diff --git a/NHSEnglandFHIRGenomicsImplementationGuide/README.md b/NHSEnglandFHIRGenomicsImplementationGuide/README.md
index 6e4c303f4..2082cf9ad 100644
--- a/NHSEnglandFHIRGenomicsImplementationGuide/README.md
+++ b/NHSEnglandFHIRGenomicsImplementationGuide/README.md
@@ -5,4 +5,4 @@ It was created on 29/09/2023 and has been set up to run every 1 month.
## Last Updated
-Updated at: Fri Dec 1 18:06:35 UTC 2023
+Updated at: Tue Dec 19 18:03:19 UTC 2023
diff --git a/NHSEnglandFHIRGenomicsImplementationGuide/backup/CodeSystem/CodeSystem-Genomics-business-status.json b/NHSEnglandFHIRGenomicsImplementationGuide/backup/CodeSystem/CodeSystem-Genomics-business-status.json
index c4a596cb3..ccd02ae9b 100644
--- a/NHSEnglandFHIRGenomicsImplementationGuide/backup/CodeSystem/CodeSystem-Genomics-business-status.json
+++ b/NHSEnglandFHIRGenomicsImplementationGuide/backup/CodeSystem/CodeSystem-Genomics-business-status.json
@@ -1,143 +1,83 @@
{
- "resourceType": "CodeSystem",
- "id": "959a0a2f-73e3-4c6e-8e99-babb6b3a4296",
- "url": "https://fhir.nhs.uk/CodeSystem/business-status-genomics",
- "identifier": [
- {
- "system": "https://fhir.nhs.uk/identifier/CodeSystem",
- "value": "business-status-genomics"
- }
- ],
- "version": "0.1.0",
- "name": "BusinessStatusGenomics",
- "title": "Business Status Genomics",
- "status": "draft",
- "date": "2022-11-25",
- "publisher": "NHS Digital",
- "contact": [
- {
- "name": "NHS Digital",
- "telecom": [
- {
- "system": "email",
- "value": "interoperabilityteam@nhs.net",
- "use": "work"
- }
- ]
- }
- ],
- "description": "Business status for test order Tasks in genomics",
- "copyright": "Copyright © 2022 NHS Digital",
- "caseSensitive": true,
- "content": "complete",
- "concept": [
- {
- "code": "InvalidRequest",
- "display": "Invalid Request"
- },
- {
- "code": "UnsatisfiedCondition",
- "display": "Unsatisfied Condition"
- },
- {
- "code": "TimeframeExceeded",
- "display": "Timeframe Exceeded"
- },
- {
- "code": "AwaitingSpecimen",
- "display": "Awaiting Specimen"
- },
- {
- "code": "AwaitingRoDAndSpecimen",
- "display": "Awaiting Record of Discussion and Specimen"
- },
- {
- "code": "SpecimenReceived",
- "display": "Specimen Received"
- },
- {
- "code": "SpecimenQualityNotOk",
- "display": "Specimen Quality Not OK"
- },
- {
- "code": "SpecimenProcessingInProgress",
- "display": "Specimen Processing In Progress"
- },
- {
- "code": "SpecimenProcessed",
- "display": "Specimen Processed"
- },
- {
- "code": "RemoteProcessingRequired",
- "display": "Remote Processing Required"
- },
- {
- "code": "SpecimenProcessingUnsuccessful",
- "display": "Specimen Processing Unsuccessful"
- },
- {
- "code": "SequencingCompleted",
- "display": "Sequencing Completed"
- },
- {
- "code": "RepeatSequencing",
- "display": "Repeat Sequencing"
- },
- {
- "code": "AlignSequencing",
- "display": "Align Sequencing"
- },
- {
- "code": "GeneticDataProcessingInProgress",
- "display": "Genetic Data Processing In Progress"
- },
- {
- "code": "RemoteGeneticDataProcessingRequired",
