } - ], - "description": "This profile defines the Genomics constraints and extensions on the EU Lab FHIR resource [EU Lab Composition](http://hl7.eu/fhir/laboratory/StructureDefinition/Composition-eu-lab).", - "purpose": "There are two use cases for Compositions within Genomics.\r\n\r\nFor Order Management, Compositions will be limited to documents generated by the central broker for capturing snapshots of Test orders and results in order to maintain historical accuracy, as per the DocumentReference generate OperationDefinition. These will typically form the first entry of a Document Bundle and as such will not be exposed via their own endpoint, nor allow creates, reads or updates from client systems on the resource itself.\r\n\r\nTo support cross border data sharing Compositions MAY be aligned to the HL7 EU Lab Composition profile as a wrap around structured reports.\r\n\r\nFor the Unified Genomic Record, Compositions will form the header or 'contents page' of the UGR itself. section elements will be used to emulate the UGR folders. ", - "copyright": "Copyright © 2026+ NHS England Licensed under the Apache License, Version 2.0 (the \\\\\\\"License\\\\\\\"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \\\\\\\"AS IS\\\\\\\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. HL7® FHIR® standard Copyright © 2011+ HL7 The HL7® FHIR® standard is used under the FHIR license. You may obtain a copy of the FHIR license at https://www.hl7.org/fhir/license.html.", - "fhirVersion": "4.0.1", - "kind": "resource", - "abstract": false, - "type": "Composition", - "baseDefinition": "http://hl7.eu/fhir/laboratory/StructureDefinition/Composition-eu-lab", - "derivation": "constraint", - "differential": { - "element": [ - { - "id": "Composition.extension:basedOn-order-or-requisition", - "path": "Composition.extension", - "sliceName": "basedOn-order-or-requisition", - "definition": "TBC. Only relevant for EU Lab aligned reports (included in HL7 EU Laboratory Report: Composition Profile). A reference to the ServiceRequest which this report is in response to." - }, - { - "id": "Composition.extension:basedOn-order-or-requisition.value[x]:valueReference", - "path": "Composition.extension.value[x]", - "sliceName": "valueReference", - "type": [ - { - "code": "Reference", - "targetProfile": [ - "http://hl7.eu/fhir/laboratory/StructureDefinition/ServiceRequest-eu-lab" - ], - "aggregation": [ - "referenced", - "bundled" - ] - } - ] - }, - { - "id": "Composition.extension:information-recipient", - "path": "Composition.extension", - "sliceName": "information-recipient", - "definition": "TBC. Only relevant for EU Lab aligned reports (included in HL7 EU Laboratory Report: Composition Profile). A reference to the recipient for a report, could potentially be used to reference additional recipients over the subject and original requester for the request." - }, - { - "id": "Composition.extension:information-recipient.value[x]", - "path": "Composition.extension.value[x]", - "sliceName": "valueReference", - "type": [ - { - "code": "Reference", - "targetProfile": [ - "https://fhir.nhs.uk/StructureDefinition/NHSEngland-PractitionerRole-Genomics", - "http://hl7.eu/fhir/laboratory/StructureDefinition/Practitioner-eu-lab", - "http://hl7.org/fhir/StructureDefinition/Device", - "http://hl7.eu/fhir/laboratory/StructureDefinition/Patient-eu-lab", - "http://hl7.org/fhir/StructureDefinition/RelatedPerson", - "http://hl7.eu/fhir/laboratory/StructureDefinition/PractitionerRole-eu-lab", - "http://hl7.org/fhir/StructureDefinition/Organization" - ], - "aggregation": [ - "referenced", - "bundled" + "name": "NHS England", + "telecom": [ + { + "system": "email", + "value": "interoperabilityteam@nhs.net", + "use": "work", + "rank": 1 + } ] - } - ] - }, - { - "id": "Composition.extension:diagnosticReport-reference", - "path": "Composition.extension", - "sliceName": "diagnosticReport-reference", - "definition": "TBC. Only relevant for EU Lab aligned reports (included in HL7 EU Laboratory Report: Composition Profile). A reference to the focal DiagnosticReport this Composition is for." - }, - { - "id": "Composition.extension:diagnosticReport-reference.value[x]", - "path": "Composition.extension.value[x]", - "type": [ - { - "code": "Reference", - "targetProfile": [ - "https://fhir.nhs.uk/StructureDefinition/NHSEngland-DiagnosticReport-GenomicReport", - "http://hl7.eu/fhir/laboratory/StructureDefinition/DiagnosticReport-eu-lab" - ], - "aggregation": [ - "referenced", - "bundled" - ] - } - ] - }, - { - "id": "Composition.status", - "path": "Composition.status", - "definition": "Fixed value of 'final'", - "fixedCode": "final" - }, - { - "id": "Composition.type", - "path": "Composition.type", - "definition": "SNOMED CT code for either a Laboratory Request (24691000000102) or Genetic report (1054161000000101)" - }, - { - "id": "Composition.type.coding", - "path": "Composition.type.coding", - "slicing": { - "discriminator": [ - { - "type": "pattern", - "path": "$this" - } - ], - "rules": "open" - } - }, - { - "id": "Composition.type.coding.display.extension:translation", - "path": "Composition.type.coding.display.extension", - "sliceName": "translation" - }, - { - "id": "Composition.type.coding.display.extension:translation.extension", - "path": "Composition.type.coding.display.extension.extension", - "min": 2 - }, - { - "id": "Composition.type.coding:codingGenomics", - "path": "Composition.type.coding", - "sliceName": "codingGenomics", - "fixedCoding": { - "system": "http://snomed.info/sct", - "code": "1054161000000101", - "display": "Genetic report" - } - }, - { - "id": "Composition.type.coding:codingGenomics.display.extension:translation", - "path": "Composition.type.coding.display.extension", - "sliceName": "translation" - }, - { - "id": "Composition.type.coding:codingGenomics.display.extension:translation.extension", - "path": "Composition.type.coding.display.extension.extension", - "min": 2 - }, - { - "id": "Composition.type.text.extension:translation", - "path": "Composition.type.text.extension", - "sliceName": "translation" - }, - { - "id": "Composition.type.text.extension:translation.extension", - "path": "Composition.type.text.extension.extension", - "min": 2 - }, - { - "id": "Composition.category", - "path": "Composition.category", - "slicing": { - "discriminator": [ - { - "type": "value", - "path": "$this" - } - ], - "rules": "open" - }, - "definition": "Fixed codes for conformance to the EU Lab Composition profile (for cross border sharing of lab reports)." - }, - { - "id": "Composition.category.coding.display.extension:translation", - "path": "Composition.category.coding.display.extension", - "sliceName": "translation" - }, - { - "id": "Composition.category.coding.display.extension:translation.extension", - "path": "Composition.category.coding.display.extension.extension", - "min": 2 - }, - { - "id": "Composition.category.text.extension:translation", - "path": "Composition.category.text.extension", - "sliceName": "translation" - }, - { - "id": "Composition.category.text.extension:translation.extension", - "path": "Composition.category.text.extension.extension", - "min": 2 - }, - { - "id": "Composition.category:studyType", - "path": "Composition.category", - "sliceName": "studyType", - "fixedCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "26436-6", - "display": "Laboratory studies (set)" - } - ] } - }, - { - "id": "Composition.category:specialty", - "path": "Composition.category", - "sliceName": "specialty", - "fixedCodeableConcept": { - "coding": [ - { - "system": "http://snomed.info/sct", - "code": "1236877003", - "display": "Genetic pathology" + ], + "description": "This profile defines the Genomics constraints and extensions on the EU Lab FHIR resource [EU Lab Composition](http://hl7.eu/fhir/laboratory/StructureDefinition/Composition-eu-lab).", + "purpose": "There are two use cases for Compositions within Genomics.\r\n\r\nFor Order Management, Compositions will be limited to documents generated by the central broker for capturing snapshots of Test orders and results in order to maintain historical accuracy, as per the DocumentReference generate OperationDefinition. These will typically form the first entry of a Document Bundle and as such will not be exposed via their own endpoint, nor allow creates, reads or updates from client systems on the resource itself.\r\n\r\nTo support cross border data sharing Compositions MAY be aligned to the HL7 EU Lab Composition profile as a wrap around structured reports.