Merge branch 'main' of https://github.com/NHSDigital/NHSDigital-FHIR-Genomics-ImplementationGuide into Patch-Testing-GOM-Package

Author: KazeemHamzat

CapabilityStatement/CapabilityStatement-genomics-requirements.json

@@ -2,10 +2,10 @@
  "resourceType": "CapabilityStatement",
  "id": "CapabilityStatement-Genomics-requirements",
  "url": "https://fhir.nhs.uk/CapabilityStatement/genomics-requirements",
- "version": "0.3.0",
+ "version": "0.3.1",
  "name": "GenomicsRequirements",
  "status": "draft",
- "date": "2026-01-14T00:00:00+00:00",
+ "date": "2026-06-11T00:00:00+00:00",
  "publisher": "digital.nhs.uk",
  "description": "Conformance requirements for NHS Digital Genomics Implementation Guide",
  "kind": "requirements",
@@ -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",

Composition/Composition-EULabGenomicReport-Example.json

@@ -26,6 +26,10 @@
       }
     }
   ],
+   "identifier": {
+  "system": "https://fhir.nhs.uk/Id/genomic-report",
+  "value": "GR-12345"
+ },
   "status": "final",
   "type": {
     "coding": [
@@ -76,6 +80,10 @@
   "section": [
     {
       "title": "Results",
+         "text": {
+    "status": "generated",
+    "div": "<div xmlns=\"http://www.w3.org/1999/xhtml\">Genomic findings.</div>"
+   },
       "code": {
         "coding": [
           {

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": "2026-06-11T10:33:00.000Z",
   "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",

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": "2026-06-11T21:00:00.000Z",
  "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",

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": "2026-06-11T11:00:00.000Z",
   "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",

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/base/StructureDefinition/patient-eu-core"
     ]
   },
   "extension": [