- "display": "Remote Genetic Data Processing Required"
- },
- {
- "code": "VariantsIdentified",
- "display": "Variants Identified"
- },
- {
- "code": "InterpretationInProgress",
- "display": "Interpretation In Progress"
- },
- {
- "code": "RemoteInterpretationRequired",
- "display": "Remote Interpretation Required"
- },
- {
- "code": "InterpretationCompleted",
- "display": "Interpretation Completed"
- },
- {
- "code": "InterpretationUnsuccessful",
- "display": "Interpretation Unsuccessful"
- },
- {
- "code": "FurtherClinicalDetailsRequired",
- "display": "Further Clinical Details Required"
- },
- {
- "code": "FurtherClinicalDetailsProvided",
- "display": "Further Clinical Details Provided"
- },
- {
- "code": "ReflexTestRequired",
- "display": "Reflex Test Required"
- },
- {
- "code": "ReflexTestComplete",
- "display": "Reflex Test Complete"
- },
- {
- "code": "DraftingReport",
- "display": "Drafting Report"
- },
- {
- "code": "ReportCompleted",
- "display": "ReportCompleted"
- }
- ]
+ "resourceType": "CodeSystem",
+ "id": "959a0a2f-73e3-4c6e-8e99-babb6b3a4296",
+ "url": "https://fhir.nhs.uk/CodeSystem/business-status-genomics",
+ "identifier": [
+ {
+ "system": "https://fhir.nhs.uk/identifier/CodeSystem",
+ "value": "business-status-genomics"
+ }
+ ],
+ "version": "0.2.0",
+ "name": "BusinessStatusGenomics",
+ "title": "Business Status Genomics",
+ "status": "draft",
+ "date": "2022-11-25",
+ "publisher": "NHS Digital",
+ "contact": [
+ {
+ "name": "NHS Digital",
+ "telecom": [
+ {
+ "system": "email",
+ "value": "interoperabilityteam@nhs.net",
+ "use": "work"
+ }
+ ]
+ }
+ ],
+ "description": "Business status for test order Tasks in genomics",
+ "copyright": "Copyright © 2022 NHS Digital",
+ "caseSensitive": true,
+ "content": "complete",
+ "concept": [
+ {
+ "code": "AwaitingSpecimen",
+ "display": "Awaiting Specimen"
+ },
+ {
+ "code": "AwaitingRoDAndSpecimen",
+ "display": "Awaiting Record of Discussion and Specimen"
+ },
+ {
+ "code": "SpecimenReceived",
+ "display": "Specimen Received"
+ },
+ {
+ "code": "RemoteProcessingRequired",
+ "display": "Remote Processing Required"
+ },
+ {
+ "code": "AlignSequencing",
+ "display": "Align Sequencing"
+ },
+ {
+ "code": "RemoteGeneticDataProcessingRequired",
+ "display": "Remote Genetic Data Processing Required"
+ },
+ {
+ "code": "VariantsIdentified",
+ "display": "Variants Identified"
+ },
+ {
+ "code": "RemoteInterpretationRequired",
+ "display": "Remote Interpretation Required"
+ },
+ {
+ "code": "FurtherClinicalDetailsRequired",
+ "display": "Further Clinical Details Required"
+ },
+ {
+ "code": "FurtherClinicalDetailsProvided",
+ "display": "Further Clinical Details Provided"
+ },
+ {
+ "code": "ReflexTestRequired",
+ "display": "Reflex Test Required"
+ },
+ {
+ "code": "ReflexTestComplete",
+ "display": "Reflex Test Complete"
+ }
+ ]
}
\ No newline at end of file
diff --git a/NHSEnglandFHIRGenomicsImplementationGuide/backup/CodeSystem/CodeSystem-Genomics-task-code.json b/NHSEnglandFHIRGenomicsImplementationGuide/backup/CodeSystem/CodeSystem-Genomics-task-code.json