\r\n\r\nFor the Unified Genomic Record, Compositions will form the header or 'contents page' of the UGR itself. section elements will be used to emulate the UGR folders. ", + "copyright": "Copyright © 2026+ NHS England Licensed under the Apache License, Version 2.0 (the \\\\\\\"License\\\\\\\"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \\\\\\\"AS IS\\\\\\\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. HL7® FHIR® standard Copyright © 2011+ HL7 The HL7® FHIR® standard is used under the FHIR license. You may obtain a copy of the FHIR license at https://www.hl7.org/fhir/license.html.", + "fhirVersion": "4.0.1", + "kind": "resource", + "abstract": false, + "type": "Composition", + "baseDefinition": "http://hl7.eu/fhir/laboratory/StructureDefinition/Composition-eu-lab", + "derivation": "constraint", + "differential": { + "element": [ + { + "id": "Composition.extension:basedOn-order-or-requisition", + "path": "Composition.extension", + "sliceName": "basedOn-order-or-requisition", + "definition": "TBC. Only relevant for EU Lab aligned reports (included in HL7 EU Laboratory Report: Composition Profile). A reference to the ServiceRequest which this report is in response to." + }, + { + "id": "Composition.extension:basedOn-order-or-requisition.value[x]:valueReference", + "path": "Composition.extension.value[x]", + "sliceName": "valueReference", + "type": [ + { + "code": "Reference", + "targetProfile": [ + "https://fhir.nhs.uk/StructureDefinition/NHSEngland-ServiceRequest-Genomics", + "http://hl7.eu/fhir/laboratory/StructureDefinition/ServiceRequest-eu-lab" + ], + "aggregation": [ + "referenced", + "bundled" + ] + } + ] + }, + { + "id": "Composition.extension:information-recipient", + "path": "Composition.extension", + "sliceName": "information-recipient", + "definition": "TBC. Only relevant for EU Lab aligned reports (included in HL7 EU Laboratory Report: Composition Profile). A reference to the recipient for a report, could potentially be used to reference additional recipients over the subject and original requester for the request." + }, + { + "id": "Composition.extension:information-recipient.value[x]", + "path": "Composition.extension.value[x]", + "type": [ + { + "code": "Reference", + "targetProfile": [ + "https://fhir.nhs.uk/StructureDefinition/NHSEngland-PractitionerRole-Genomics", + "http://hl7.eu/fhir/laboratory/StructureDefinition/Practitioner-eu-lab", + "http://hl7.org/fhir/StructureDefinition/Device", + "http://hl7.eu/fhir/laboratory/StructureDefinition/Patient-eu-lab", + "http://hl7.org/fhir/StructureDefinition/RelatedPerson", + "http://hl7.eu/fhir/laboratory/StructureDefinition/PractitionerRole-eu-lab", + "http://hl7.org/fhir/StructureDefinition/Organization" + ], + "aggregation": [ + "referenced", + "bundled" + ] + } + ] + }, + { + "id": "Composition.extension:diagnosticReport-reference", + "path": "Composition.extension", + "sliceName": "diagnosticReport-reference", + "definition": "TBC. Only relevant for EU Lab aligned reports (included in HL7 EU Laboratory Report: Composition Profile). A reference to the focal DiagnosticReport this Composition is for." + }, + { + "id": "Composition.extension:diagnosticReport-reference.url", + "path": "Composition.extension.url", + "fixedUri": "diagnosticReport-reference" + }, + { + "id": "Composition.extension:diagnosticReport-reference.value[x]", + "path": "Composition.extension.value[x]", + "type": [ + { + "code": "Reference", + "targetProfile": [ + "https://fhir.nhs.uk/StructureDefinition/NHSEngland-DiagnosticReport-GenomicReport", + "http://hl7.eu/fhir/laboratory/StructureDefinition/DiagnosticReport-eu-lab" + ], + "aggregation": [ + "referenced", + "bundled" + ] + } + ] + }, + { + "id": "Composition.status", + "path": "Composition.status", + "definition": "Fixed value of 'final'", + "fixedCode": "final" + }, + { + "id": "Composition.type", + "path": "Composition.type", + "definition": "SNOMED CT code for either a Laboratory Request (24691000000102) or Genetic report (1054161000000101)" + }, + { + "id": "Composition.type.coding", + "path": "Composition.type.coding", + "slicing": { + "discriminator": [ + { + "type": "pattern", + "path": "$this" + } + ], + "rules": "open" + } + }, + { + "id": "Composition.type.coding.display.extension:translation", + "path": "Composition.type.coding.display.extension", + "sliceName": "translation" + }, + { + "id": "Composition.type.coding.display.extension:translation.extension", + "path": "Composition.type.coding.display.extension.extension", + "min": 2 + }, + { + "id": "Composition.type.coding:codingGenomics", + "path": "Composition.type.coding", + "sliceName": "codingGenomics", + "fixedCoding": { + "system": "http://snomed.info/sct", + "code": "1054161000000101", + "display": "Genetic report" + } + }, + { + "id": "Composition.type.coding:codingGenomics.display.extension:translation", + "path": "Composition.type.coding.display.extension", + "sliceName": "translation" + }, + { + "id": "Composition.type.coding:codingGenomics.display.extension:translation.extension", + "path": "Composition.type.coding.display.extension.extension", + "min": 2 + }, + { + "id": "Composition.type.text.extension:translation", + "path": "Composition.type.text.extension", + "sliceName": "translation" + }, + { + "id": "Composition.type.text.extension:translation.extension", + "path": "Composition.type.text.extension.extension", + "min": 2 + }, + { + "id": "Composition.category", + "path": "Composition.category", + "slicing": { + "discriminator": [ + { + "type": "value", + "path": "$this" + } + ], + "rules": "open" + }, + "definition": "Fixed codes for conformance to the EU Lab Composition profile (for cross border sharing of lab reports)." + }, + { + "id": "Composition.category.coding.display.extension:translation", + "path": "Composition.category.coding.display.extension", + "sliceName": "translation" + }, + { + "id": "Composition.category.coding.display.extension:translation.extension", + "path": "Composition.category.coding.display.extension.extension", + "min": 2 + }, + { + "id": "Composition.category.text.extension:translation", + "path": "Composition.category.text.extension", + "sliceName": "translation" + }, + { + "id": "Composition.category.text.extension:translation.extension", + "path": "Composition.category.text.extension.extension", + "min": 2 + }, + { + "id": "Composition.category:studyType", + "path": "Composition.category", + "sliceName": "studyType", + "fixedCodeableConcept": { + "coding": [ + { + "system": "http://loinc.org", + "code": "26436-6", + "display": "Laboratory studies (set)" + } + ] + } + }, + { + "id": "Composition.category:specialty", + "path": "Composition.category", + "sliceName": "specialty", + "fixedCodeableConcept": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "1236877003", + "display": "Genetic pathology" + } + ] + } + }, + { + "id": "Composition.subject", + "path": "Composition.subject", + "definition": "Matches subject reference included in either the DiagnosticReport or ServiceRequest", + "type": [ + { + "code": "Reference", + "targetProfile": [ + "https://fhir.nhs.uk/StructureDefinition/NHSEngland-Patient-Genomics", + "http://hl7.eu/fhir/laboratory/StructureDefinition/Patient-eu-lab", + "http://hl7.eu/fhir/laboratory/StructureDefinition/Patient-animal-eu-lab", + "http://hl7.org/fhir/StructureDefinition/Group", + "http://hl7.org/fhir/StructureDefinition/Location", + "http://hl7.org/fhir/StructureDefinition/Device" + ], + "aggregation": [ + "referenced", + "bundled" + ] + } + ] + }, + { + "id": "Composition.date", + "path": "Composition.date", + "definition": "SHALL be the dateTime the Composition was generated by the central broker" + }, + { + "id": "Composition.author", + "path": "Composition.author", + "definition": "Fixed to an identifier for the central broker (TBC). The author for the underlying ServiceRequest or DiagnosticReport can be retrieved by interrogating the appropriate resources." + }, + { + "id": "Composition.title", + "path": "Composition.title", + "definition": "SHALL match the SNOMED CT display used within Composition.type", + "fixedString": "Genetic report" + }, + { + "id": "Composition.section", + "path": "Composition.section", + "definition": "To conform to EU Lab, SHOULD include references to the results that form part of the genomic report. For the UGR, will include sections that conform to the UGR folders, this work is currently in development." + }, + { + "id": "Composition.section.code.coding.display.extension:translation", + "path": "Composition.section.code.coding.display.extension", + "sliceName": "translation" + }, + { + "id": "Composition.section.code.coding.display.extension:translation.extension", + "path": "Composition.section.code.coding.display.extension.extension", + "min": 2 + }, + { + "id": "Composition.section.code.text.extension:translation", + "path": "Composition.section.code.text.extension", + "sliceName": "translation" + }, + { + "id": "Composition.section.code.text.extension:translation.extension", + "path": "Composition.section.code.text.extension.extension", + "min": 2 + }, + { + "id": "Composition.section:sectionUGR", + "path": "Composition.section", + "sliceName": "sectionUGR", + "definition": "Sections included within the UGR: patient-demographics | investigations-and-procedures-requested | investigation-results | consent-for-information-sharing | family-history " + }, + { + "id": "Composition.section:sectionUGR.code", + "path": "Composition.section.code", + "binding": { + "strength": "extensible", + "description": "UK Core Composition Section Codes", + "valueSet": "https://fhir.hl7.org.uk/ValueSet/UKCore-CompositionSectionCode" + } } - ] - } - }, - { - "id": "Composition.subject", - "path": "Composition.subject", - "definition": "Matches subject reference included in either the DiagnosticReport or ServiceRequest", - "type": [ - { - "code": "Reference", - "targetProfile": [ - "http://hl7.eu/fhir/laboratory/StructureDefinition/Patient-eu-lab", - "http://hl7.org/fhir/StructureDefinition/Group", - "http://hl7.org/fhir/StructureDefinition/Location", - "http://hl7.org/fhir/StructureDefinition/Device" - ], - "aggregation": [ - "referenced", - "bundled" - ] - } ] - }, - { - "id": "Composition.date", - "path": "Composition.date", - "definition": "SHALL be the dateTime the Composition was generated by the central broker" - }, - { - "id": "Composition.author", - "path": "Composition.author", - "definition": "Fixed to an identifier for the central broker (TBC). The author for the underlying ServiceRequest or DiagnosticReport can be retrieved by interrogating the appropriate resources." - }, - { - "id": "Composition.title", - "path": "Composition.title", - "definition": "SHALL match the SNOMED CT display used within Composition.type", - "fixedString": "Genetic report" - }, - { - "id": "Composition.section", - "path": "Composition.section", - "definition": "To conform to EU Lab, SHOULD include references to the results that form part of the genomic report. For the UGR, will include sections that conform to the UGR folders, this work is currently in development." - }, - { - "id": "Composition.section.code.coding.display.extension:translation", - "path": "Composition.section.code.coding.display.extension", - "sliceName": "translation" - }, - { - "id": "Composition.section.code.coding.display.extension:translation.extension", - "path": "Composition.section.code.coding.display.extension.extension", - "min": 2 - }, - { - "id": "Composition.section.code.text.extension:translation", - "path": "Composition.section.code.text.extension", - "sliceName": "translation" - }, - { - "id": "Composition.section.code.text.extension:translation.extension", - "path": "Composition.section.code.text.extension.extension", - "min": 2 - }, - { - "id": "Composition.section:sectionUGR", - "path": "Composition.section", - "sliceName": "sectionUGR", - "definition": "Sections included within the UGR: patient-demographics | investigations-and-procedures-requested | investigation-results | consent-for-information-sharing | family-history " - }, - { - "id": "Composition.section:sectionUGR.code", - "path": "Composition.section.code", - "binding": { - "strength": "extensible", - "description": "UK Core Composition Section Codes", - "valueSet": "https://fhir.hl7.org.uk/ValueSet/UKCore-CompositionSectionCode" - } - } - ] - } + } } \ No newline at end of file From 6642d20dca55d0c6c5a0601b79c9995ea14014d9 Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Sat, 6 Jun 2026 09:50:07 +0100 Subject: [PATCH 44/80] Validation Issues: Slicing Validation Issues: Slicing --- ...ngland-Composition-GenomicsEULabReport.json | 18 ++---------------- 1 file changed, 2 insertions(+), 16 deletions(-) diff --git a/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json b/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json index f6ccc9a..24ab95e 100644 --- a/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json +++ b/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json @@ -2,11 +2,11 @@ "resourceType": "StructureDefinition", "id": "NHSEngland-Composition-GenomicsEULabReport", "url": "https://fhir.nhs.uk/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport", - "version": "0.3.0", + "version": "0.4.0", "name": "NHSEngland_Composition_GenomicsEULabReport", "title": "NHSEngland Composition GenomicsEULabReport", "status": "active", - "date": "2026-04-16", + "date": "2026-06-03", "publisher": "NHS England", "contact": [ { @@ -90,11 +90,6 @@ "sliceName": "diagnosticReport-reference", "definition": "TBC. Only relevant for EU Lab aligned reports (included in HL7 EU Laboratory Report: Composition Profile). A reference to the focal DiagnosticReport this Composition is for." }, - { - "id": "Composition.extension:diagnosticReport-reference.url", - "path": "Composition.extension.url", - "fixedUri": "diagnosticReport-reference" - }, { "id": "Composition.extension:diagnosticReport-reference.value[x]", "path": "Composition.extension.value[x]", @@ -179,15 +174,6 @@ { "id": "Composition.category", "path": "Composition.category", - "slicing": { - "discriminator": [ - { - "type": "value", - "path": "$this" - } - ], - "rules": "open" - }, "definition": "Fixed codes for conformance to the EU Lab Composition profile (for cross border sharing of lab reports)." }, { From 9dc6870dbe737e9e8120ef2e624d9bef053d1589 Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Sat, 6 Jun 2026 09:58:29 +0100 Subject: [PATCH 45/80] Add mcode Add mcode --- StructureDefinition/NHSEngland-BodyStructure-GenomicsmCODE.json | 1 - private.package.yaml | 2 +- 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/StructureDefinition/NHSEngland-BodyStructure-GenomicsmCODE.json b/StructureDefinition/NHSEngland-BodyStructure-GenomicsmCODE.json index e41b28c..3544181 100644 --- a/StructureDefinition/NHSEngland-BodyStructure-GenomicsmCODE.json +++ b/StructureDefinition/NHSEngland-BodyStructure-GenomicsmCODE.json @@ -54,7 +54,6 @@ { "code": "Reference", "targetProfile": [ - "https://fhir.nhs.uk/StructureDefinition/NHSEngland-Patient-Genomics", "http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-cancer-patient" ], "aggregation": [ diff --git a/private.package.yaml b/private.package.yaml index 5e6e0b7..bf7f55a 100644 --- a/private.package.yaml +++ b/private.package.yaml @@ -33,7 +33,7 @@ implementationguides: name: hl7.fhir.us.mcode version: 4.0.0 installMode: STORE_AND_INSTALL - fetchDependencies: false + fetchDependencies: true fhir-r4-nhsengland-pathology: name: fhir.r4.nhsengland.pathology version: 0.1.4-alpha From 56490a12e6e05c6058e3a7db740e966670a06ce5 Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Sat, 6 Jun 2026 10:06:08 +0100 Subject: [PATCH 46/80] Testing "hl7.fhir.us.mcode.r4": "4.0.0-ballot", Testing "hl7.fhir.us.mcode.r4": "4.0.0-ballot", --- fhirpkg.lock.json | 2 +- private.package.yaml | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/fhirpkg.lock.json b/fhirpkg.lock.json index 6efab8e..7606172 100644 --- a/fhirpkg.lock.json +++ b/fhirpkg.lock.json @@ -8,7 +8,7 @@ "hl7.fhir.uv.ips": "2.0.0", "hl7.fhir.eu.laboratory": "0.1.1", "ihe.iti.pcf": "1.1.0", - "hl7.fhir.us.mcode": "4.0.0", + "hl7.fhir.us.mcode.r4": "4.0.0-ballot", "fhir.r4.nhsengland.pathology": "0.1.4-alpha", "fhir.r4.nhsengland.nhse-identifiers": "0.1.1-alpha", "fhir.r4.ukcore.stu3.currentbuild": "0.28.0-pre-release" diff --git a/private.package.yaml b/private.package.yaml index bf7f55a..14a905c 100644 --- a/private.package.yaml +++ b/private.package.yaml @@ -30,8 +30,8 @@ implementationguides: installMode: STORE_AND_INSTALL fetchDependencies: false hl7-fhir-us-mcode: - name: hl7.fhir.us.mcode - version: 4.0.0 + name: hl7.fhir.us.mcode.r4 + version: 4.0.0-ballot installMode: STORE_AND_INSTALL fetchDependencies: true fhir-r4-nhsengland-pathology: From 4dd98e3a3c3762bffd7335b4e810b2cd16eb4cfd Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Sat, 6 Jun 2026 10:24:46 +0100 Subject: [PATCH 47/80] Revert Revert --- fhirpkg.lock.json | 2 +- private.package.yaml | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/fhirpkg.lock.json b/fhirpkg.lock.json index 7606172..6efab8e 100644 --- a/fhirpkg.lock.json +++ b/fhirpkg.lock.json @@ -8,7 +8,7 @@ "hl7.fhir.uv.ips": "2.0.0", "hl7.fhir.eu.laboratory": "0.1.1", "ihe.iti.pcf": "1.1.0", - "hl7.fhir.us.mcode.r4": "4.0.0-ballot", + "hl7.fhir.us.mcode": "4.0.0", "fhir.r4.nhsengland.pathology": "0.1.4-alpha", "fhir.r4.nhsengland.nhse-identifiers": "0.1.1-alpha", "fhir.r4.ukcore.stu3.currentbuild": "0.28.0-pre-release" diff --git a/private.package.yaml b/private.package.yaml index 14a905c..b43857f 100644 --- a/private.package.yaml +++ b/private.package.yaml @@ -30,15 +30,15 @@ implementationguides: installMode: STORE_AND_INSTALL fetchDependencies: false hl7-fhir-us-mcode: - name: hl7.fhir.us.mcode.r4 - version: 4.0.0-ballot + name: hl7.fhir.us.mcode + version: 4.0.0 installMode: STORE_AND_INSTALL fetchDependencies: true fhir-r4-nhsengland-pathology: name: fhir.r4.nhsengland.pathology version: 0.1.4-alpha installMode: STORE_AND_INSTALL - fetchDependencies: false + fetchDependencies: true hl7-fhir-uv-tools-r4: name: hl7.fhir.uv.tools.r4 version: 1.1.2 From da828452c122bf4903fd414341df5cf18e1da5ba Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Sat, 6 Jun 2026 10:32:22 +0100 Subject: [PATCH 48/80] Testing Testing --- private.package.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/private.package.yaml b/private.package.yaml index b43857f..1e1f7fa 100644 --- a/private.package.yaml +++ b/private.package.yaml @@ -3,7 +3,7 @@ implementationguides: name: hl7.fhir.uv.extensions.r4 version: 5.3.0-ballot-tc1 installMode: STORE_AND_INSTALL - fetchDependencies: false + fetchDependencies: true hl7-fhir-uv-xver-r5-r4: name: hl7.fhir.uv.xver-r5.r4 version: 0.1.0 @@ -13,7 +13,7 @@ implementationguides: name: hl7.fhir.uv.genomics-reporting version: 3.0.0 installMode: STORE_AND_INSTALL - fetchDependencies: false + fetchDependencies: true hl7-fhir-uv-ips: name: hl7.fhir.uv.ips version: 2.0.0 @@ -43,6 +43,7 @@ implementationguides: name: hl7.fhir.uv.tools.r4 version: 1.1.2 installMode: STORE_AND_INSTALL + fetchDependencies: true fhir-r4-nhsengland-nhse-identifiers: name: fhir.r4.nhsengland.nhse-identifiers version: 0.1.1-alpha From 9dc2532a7bac5b1bbdb3cb4f5c8f65c7621a3705 Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Sat, 6 Jun 2026 10:37:09 +0100 Subject: [PATCH 49/80] Testing Testing --- private.package.