new file mode 100644
index 000000000..2822e5fe1
--- /dev/null
+++ b/NHSEnglandFHIRGenomicsImplementationGuide/backup/CodeSystem/CodeSystem-Genomics-task-code.json
@@ -0,0 +1,188 @@
+{
+ "resourceType": "CodeSystem",
+ "url": "https://fhir.nhs.uk/CodeSystem/task-code-genomics",
+ "identifier": [
+ {
+ "system": "https://fhir.nhs.uk/identifier/CodeSystem",
+ "value": "task-code-genomics"
+ }
+ ],
+ "version": "0.1.0",
+ "name": "TaskCodeGenomics",
+ "title": "Task Code Genomics",
+ "status": "draft",
+ "date": "2023-12-06T10:54:00+00:00",
+ "publisher": "NHS England",
+ "contact": [
+ {
+ "name": "NHS England",
+ "telecom": [
+ {
+ "system": "email",
+ "value": "interoperabilityteam@nhs.net",
+ "use": "work"
+ }
+ ]
+ }
+ ],
+ "description": "A set of codes use to identify the type of task for Genomic Order Management",
+ "copyright": "Copyright © 2023 NHS England",
+ "caseSensitive": true,
+ "content": "complete",
+ "concept": [
+ {
+ "code": "RequestGenomicTest",
+ "display": "Request Genomic Test",
+ "designation": [
+ {
+ "use": {
+ "system": "http://snomed.info/sct",
+ "code": "900000000000013009",
+ "display": "Synonym"
+ },
+ "value": "10.00"
+ }
+ ]
+ },
+ {
+ "code": "ProcessGenomicTestRequest",
+ "display": "Process Genomic Test Request",
+ "designation": [
+ {
+ "use": {
+ "system": "http://snomed.info/sct",
+ "code": "900000000000013009",
+ "display": "Synonym"
+ },
+ "value": "50.00"
+ }
+ ]
+ },
+ {
+ "code": "RequestSampleAlignment",
+ "display": "Request & Sample Alignment",
+ "designation": [
+ {
+ "use": {
+ "system": "http://snomed.info/sct",
+ "code": "900000000000013009",
+ "display": "Synonym"
+ },
+ "value": "100.00"
+ }
+ ]
+ },
+ {
+ "code": "SamplePreparation",
+ "display": "Sample Preparation",
+ "designation": [
+ {
+ "use": {
+ "system": "http://snomed.info/sct",
+ "code": "900000000000013009",
+ "display": "Synonym"
+ },
+ "value": "150.00"
+ }
+ ]
+ },
+ {
+ "code": "SampleProcessing",
+ "display": "Sample Processing",
+ "designation": [
+ {
+ "use": {
+ "system": "http://snomed.info/sct",
+ "code": "900000000000013009",
+ "display": "Synonym"
+ },
+ "value": "200.00"
+ }
+ ]
+ },
+ {
+ "code": "GeneticGenomicDataProcessing",
+ "display": "Genetic/Genomic Data Processing",
+ "designation": [
+ {
+ "use": {
+ "system": "http://snomed.info/sct",
+ "code": "900000000000013009",
+ "display": "Synonym"
+ },
+ "value": "250.00"
+ }
+ ]
+ },
+ {
+ "code": "Interpretation",
+ "display": "Interpretation",
+ "designation": [
+ {
+ "use": {
+ "system": "http://snomed.info/sct",
+ "code": "900000000000013009",
+ "display": "Synonym"
+ },
+ "value": "300.00"
+ }
+ ]
+ },
+ {
+ "code": "ProduceInterimReport",
+ "display": "Produce Interim Report",
+ "designation": [
+ {
+ "use": {
+ "system": "http://snomed.info/sct",
+ "code": "900000000000013009",
+ "display": "Synonym"
+ },
+ "value": "350.00"
+ }
+ ]
+ },
+ {
+ "code": "GenomicMDT",
+ "display": "Genomic MDT",
+ "designation": [
+ {
+ "use": {
+ "system": "http://snomed.info/sct",
+ "code": "900000000000013009",