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/private.package.yaml b/private.package.yaml index 1e1f7fa..9d7ad39 100644 --- a/private.package.yaml +++ b/private.package.yaml @@ -3,7 +3,7 @@ implementationguides: name: hl7.fhir.uv.extensions.r4 version: 5.3.0-ballot-tc1 installMode: STORE_AND_INSTALL - fetchDependencies: true + fetchDependencies: false hl7-fhir-uv-xver-r5-r4: name: hl7.fhir.uv.xver-r5.r4 version: 0.1.0 @@ -13,7 +13,7 @@ implementationguides: name: hl7.fhir.uv.genomics-reporting version: 3.0.0 installMode: STORE_AND_INSTALL - fetchDependencies: true + fetchDependencies: false hl7-fhir-uv-ips: name: hl7.fhir.uv.ips version: 2.0.0 @@ -38,12 +38,12 @@ implementationguides: name: fhir.r4.nhsengland.pathology version: 0.1.4-alpha installMode: STORE_AND_INSTALL - fetchDependencies: true + fetchDependencies: false hl7-fhir-uv-tools-r4: name: hl7.fhir.uv.tools.r4 version: 1.1.2 installMode: STORE_AND_INSTALL - fetchDependencies: true + fetchDependencies: false fhir-r4-nhsengland-nhse-identifiers: name: fhir.r4.nhsengland.nhse-identifiers version: 0.1.1-alpha From 20adbb3dce3931ebb359ba2c6cfd447838fd4430 Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Sat, 6 Jun 2026 10:48:11 +0100 Subject: [PATCH 50/80] Testing hl7.fhir.uv.tools.r4 Testing hl7.fhir.uv.tools.r4 --- fhirpkg.lock.json | 1 - private.package.yaml | 3 +-- 2 files changed, 1 insertion(+), 3 deletions(-) diff --git a/fhirpkg.lock.json b/fhirpkg.lock.json index 6efab8e..1a787f5 100644 --- a/fhirpkg.lock.json +++ b/fhirpkg.lock.json @@ -2,7 +2,6 @@ "updated": "2026-05-06T10:21:55.9845039+01:00", "dependencies": { "hl7.fhir.r4.core": "4.0.1", - "hl7.fhir.uv.extensions.r4": "5.3.0-ballot-tc1", "hl7.fhir.uv.xver-r5.r4": "0.1.0", "hl7.fhir.uv.genomics-reporting": "3.0.0", "hl7.fhir.uv.ips": "2.0.0", diff --git a/private.package.yaml b/private.package.yaml index 9d7ad39..5e6e0b7 100644 --- a/private.package.yaml +++ b/private.package.yaml @@ -33,7 +33,7 @@ implementationguides: name: hl7.fhir.us.mcode version: 4.0.0 installMode: STORE_AND_INSTALL - fetchDependencies: true + fetchDependencies: false fhir-r4-nhsengland-pathology: name: fhir.r4.nhsengland.pathology version: 0.1.4-alpha @@ -43,7 +43,6 @@ implementationguides: name: hl7.fhir.uv.tools.r4 version: 1.1.2 installMode: STORE_AND_INSTALL - fetchDependencies: false fhir-r4-nhsengland-nhse-identifiers: name: fhir.r4.nhsengland.nhse-identifiers version: 0.1.1-alpha From 58613157ff8d636c23f586416944d45c4ff65efe Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Sat, 6 Jun 2026 10:56:46 +0100 Subject: [PATCH 51/80] Add mcode Add mcode --- private.package.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/private.package.yaml b/private.package.yaml index 5e6e0b7..bf7f55a 100644 --- a/private.package.yaml +++ b/private.package.yaml @@ -33,7 +33,7 @@ implementationguides: name: hl7.fhir.us.mcode version: 4.0.0 installMode: STORE_AND_INSTALL - fetchDependencies: false + fetchDependencies: true fhir-r4-nhsengland-pathology: name: fhir.r4.nhsengland.pathology version: 0.1.4-alpha From 85447d9131f58afe8239032152b3c43097fe6da7 Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Sat, 6 Jun 2026 11:04:22 +0100 Subject: [PATCH 52/80] Use mcode 3.0.0 Use mcode 3.0.0 --- private.package.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/private.package.yaml b/private.package.yaml index bf7f55a..945d20f 100644 --- a/private.package.yaml +++ b/private.package.yaml @@ -31,7 +31,7 @@ implementationguides: fetchDependencies: false hl7-fhir-us-mcode: name: hl7.fhir.us.mcode - version: 4.0.0 + version: 3.0.0 installMode: STORE_AND_INSTALL fetchDependencies: true fhir-r4-nhsengland-pathology: From 8c6480f391cca6ba537b1d44c42dab88841eef86 Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Sat, 6 Jun 2026 11:24:21 +0100 Subject: [PATCH 53/80] Testing "hl7.fhir.us.mcode": "3.0.0", Testing "hl7.fhir.us.mcode": "3.0.0", --- fhirpkg.lock.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/fhirpkg.lock.json b/fhirpkg.lock.json index 1a787f5..e22b7cf 100644 --- a/fhirpkg.lock.json +++ b/fhirpkg.lock.json @@ -7,7 +7,7 @@ "hl7.fhir.uv.ips": "2.0.0", "hl7.fhir.eu.laboratory": "0.1.1", "ihe.iti.pcf": "1.1.0", - "hl7.fhir.us.mcode": "4.0.0", + "hl7.fhir.us.mcode": "3.0.0", "fhir.r4.nhsengland.pathology": "0.1.4-alpha", "fhir.r4.nhsengland.nhse-identifiers": "0.1.1-alpha", "fhir.r4.ukcore.stu3.currentbuild": "0.28.0-pre-release" From 45536a9a054d13d2733219de1239c007e3d06541 Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Sat, 6 Jun 2026 11:41:13 +0100 Subject: [PATCH 54/80] Testing "hl7.fhir.us.mcode": "4.0.0", Testing "hl7.fhir.us.mcode": "4.0.0", --- fhirpkg.lock.json | 2 +- private.package.yaml | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/fhirpkg.lock.json b/fhirpkg.lock.json index e22b7cf..1a787f5 100644 --- a/fhirpkg.lock.json +++ b/fhirpkg.lock.json @@ -7,7 +7,7 @@ "hl7.fhir.uv.ips": "2.0.0", "hl7.fhir.eu.laboratory": "0.1.1", "ihe.iti.pcf": "1.1.0", - "hl7.fhir.us.mcode": "3.0.0", + "hl7.fhir.us.mcode": "4.0.0", "fhir.r4.nhsengland.pathology": "0.1.4-alpha", "fhir.r4.nhsengland.nhse-identifiers": "0.1.1-alpha", "fhir.r4.ukcore.stu3.currentbuild": "0.28.0-pre-release" diff --git a/private.package.yaml b/private.package.yaml index 945d20f..5e6e0b7 100644 --- a/private.package.yaml +++ b/private.package.yaml @@ -31,9 +31,9 @@ implementationguides: fetchDependencies: false hl7-fhir-us-mcode: name: hl7.fhir.us.mcode - version: 3.0.0 + version: 4.0.0 installMode: STORE_AND_INSTALL - fetchDependencies: true + fetchDependencies: false fhir-r4-nhsengland-pathology: name: fhir.r4.nhsengland.pathology version: 0.1.4-alpha From 6984b809422567e942ccc4242ff2c3ed5e278cb5 Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Sat, 6 Jun 2026 13:40:35 +0100 Subject: [PATCH 55/80] Re-arrange Re-arrange --- ...gland-Composition-GenomicsEULabReport.json | 30 +++++++++---------- 1 file changed, 15 insertions(+), 15 deletions(-) diff --git a/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json b/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json index 24ab95e..3db0890 100644 --- a/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json +++ b/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json @@ -267,6 +267,21 @@ "path": "Composition.section", "definition": "To conform to EU Lab, SHOULD include references to the results that form part of the genomic report. For the UGR, will include sections that conform to the UGR folders, this work is currently in development." }, + { + "id": "Composition.section:sectionUGR", + "path": "Composition.section", + "sliceName": "sectionUGR", + "definition": "Sections included within the UGR: patient-demographics | investigations-and-procedures-requested | investigation-results | consent-for-information-sharing | family-history " + }, + { + "id": "Composition.section:sectionUGR.code", + "path": "Composition.section.code", + "binding": { + "strength": "extensible", + "description": "UK Core Composition Section Codes", + "valueSet": "https://fhir.hl7.org.uk/ValueSet/UKCore-CompositionSectionCode" + } + }, { "id": "Composition.section.code.coding.display.extension:translation", "path": "Composition.section.code.coding.display.extension", @@ -286,21 +301,6 @@ "id": "Composition.section.code.text.extension:translation.extension", "path": "Composition.section.code.text.extension.extension", "min": 2 - }, - { - "id": "Composition.section:sectionUGR", - "path": "Composition.section", - "sliceName": "sectionUGR", - "definition": "Sections included within the UGR: patient-demographics | investigations-and-procedures-requested | investigation-results | consent-for-information-sharing | family-history " - }, - { - "id": "Composition.section:sectionUGR.code", - "path": "Composition.section.code", - "binding": { - "strength": "extensible", - "description": "UK Core Composition Section Codes", - "valueSet": "https://fhir.hl7.org.uk/ValueSet/UKCore-CompositionSectionCode" - } } ] } From d59f5e09d131deb12131f800f53528553b29f336 Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Sat, 6 Jun 2026 15:33:10 +0100 Subject: [PATCH 56/80] Update NHSEngland-Composition-GenomicsEULabReport Update NHSEngland-Composition-GenomicsEULabReport --- ...gland-Composition-GenomicsEULabReport.json | 42 +++---------------- 1 file changed, 6 insertions(+), 36 deletions(-) diff --git a/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json b/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json index 3db0890..9703425 100644 --- a/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json +++ b/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json @@ -131,17 +131,7 @@ "rules": "open" } }, - { - "id": "Composition.type.coding.display.extension:translation", - "path": "Composition.type.coding.display.extension", - "sliceName": "translation" - }, - { - "id": "Composition.type.coding.display.extension:translation.extension", - "path": "Composition.type.coding.display.extension.extension", - "min": 2 - }, - { + { "id": "Composition.type.coding:codingGenomics", "path": "Composition.type.coding", "sliceName": "codingGenomics", @@ -161,14 +151,14 @@ "path": "Composition.type.coding.display.extension.extension", "min": 2 }, - { - "id": "Composition.type.text.extension:translation", - "path": "Composition.type.text.extension", + { + "id": "Composition.type.coding.display.extension:translation", + "path": "Composition.type.coding.display.extension", "sliceName": "translation" }, { - "id": "Composition.type.text.extension:translation.extension", - "path": "Composition.type.text.extension.extension", + "id": "Composition.type.coding.display.extension:translation.extension", + "path": "Composition.type.coding.display.extension.extension", "min": 2 }, { @@ -176,26 +166,6 @@ "path": "Composition.category", "definition": "Fixed codes for conformance to the EU Lab Composition profile (for cross border sharing of lab reports)." }, - { - "id": "Composition.category.coding.display.extension:translation", - "path": "Composition.category.coding.display.extension", - "sliceName": "translation" - }, - { - "id": "Composition.category.coding.display.extension:translation.extension", - "path": "Composition.category.coding.display.extension.extension", - "min": 2 - }, - { - "id": "Composition.category.text.extension:translation", - "path": "Composition.category.text.extension", - "sliceName": "translation" - }, - { - "id": "Composition.category.text.extension:translation.extension", - "path": "Composition.category.text.extension.extension", - "min": 2 - }, { "id": "Composition.category:studyType", "path": "Composition.category", From 4afb6a01dc7baa2a280dfb5fa49a96f39c31089c Mon Sep 17 00:00:00 2001 From: KazeemHamzat Date: Sat, 6 Jun 2026 15:46:05 +0100 Subject: [PATCH 57/80] Test Test --- fhirpkg.lock.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/fhirpkg.lock.json b/fhirpkg.lock.json index 1a787f5..09a6f4b 100644 --- a/fhirpkg.lock.json +++ b/fhirpkg.lock.json @@ -1,5 +1,5 @@ { - "updated": "2026-05-06T10:21:55.9845039+01:00", + "updated": "2026-06-06T15:25:27.6236512+01:00", "dependencies": { "hl7.fhir.r4.core": "4.0.1", "hl7.fhir.uv.xver-r5.r4": "0.1.0", From ab69ad7ba2a264a12a8e264d252591d24de4ad87 Mon Sep 17 00:00:00 2001 From: KazeemHamzat Date: Sat, 6 Jun 2026 16:14:48 +0100 Subject: [PATCH 58/80] Update Eu-Lab Update Eu-Lab --- ...gland-Composition-GenomicsEULabReport.json | 70 ++++++++++++++++--- fhirpkg.lock.json | 2 +- 2 files changed, 61 insertions(+), 11 deletions(-) diff --git a/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json b/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json index 9703425..4eef2a1 100644 --- a/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json +++ b/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json @@ -131,7 +131,17 @@ "rules": "open" } }, - { + { + "id": "Composition.type.coding.display.extension:translation", + "path": "Composition.type.coding.display.extension", + "sliceName": "translation" + }, + { + "id": "Composition.type.coding.display.extension:translation.extension", + "path": "Composition.type.coding.display.extension.extension", + "min": 2 + }, + { "id": "Composition.type.coding:codingGenomics", "path": "Composition.type.coding", "sliceName": "codingGenomics", @@ -151,14 +161,14 @@ "path": "Composition.type.coding.display.extension.extension", "min": 2 }, - { - "id": "Composition.type.coding.display.extension:translation", - "path": "Composition.type.coding.display.extension", + { + "id": "Composition.type.text.extension:translation", + "path": "Composition.type.text.extension", "sliceName": "translation" }, { - "id": "Composition.type.coding.display.extension:translation.extension", - "path": "Composition.type.coding.display.extension.extension", + "id": "Composition.type.text.extension:translation.extension", + "path": "Composition.type.text.extension.extension", "min": 2 }, { @@ -166,6 +176,26 @@ "path": "Composition.category", "definition": "Fixed codes for conformance to the EU Lab Composition profile (for cross border sharing of lab reports)." }, + { + "id": "Composition.category.coding.display.extension:translation", + "path": "Composition.category.coding.display.extension", + "sliceName": "translation" + }, + { + "id": "Composition.category.coding.display.extension:translation.extension", + "path": "Composition.category.coding.display.extension.extension", + "min": 2 + }, + { + "id": "Composition.category.text.extension:translation", + "path": "Composition.category.text.extension", + "sliceName": "translation" + }, + { + "id": "Composition.category.text.extension:translation.extension", + "path": "Composition.category.text.extension.extension", + "min": 2 + }, { "id": "Composition.category:studyType", "path": "Composition.category", @@ -237,6 +267,26 @@ "path": "Composition.section", "definition": "To conform to EU Lab, SHOULD include references to the results that form part of the genomic report. For the UGR, will include sections that conform to the UGR folders, this work is currently in development." }, + { + "id": "Composition.section.code.coding.display.extension:translation", + "path": "Composition.section.code.coding.display.extension", + "sliceName": "translation" + }, + { + "id": "Composition.section.code.coding.display.extension:translation.extension", + "path": "Composition.section.code.coding.display.extension.extension", + "min": 2 + }, + { + "id": "Composition.section.code.text.extension:translation", + "path": "Composition.section.code.text.extension", + "sliceName": "translation" + }, + { + "id": "Composition.section.code.text.extension:translation.extension", + "path": "Composition.section.code.text.extension.extension", + "min": 2 + }, { "id": "Composition.section:sectionUGR", "path": "Composition.section", @@ -253,22 +303,22 @@ } }, { - "id": "Composition.section.code.coding.display.extension:translation", + "id": "Composition.section:sectionUGR.code.coding.display.extension:translation", "path": "Composition.section.code.coding.display.extension", "sliceName": "translation" }, { - "id": "Composition.section.code.coding.display.extension:translation.extension", + "id": "Composition.section:sectionUGR.code.coding.display.extension:translation.extension", "path": "Composition.section.code.coding.display.extension.extension", "min": 2 }, { - "id": "Composition.section.code.text.extension:translation", + "id": "Composition.section:sectionUGR.code.text.extension:translation", "path": "Composition.section.code.text.extension", "sliceName": "translation" }, { - "id": "Composition.section.code.text.extension:translation.extension", + "id": "Composition.section:sectionUGR.code.text.extension:translation.extension", "path": "Composition.section.code.text.extension.extension", "min": 2 } diff --git a/fhirpkg.lock.json b/fhirpkg.lock.json index 09a6f4b..198c065 100644 --- a/fhirpkg.lock.json +++ b/fhirpkg.lock.json @@ -13,4 +13,4 @@ "fhir.r4.ukcore.stu3.currentbuild": "0.28.0-pre-release" }, "missing": {} -} \ No newline at end of file +} From 83e5ba3c633a3f2c2d8c869e8177f79080a3ef11 Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Sat, 6 Jun 2026 17:14:25 +0100 Subject: [PATCH 59/80] New Model New Model --- ...gland-Composition-GenomicsEULabReport.json | 56 ++++--------------- 1 file changed, 11 insertions(+), 45 deletions(-) diff --git a/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json b/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json index 9703425..ee08a89 100644 --- a/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json +++ b/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json @@ -107,59 +107,25 @@ } ] }, - { - "id": "Composition.status", - "path": "Composition.status", - "definition": "Fixed value of 'final'", - "fixedCode": "final" - }, { "id": "Composition.type", "path": "Composition.type", - "definition": "SNOMED CT code for either a Laboratory Request (24691000000102) or Genetic report (1054161000000101)" - }, - { - "id": "Composition.type.coding", - "path": "Composition.type.coding", - "slicing": { - "discriminator": [ + "definition": "SNOMED CT code for either a Laboratory Request (24691000000102) or Genetic report (1054161000000101)", + "min": 1, + "patternCodeableConcept": { + "coding": [ { - "type": "pattern", - "path": "$this" + "system": "http://snomed.info/sct", + "code": "105416100000010" } - ], - "rules": "open" - } - }, - { - "id": "Composition.type.coding:codingGenomics", - "path": "Composition.type.coding", - "sliceName": "codingGenomics", - "fixedCoding": { - "system": "http://snomed.info/sct", - "code": "1054161000000101", - "display": "Genetic report" + ] } }, { - "id": "Composition.type.coding:codingGenomics.display.extension:translation", - "path": "Composition.type.coding.display.extension", - "sliceName": "translation" - }, - { - "id": "Composition.type.coding:codingGenomics.display.extension:translation.extension", - "path": "Composition.type.coding.display.extension.extension", - "min": 2 - }, - { - "id": "Composition.type.coding.display.extension:translation", - "path": "Composition.type.coding.display.extension", - "sliceName": "translation" - }, - { - "id": "Composition.type.coding.display.extension:translation.extension", - "path": "Composition.type.coding.display.extension.extension", - "min": 2 + "id": "Composition.status", + "path": "Composition.status", + "definition": "Fixed value of 