+ "display": "Synonym"
+ },
+ "value": "400.00"
+ }
+ ]
+ },
+ {
+ "code": "ProduceFinalReport",
+ "display": "Produce Final Report",
+ "designation": [
+ {
+ "use": {
+ "system": "http://snomed.info/sct",
+ "code": "900000000000013009",
+ "display": "Synonym"
+ },
+ "value": "450.00"
+ }
+ ]
+ },
+ {
+ "code": "DistributeReport",
+ "display": "Distribute Report",
+ "designation": [
+ {
+ "use": {
+ "system": "http://snomed.info/sct",
+ "code": "900000000000013009",
+ "display": "Synonym"
+ },
+ "value": "500.00"
+ }
+ ]
+ }
+ ]
+}
\ No newline at end of file
diff --git a/NHSEnglandFHIRGenomicsImplementationGuide/backup/CodeSystem/CodeSystem-Genomics-task-statusReason.json b/NHSEnglandFHIRGenomicsImplementationGuide/backup/CodeSystem/CodeSystem-Genomics-task-statusReason.json
new file mode 100644
index 000000000..4304d4917
--- /dev/null
+++ b/NHSEnglandFHIRGenomicsImplementationGuide/backup/CodeSystem/CodeSystem-Genomics-task-statusReason.json
@@ -0,0 +1,54 @@
+{
+ "resourceType": "CodeSystem",
+ "url": "https://fhir.nhs.uk/CodeSystem/task-statusReason-genomics",
+ "identifier": [
+ {
+ "system": "https://fhir.nhs.uk/identifier/CodeSystem",
+ "value": "task-statusReason-genomics"
+ }
+ ],
+ "version": "0.1.0",
+ "name": "TaskStatusReasonGenomics",
+ "title": "Task StatusReason Genomics",
+ "status": "draft",
+ "date": "2023-12-06",
+ "publisher": "NHS England",
+ "contact": [
+ {
+ "name": "NHS England",
+ "telecom": [
+ {
+ "system": "email",
+ "value": "interoperabilityteam@nhs.net",
+ "use": "work"
+ }
+ ]
+ }
+ ],
+ "description": "Status reasons for Tasks in genomics",
+ "copyright": "Copyright © 2023 NHS England",
+ "caseSensitive": true,
+ "content": "complete",
+ "concept": [
+ {
+ "code": "InvalidRequest",
+ "display": "Invalid Request"
+ },
+ {
+ "code": "PipelineActivityFailure",
+ "display": "Pipeline Activity Failure"
+ },
+ {
+ "code": "TaskTimeExceeded",
+ "display": "Task Time Exceeded"
+ },
+ {
+ "code": "UnableToInterpret",
+ "display": "Unable To Interpret"
+ },
+ {
+ "code": "SpecimenQualityNotOK",
+ "display": "Specimen Quality Not OK"
+ }
+ ]
+}
\ No newline at end of file
diff --git a/NHSEnglandFHIRGenomicsImplementationGuide/backup/NamingSystem/NamingSystem-England-GenomicTestDirectory.json b/NHSEnglandFHIRGenomicsImplementationGuide/backup/NamingSystem/NamingSystem-England-GenomicTestDirectory.json
new file mode 100644
index 000000000..631ba4b3d
--- /dev/null
+++ b/NHSEnglandFHIRGenomicsImplementationGuide/backup/NamingSystem/NamingSystem-England-GenomicTestDirectory.json
@@ -0,0 +1,43 @@
+{
+ "resourceType": "NamingSystem",
+ "id": "England-GenomicTestDirectory",
+ "name": "EnglandGenomicTestDirectory",
+ "status": "draft",
+ "kind": "codesystem",
+ "date": "2023-12-04",
+ "publisher": "NHS England",
+ "contact": [
+ {
+ "name": "NHS England",
+ "telecom": [
+ {
+ "system": "email",
+ "value": "interoperabilityteam@nhs.net",
+ "use": "work",
+ "rank": 1
+ }
+ ]
+ },
+ {
+ "name": "NHS Genomic Medicine Service",
+ "telecom": [
+ {
+ "system": "email",