'final'", + "fixedCode": "final" }, { "id": "Composition.category", From 96348d1eae49175f02372b08eb0cb1d10ca9846b Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Sat, 6 Jun 2026 17:59:50 +0100 Subject: [PATCH 60/80] Testing Category Testing Category --- ...gland-Composition-GenomicsEULabReport.json | 33 ++++--------------- 1 file changed, 7 insertions(+), 26 deletions(-) diff --git a/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json b/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json index fb211c0..9bfdb30 100644 --- a/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json +++ b/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json @@ -107,7 +107,14 @@ } ] }, + { + "id": "Composition.status", + "path": "Composition.status", + "definition": "Fixed value of 'final'", + "fixedCode": "final" + }, + { "id": "Composition.type", "path": "Composition.type", "definition": "SNOMED CT code for either a Laboratory Request (24691000000102) or Genetic report (1054161000000101)", @@ -120,37 +127,11 @@ ] } }, - { - "id": "Composition.status", - "path": "Composition.status", - "definition": "Fixed value of 'final'", - "fixedCode": "final" - }, { "id": "Composition.category", "path": "Composition.category", "definition": "Fixed codes for conformance to the EU Lab Composition profile (for cross border sharing of lab reports)." }, - { - "id": "Composition.category.coding.display.extension:translation", - "path": "Composition.category.coding.display.extension", - "sliceName": "translation" - }, - { - "id": "Composition.category.coding.display.extension:translation.extension", - "path": "Composition.category.coding.display.extension.extension", - "min": 2 - }, - { - "id": "Composition.category.text.extension:translation", - "path": "Composition.category.text.extension", - "sliceName": "translation" - }, - { - "id": "Composition.category.text.extension:translation.extension", - "path": "Composition.category.text.extension.extension", - "min": 2 - }, { "id": "Composition.category:studyType", "path": "Composition.category", From d1ef915b2ad5a1cedf72c91581cdede5f824f73b Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Sat, 6 Jun 2026 18:17:29 +0100 Subject: [PATCH 61/80] Update Update --- ...gland-Composition-GenomicsEULabReport.json | 49 ++----------------- 1 file changed, 3 insertions(+), 46 deletions(-) diff --git a/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json b/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json index 9bfdb30..592628d 100644 --- a/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json +++ b/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json @@ -107,14 +107,13 @@ } ] }, - { "id": "Composition.status", "path": "Composition.status", "definition": "Fixed value of 'final'", "fixedCode": "final" }, - { + { "id": "Composition.type", "path": "Composition.type", "definition": "SNOMED CT code for either a Laboratory Request (24691000000102) or Genetic report (1054161000000101)", @@ -200,63 +199,21 @@ }, { "id": "Composition.section", - "path": "Composition.section", - "definition": "To conform to EU Lab, SHOULD include references to the results that form part of the genomic report. For the UGR, will include sections that conform to the UGR folders, this work is currently in development." - }, - { - "id": "Composition.section.code.coding.display.extension:translation", - "path": "Composition.section.code.coding.display.extension", - "sliceName": "translation" - }, - { - "id": "Composition.section.code.coding.display.extension:translation.extension", - "path": "Composition.section.code.coding.display.extension.extension", - "min": 2 - }, - { - "id": "Composition.section.code.text.extension:translation", - "path": "Composition.section.code.text.extension", - "sliceName": "translation" - }, - { - "id": "Composition.section.code.text.extension:translation.extension", - "path": "Composition.section.code.text.extension.extension", - "min": 2 + "path": "Composition.section" }, { "id": "Composition.section:sectionUGR", "path": "Composition.section", "sliceName": "sectionUGR", - "definition": "Sections included within the UGR: patient-demographics | investigations-and-procedures-requested | investigation-results | consent-for-information-sharing | family-history " + "definition": "Sections included within UGR" }, { "id": "Composition.section:sectionUGR.code", "path": "Composition.section.code", "binding": { "strength": "extensible", - "description": "UK Core Composition Section Codes", "valueSet": "https://fhir.hl7.org.uk/ValueSet/UKCore-CompositionSectionCode" } - }, - { - "id": "Composition.section:sectionUGR.code.coding.display.extension:translation", - "path": "Composition.section.code.coding.display.extension", - "sliceName": "translation" - }, - { - "id": "Composition.section:sectionUGR.code.coding.display.extension:translation.extension", - "path": "Composition.section.code.coding.display.extension.extension", - "min": 2 - }, - { - "id": "Composition.section:sectionUGR.code.text.extension:translation", - "path": "Composition.section.code.text.extension", - "sliceName": "translation" - }, - { - "id": "Composition.section:sectionUGR.code.text.extension:translation.extension", - "path": "Composition.section.code.text.extension.extension", - "min": 2 } ] } From 7107164f92d070cb5f969c61cd53e977bc193582 Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Sat, 6 Jun 2026 18:29:01 +0100 Subject: [PATCH 62/80] Update Update --- .../NHSEngland-Composition-GenomicsEULabReport.json | 4 ---- 1 file changed, 4 deletions(-) diff --git a/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json b/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json index 592628d..7d87bba 100644 --- a/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json +++ b/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json @@ -197,10 +197,6 @@ "definition": "SHALL match the SNOMED CT display used within Composition.type", "fixedString": "Genetic report" }, - { - "id": "Composition.section", - "path": "Composition.section" - }, { "id": "Composition.section:sectionUGR", "path": "Composition.section", From 0e3eb2220777fdf14914450aceb43c5329be3ef4 Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Sat, 6 Jun 2026 18:53:25 +0100 Subject: [PATCH 63/80] Update Update --- ...NHSEngland-Composition-GenomicsEULabReport.json | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json b/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json index 7d87bba..e994fba 100644 --- a/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json +++ b/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json @@ -197,6 +197,20 @@ "definition": "SHALL match the SNOMED CT display used within Composition.type", "fixedString": "Genetic report" }, + { + "id": "Composition.section", + "path": "Composition.section", + "slicing": { + "discriminator": [ + { + "type": "value", + "path": "code" + } + ], + "rules": "open" + }, + "definition": "Sections included in the Genomics / UGR Composition." + }, { "id": "Composition.section:sectionUGR", "path": "Composition.section", From b6cbb33009b5f13e59ed99cc772012a1038cd91c Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Sat, 6 Jun 2026 19:23:45 +0100 Subject: [PATCH 64/80] Update Update --- ...ngland-Composition-GenomicsEULabReport.json | 18 +++--------------- 1 file changed, 3 insertions(+), 15 deletions(-) diff --git a/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json b/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json index e994fba..4da2196 100644 --- a/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json +++ b/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json @@ -197,25 +197,13 @@ "definition": "SHALL match the SNOMED CT display used within Composition.type", "fixedString": "Genetic report" }, - { - "id": "Composition.section", - "path": "Composition.section", - "slicing": { - "discriminator": [ - { - "type": "value", - "path": "code" - } - ], - "rules": "open" - }, - "definition": "Sections included in the Genomics / UGR Composition." - }, { "id": "Composition.section:sectionUGR", "path": "Composition.section", "sliceName": "sectionUGR", - "definition": "Sections included within UGR" + "definition": "Sections included within UGR", + "min": 0, + "max": "*" }, { "id": "Composition.section:sectionUGR.code", From 11ce98df38cc8e5b3eaab5070646aec2d2aaefc0 Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Sat, 6 Jun 2026 19:31:37 +0100 Subject: [PATCH 65/80] Remove ugr remove --- ...SEngland-Composition-GenomicsEULabReport.json | 16 ---------------- 1 file changed, 16 deletions(-) diff --git a/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json b/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json index 4da2196..da7b866 100644 --- a/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json +++ b/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json @@ -196,22 +196,6 @@ "path": "Composition.title", "definition": "SHALL match the SNOMED CT display used within Composition.type", "fixedString": "Genetic report" - }, - { - "id": "Composition.section:sectionUGR", - "path": "Composition.section", - "sliceName": "sectionUGR", - "definition": "Sections included within UGR", - "min": 0, - "max": "*" - }, - { - "id": "Composition.section:sectionUGR.code", - "path": "Composition.section.code", - "binding": { - "strength": "extensible", - "valueSet": "https://fhir.hl7.org.uk/ValueSet/UKCore-CompositionSectionCode" - } } ] } From ce05a8fdbe5ebebebe40bca2694df194ac3de014 Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Sat, 6 Jun 2026 20:28:55 +0100 Subject: [PATCH 66/80] Remove Extension constraint Remove Extension constraint --- ...gland-Composition-GenomicsEULabReport.json | 73 ++++--------------- 1 file changed, 16 insertions(+), 57 deletions(-) diff --git a/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json b/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json index da7b866..c9de118 100644 --- a/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json +++ b/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json @@ -38,75 +38,18 @@ "sliceName": "basedOn-order-or-requisition", "definition": "TBC. Only relevant for EU Lab aligned reports (included in HL7 EU Laboratory Report: Composition Profile). A reference to the ServiceRequest which this report is in response to." }, - { - "id": "Composition.extension:basedOn-order-or-requisition.value[x]:valueReference", - "path": "Composition.extension.value[x]", - "sliceName": "valueReference", - "type": [ - { - "code": "Reference", - "targetProfile": [ - "https://fhir.nhs.uk/StructureDefinition/NHSEngland-ServiceRequest-Genomics", - "http://hl7.eu/fhir/laboratory/StructureDefinition/ServiceRequest-eu-lab" - ], - "aggregation": [ - "referenced", - "bundled" - ] - } - ] - }, { "id": "Composition.extension:information-recipient", "path": "Composition.extension", "sliceName": "information-recipient", "definition": "TBC. Only relevant for EU Lab aligned reports (included in HL7 EU Laboratory Report: Composition Profile). A reference to the recipient for a report, could potentially be used to reference additional recipients over the subject and original requester for the request." }, - { - "id": "Composition.extension:information-recipient.value[x]", - "path": "Composition.extension.value[x]", - "type": [ - { - "code": "Reference", - "targetProfile": [ - "https://fhir.nhs.uk/StructureDefinition/NHSEngland-PractitionerRole-Genomics", - "http://hl7.eu/fhir/laboratory/StructureDefinition/Practitioner-eu-lab", - "http://hl7.org/fhir/StructureDefinition/Device", - "http://hl7.eu/fhir/laboratory/StructureDefinition/Patient-eu-lab", - "http://hl7.org/fhir/StructureDefinition/RelatedPerson", - "http://hl7.eu/fhir/laboratory/StructureDefinition/PractitionerRole-eu-lab", - "http://hl7.org/fhir/StructureDefinition/Organization" - ], - "aggregation": [ - "referenced", - "bundled" - ] - } - ] - }, { "id": "Composition.extension:diagnosticReport-reference", "path": "Composition.extension", "sliceName": "diagnosticReport-reference", "definition": "TBC. Only relevant for EU Lab aligned reports (included in HL7 EU Laboratory Report: Composition Profile). A reference to the focal DiagnosticReport this Composition is for." }, - { - "id": "Composition.extension:diagnosticReport-reference.value[x]", - "path": "Composition.extension.value[x]", - "type": [ - { - "code": "Reference", - "targetProfile": [ - "https://fhir.nhs.uk/StructureDefinition/NHSEngland-DiagnosticReport-GenomicReport", - "http://hl7.eu/fhir/laboratory/StructureDefinition/DiagnosticReport-eu-lab" - ], - "aggregation": [ - "referenced", - "bundled" - ] - } - ] - }, { "id": "Composition.status", "path": "Composition.status", @@ -196,6 +139,22 @@ "path": "Composition.title", "definition": "SHALL match the SNOMED CT display used within Composition.type", "fixedString": "Genetic report" + }, + { + "id": "Composition.section:sectionUGR", + "path": "Composition.section", + "sliceName": "sectionUGR", + "definition": "Sections included within UGR", + "min": 0, + "max": "*" + }, + { + "id": "Composition.section:sectionUGR.code", + "path": "Composition.section.code", + "binding": { + "strength": "extensible", + "valueSet": "https://fhir.hl7.org.uk/ValueSet/UKCore-CompositionSectionCode" + } } ] } From 87e53300d148e2b8ca00c9fc6d7ef5e756f0409b Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Sat, 6 Jun 2026 20:38:11 +0100 Subject: [PATCH 67/80] Remove extension Remove extension --- ...ngland-Composition-GenomicsEULabReport.json | 18 ------------------ 1 file changed, 18 deletions(-) diff --git a/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json b/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json index c9de118..6108c2c 100644 --- a/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json +++ b/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json @@ -32,24 +32,6 @@ "derivation": "constraint", "differential": { "element": [ - { - "id": "Composition.extension:basedOn-order-or-requisition", - "path": "Composition.extension", - "sliceName": "basedOn-order-or-requisition", - "definition": "TBC. Only relevant for EU Lab aligned reports (included in HL7 EU Laboratory Report: Composition Profile). A reference to the ServiceRequest which this report is in response to." - }, - { - "id": "Composition.extension:information-recipient", - "path": "Composition.extension", - "sliceName": "information-recipient", - "definition": "TBC. Only relevant for EU Lab aligned reports (included in HL7 EU Laboratory Report: Composition Profile). A reference to the recipient for a report, could potentially be used to reference additional recipients over the subject and original requester for the request." - }, - { - "id": "Composition.extension:diagnosticReport-reference", - "path": "Composition.extension", - "sliceName": "diagnosticReport-reference", - "definition": "TBC. Only relevant for EU Lab aligned reports (included in HL7 EU Laboratory Report: Composition Profile). A reference to the focal DiagnosticReport this Composition is for." - }, { "id": "Composition.status", "path": "Composition.status", From 7b21b5c58fb133184e2f8692c3f87da01f8b5f28 Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Sat, 6 Jun 2026 21:09:04 +0100 Subject: [PATCH 68/80] Remove nhs as traget Profile Remove nhs as traget Profile --- .../NHSEngland-Composition-GenomicsEULabReport.json | 1 - package.json | 3 ++- private.package.yaml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json b/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json index 6108c2c..92131a3 100644 --- a/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json +++ b/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json @@ -92,7 +92,6 @@ { "code": "Reference", "targetProfile": [ - "https://fhir.nhs.uk/StructureDefinition/NHSEngland-Patient-Genomics", "http://hl7.eu/fhir/laboratory/StructureDefinition/Patient-eu-lab", "http://hl7.eu/fhir/laboratory/StructureDefinition/Patient-animal-eu-lab", "http://hl7.org/fhir/StructureDefinition/Group", diff --git a/package.json b/package.json index eabc112..e8a5a6d 100644 --- a/package.json +++ b/package.json @@ -3,7 +3,8 @@ "description": "FHIR Genomics Implementation Guide", "author": "nhsdigital", "dependencies": { - "hl7.fhir.r4.core": "4.0.1" + "hl7.fhir.r4.core": "4.0.1", + "hl7.fhir.us.mcode":"4..0.0" }, "fhirVersions": [ "4.0.1" diff --git a/private.package.yaml b/private.package.yaml index 5e6e0b7..a6ea14d 100644 --- a/private.package.yaml +++ b/private.package.yaml @@ -23,7 +23,7 @@ implementationguides: name: hl7.fhir.eu.laboratory version: 0.1.1 installMode: STORE_AND_INSTALL - fetchDependencies: false + fetchDependencies: true ihe-iti-pcf: name: ihe.iti.pcf version: 1.1.0 From 23ccf83e764bdb4bcaab56be26cd10b90cc6c695 Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Sat, 6 Jun 2026 21:31:19 +0100 Subject: [PATCH 69/80] Update package.json Update package.json --- fhirpkg.lock.json | 16 ++++------------ package.json | 2 +- 2 files changed, 5 insertions(+), 13 deletions(-) diff --git a/fhirpkg.lock.json b/fhirpkg.lock.json index 198c065..45a89ed 100644 --- a/fhirpkg.lock.json +++ b/fhirpkg.lock.json @@ -1,16 +1,8 @@ { - "updated": "2026-06-06T15:25:27.6236512+01:00", + "updated": "2026-05-06T10:21:55.9845039+01:00", "dependencies": { - "hl7.fhir.r4.core": "4.0.1", - "hl7.fhir.uv.xver-r5.r4": "0.1.0", - "hl7.fhir.uv.genomics-reporting": "3.0.0", - "hl7.fhir.uv.ips": "2.0.0", - "hl7.fhir.eu.laboratory": "0.1.1", - "ihe.iti.pcf": "1.1.0", - "hl7.fhir.us.mcode": "4.0.0", - "fhir.r4.nhsengland.pathology": "0.1.4-alpha", - "fhir.r4.nhsengland.nhse-identifiers": "0.1.1-alpha", - "fhir.r4.ukcore.stu3.currentbuild": "0.28.0-pre-release" + "hl7.fhir.r4.core": "4.0.1", + "hl7.fhir.us.mcode":"4.0.0" }, "missing": {} -} +} \ No newline at end of file diff --git a/package.json b/package.json index e8a5a6d..b42e325 100644 --- a/package.json +++ b/package.json @@ -4,7 +4,7 @@ "author": "nhsdigital", "dependencies": { "hl7.fhir.r4.core": "4.0.1", - "hl7.fhir.us.mcode":"4..0.0" + "hl7.fhir.us.mcode":"4.0.0" }, "fhirVersions": [ "4.0.1" From 3a55358fe16476d979eed6c549d3083d936a5e2e Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Sat, 6 Jun 2026 21:54:11 +0100 Subject: [PATCH 70/80] Add extension Add extension --- fhirpkg.lock.json | 5 +++-- package.json | 3 ++- 2 files changed, 5 insertions(+), 3 deletions(-) diff --git a/fhirpkg.lock.json b/fhirpkg.lock.json index 45a89ed..0015187 100644 --- a/fhirpkg.lock.json +++ b/fhirpkg.lock.json @@ -1,8 +1,9 @@ { "updated": "2026-05-06T10:21:55.9845039+01:00", "dependencies": { - "hl7.fhir.r4.core": "4.0.1", - "hl7.fhir.us.mcode":"4.0.0" + "hl7.fhir.r4.core": "4.0.1", + "hl7.fhir.us.mcode":"4.0.0", + "hl7.fhir.uv.extensions.r4": "5.0.0" }, "missing": {} } \ No newline at end of file diff --git a/package.json b/package.json index b42e325..6446235 100644 --- a/package.json +++ b/package.json @@ -4,7 +4,8 @@ "author": "nhsdigital", "dependencies": { "hl7.fhir.r4.core": "4.0.1", - "hl7.fhir.us.mcode":"4.0.0" + "hl7.fhir.us.mcode":"4.0.0", + "hl7.fhir.uv.extensions.r4": "5.0.0" }, "fhirVersions": [ "4.0.1" From 4696d5d4a3a87a2f38476d92ebda550c28c3b8e4 Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Sat, 6 Jun 2026 22:03:53 +0100 Subject: [PATCH 71/80] Using hl7.fhir.uv.extensions.r4 5.0.0 Using hl7.fhir.uv.extensions.r4 5.0.0 --- private.package.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/private.package.yaml b/private.package.yaml index a6ea14d..debea03 100644 --- a/private.package.yaml +++ b/private.package.yaml @@ -1,7 +1,7 @@ implementationguides: hl7-fhir-uv-extensions-r4: name: hl7.fhir.uv.extensions.r4 - version: 5.3.0-ballot-tc1 + version: 5.0.0 installMode: STORE_AND_INSTALL fetchDependencies: false hl7-fhir-uv-xver-r5-r4: From 096a132e0dd4be84fc0466630e1da71b11b93bff Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Sat, 6 Jun 2026 22:11:39 +0100 Subject: [PATCH 72/80] Add "hl7.fhir.r4.core": "4.0.1" Add "hl7.fhir.r4.core": "4.0.1" --- fhirpkg.lock.json | 4 +--- package.json | 4 +--- private.package.yaml | 2 +- 3 files changed, 3 insertions(+), 7 deletions(-) diff --git a/fhirpkg.lock.json b/fhirpkg.lock.json index 0015187..3fc5928 100644 --- a/fhirpkg.lock.json +++ b/fhirpkg.lock.json @@ -1,9 +1,7 @@ { "updated": "2026-05-06T10:21:55.9845039+01:00", "dependencies": { - "hl7.fhir.r4.core": "4.0.1", - "hl7.fhir.us.mcode":"4.0.0", - "hl7.fhir.uv.extensions.r4": "5.0.0" + "hl7.fhir.r4.core": "4.0.1" }, "missing": {} } \ No newline at end of file diff --git a/package.json b/package.json index 6446235..eabc112 100644 --- a/package.json +++ b/package.json @@ -3,9 +3,7 @@ "description": "FHIR Genomics Implementation Guide", "author": "nhsdigital", "dependencies": { - "hl7.fhir.r4.core": "4.0.1", - "hl7.fhir.us.mcode":"4.0.0", - "hl7.fhir.uv.extensions.r4": "5.0.0" + "hl7.fhir.r4.core": "4.0.1" }, "fhirVersions": [ "4.0.1" diff --git a/private.package.yaml b/private.package.yaml index debea03..9dc0eca 100644 --- a/private.package.yaml +++ b/private.package.yaml @@ -1,7 +1,7 @@ implementationguides: hl7-fhir-uv-extensions-r4: name: hl7.fhir.uv.extensions.r4 - version: 5.0.0 + version: 5.3.0 installMode: STORE_AND_INSTALL fetchDependencies: false hl7-fhir-uv-xver-r5-r4: From ecf21a2b18e0e33fa2bb4948abf2c66579a952ed Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Sat, 6 Jun 2026 22:19:52 +0100 Subject: [PATCH 73/80] Update Update --- private.package.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/private.package.yaml b/private.package.yaml index 9dc0eca..432658d 100644 --- a/private.package.yaml +++ b/private.package.yaml @@ -1,7 +1,7 @@ implementationguides: hl7-fhir-uv-extensions-r4: name: hl7.fhir.uv.extensions.r4 - version: 5.3.0 + version: 1.0.0 installMode: STORE_AND_INSTALL fetchDependencies: false hl7-fhir-uv-xver-r5-r4: From da67cdcd6b2cdffc7342b3dfbb9d9ba585fbbb6d Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Sat, 6 Jun 2026 22:27:34 +0100 Subject: [PATCH 74/80] Remove Remove --- private.package.yaml | 5 ----- 1 file changed, 5 deletions(-) diff --git a/private.package.yaml b/private.package.yaml index 432658d..c120de9 100644 --- a/private.package.yaml +++ b/private.package.yaml @@ -1,9 +1,4 @@ implementationguides: - hl7-fhir-uv-extensions-r4: - name: hl7.fhir.uv.extensions.r4 - version: 1.0.0 - installMode: STORE_AND_INSTALL - fetchDependencies: false hl7-fhir-uv-xver-r5-r4: name: hl7.fhir.uv.xver-r5.r4 version: 0.1.0 From c2ed5205e7d0d0d96a10f4a6dcb513ffbf86bdf5 Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Sat, 6 Jun 2026 22:45:20 +0100 Subject: [PATCH 75/80] Reset Eu-lab --- private.package.yaml | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/private.package.yaml b/private.package.yaml index c120de9..197f194 100644 --- a/private.package.yaml +++ b/private.package.yaml @@ -1,4 +1,9 @@ implementationguides: + hl7-fhir-uv-extensions-r4: + name: hl7.fhir.uv.extensions.r4 + version: 1.0.0 + installMode: STORE_AND_INSTALL + fetchDependencies: false hl7-fhir-uv-xver-r5-r4: name: hl7.fhir.uv.xver-r5.r4 version: 0.1.0 @@ -18,7 +23,7 @@ implementationguides: name: hl7.fhir.eu.laboratory version: 0.1.1 installMode: STORE_AND_INSTALL - fetchDependencies: true + fetchDependencies: false ihe-iti-pcf: name: ihe.iti.pcf version: 1.1.0 From b978323be88ce027312af9aecfd570573726955b Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Sat, 6 Jun 2026 22:49:09 +0100 Subject: [PATCH 76/80] Update Update --- private.package.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/private.package.yaml b/private.package.yaml index 197f194..5e6e0b7 100644 --- a/private.package.yaml +++ b/private.package.yaml @@ -1,7 +1,7 @@ implementationguides: hl7-fhir-uv-extensions-r4: name: hl7.fhir.uv.extensions.r4 - version: 1.0.0 + version: 5.3.0-ballot-tc1 installMode: STORE_AND_INSTALL fetchDependencies: false hl7-fhir-uv-xver-r5-r4: From 6fa05c3ab0bd4024645b14922efb6ac9cbb61cfe Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Sat, 6 Jun 2026 22:57:20 +0100 Subject: [PATCH 77/80] Mcode Mcode --- .../NHSEngland-Composition-GenomicsEULabReport.json | 2 +- private.package.yaml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json b/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json index 92131a3..13ec9f4 100644 --- a/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json +++ b/StructureDefinition/NHSEngland-Composition-GenomicsEULabReport.json @@ -92,7 +92,7 @@ { "code": "Reference", "targetProfile": [ - "http://hl7.eu/fhir/laboratory/StructureDefinition/Patient-eu-lab", + "http://hl7.eu/fhir/base/StructureDefinition/patient-eu-core", "http://hl7.eu/fhir/laboratory/StructureDefinition/Patient-animal-eu-lab", "http://hl7.org/fhir/StructureDefinition/Group", "http://hl7.org/fhir/StructureDefinition/Location", diff --git a/private.package.yaml b/private.package.yaml index 5e6e0b7..bf7f55a 100644 --- a/private.package.yaml +++ b/private.package.yaml @@ -33,7 +33,7 @@ implementationguides: name: hl7.fhir.us.mcode version: 4.0.0 installMode: STORE_AND_INSTALL - fetchDependencies: false + fetchDependencies: true fhir-r4-nhsengland-pathology: name: fhir.r4.nhsengland.pathology version: 0.1.4-alpha From f8205904531d4752859ea5e93685f4510053503e Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Sat, 6 Jun 2026 23:31:25 +0100 Subject: [PATCH 78/80] Update update --- private.package.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/private.package.yaml b/private.package.yaml index bf7f55a..5e6e0b7 100644 --- a/private.package.yaml +++ b/private.package.yaml @@ -33,7 +33,7 @@ implementationguides: name: hl7.fhir.us.mcode version: 4.0.0 installMode: STORE_AND_INSTALL - fetchDependencies: true + fetchDependencies: false fhir-r4-nhsengland-pathology: name: fhir.r4.nhsengland.pathology version: 0.1.4-alpha From 1032641ffb36fc847ff7dec61a1fd2a74717fdaa Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Sat, 6 Jun 2026 23:48:36 +0100 Subject: [PATCH 79/80] Remove bundle Remove bundle --- .../NHSEngland-BodyStructure-GenomicsmCODE.json | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/StructureDefinition/NHSEngland-BodyStructure-GenomicsmCODE.json b/StructureDefinition/NHSEngland-BodyStructure-GenomicsmCODE.json index 3544181..f219cfa 100644 --- a/StructureDefinition/NHSEngland-BodyStructure-GenomicsmCODE.json +++ b/StructureDefinition/NHSEngland-BodyStructure-GenomicsmCODE.json @@ -57,8 +57,7 @@ "http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-cancer-patient" ], "aggregation": [ - "referenced", - "bundled" + "referenced" ] } ] From 8dc7295ae811f0c529af9103c9e55a309de6e575 Mon Sep 17 00:00:00 2001 From: Kazeem Hamzat Date: Sat, 6 Jun 2026 23:54:06 +0100 Subject: [PATCH 80/80] Remove B.patient { "id": "BodyStructure.patient", "path": "BodyStructure.patient", "type": [ { "code": "Reference", "targetProfile": [ "http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-cancer-patient" ], "aggregation": [ "referenced", "bundled" ] } ] } --- .../NHSEngland-BodyStructure-GenomicsmCODE.json | 15 --------------- 1 file changed, 15 deletions(-) diff --git a/StructureDefinition/NHSEngland-BodyStructure-GenomicsmCODE.json b/StructureDefinition/NHSEngland-BodyStructure-GenomicsmCODE.json index f219cfa..dd36bdb 100644 --- a/StructureDefinition/NHSEngland-BodyStructure-GenomicsmCODE.json +++ b/StructureDefinition/NHSEngland-BodyStructure-GenomicsmCODE.json @@ -46,21 +46,6 @@ "id": "BodyStructure.locationQualifier", "path": "BodyStructure.locationQualifier", "definition": "SHALL be provided where relevant. SHOULD use SNOMED CT encoding." - }, - { - "id": "BodyStructure.patient", - "path": "BodyStructure.patient", - "type": [ - { - "code": "Reference", - "targetProfile": [ - "http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-cancer-patient" - ], - "aggregation": [ - "referenced" - ] - } - ] } ] }