+ "value": "england.genomics@nhs.net",
+ "use": "work",
+ "rank": 1
+ }
+ ]
+ }
+ ],
+ "responsible": "NHS Genomic Interop Programme",
+ "description": "NamingSystem for Genomic Test Directory Codes",
+ "usage": "Used to define the system for Genomic Test Directory codes within ServiceRequest resources",
+ "uniqueId": [
+ {
+ "type": "uri",
+ "value": "https://fhir.nhs.uk/CodeSystem/England-GenomicTestDirectory",
+ "preferred": true
+ }
+ ]
+}
\ No newline at end of file
diff --git a/NHSEnglandFHIRGenomicsImplementationGuide/backup/NamingSystem/NamingSystem-Genomics-order-number.json b/NHSEnglandFHIRGenomicsImplementationGuide/backup/NamingSystem/NamingSystem-Genomics-order-number.json
index bedcdc890..41f663776 100644
--- a/NHSEnglandFHIRGenomicsImplementationGuide/backup/NamingSystem/NamingSystem-Genomics-order-number.json
+++ b/NHSEnglandFHIRGenomicsImplementationGuide/backup/NamingSystem/NamingSystem-Genomics-order-number.json
@@ -6,6 +6,30 @@
"kind": "identifier",
"date": "2023-09-15",
"publisher": "NHS England",
+ "contact": [
+ {
+ "name": "NHS England",
+ "telecom": [
+ {
+ "system": "email",
+ "value": "interoperabilityteam@nhs.net",
+ "use": "work",
+ "rank": 1
+ }
+ ]
+ },
+ {
+ "name": "NHS Genomic Medicine Service",
+ "telecom": [
+ {
+ "system": "email",
+ "value": "england.genomics@nhs.net",
+ "use": "work",
+ "rank": 1
+ }
+ ]
+ }
+ ],
"responsible": "NHS Genomic Interop Programme",
"description": "Genomic Medicine Service Unique Order Number",
"usage": "Assigned by central GMS system on receipt of a test order",
diff --git a/NHSEnglandFHIRGenomicsImplementationGuide/backup/NamingSystem/NamingSystem-Genomics-pedigree-number.json b/NHSEnglandFHIRGenomicsImplementationGuide/backup/NamingSystem/NamingSystem-Genomics-pedigree-number.json
index 5ed9dbd2a..eea62e324 100644
--- a/NHSEnglandFHIRGenomicsImplementationGuide/backup/NamingSystem/NamingSystem-Genomics-pedigree-number.json
+++ b/NHSEnglandFHIRGenomicsImplementationGuide/backup/NamingSystem/NamingSystem-Genomics-pedigree-number.json
@@ -5,7 +5,31 @@
"status": "draft",
"kind": "identifier",
"date": "2022-12-05",
- "publisher": "NHS Digital",
+ "publisher": "NHS England",
+ "contact": [
+ {
+ "name": "NHS England",
+ "telecom": [
+ {
+ "system": "email",
+ "value": "interoperabilityteam@nhs.net",
+ "use": "work",
+ "rank": 1
+ }
+ ]
+ },
+ {
+ "name": "NHS Genomic Medicine Service",
+ "telecom": [
+ {
+ "system": "email",
+ "value": "england.genomics@nhs.net",
+ "use": "work",
+ "rank": 1
+ }
+ ]
+ }
+ ],
"responsible": "NHS Genomic Interop Programme",
"description": "Clinical genetics no/pedigree number",
"usage": "Patient's genetic/pedigree number which links their family.",
diff --git a/NHSEnglandFHIRGenomicsImplementationGuide/backup/Task/Task-NonWGSRareDiseaseTestOrder-Example.json b/NHSEnglandFHIRGenomicsImplementationGuide/backup/Task/Task-NonWGSRareDiseaseTestOrder-Example.json
index 027212a92..72bf13cc5 100644
--- a/NHSEnglandFHIRGenomicsImplementationGuide/backup/Task/Task-NonWGSRareDiseaseTestOrder-Example.json
+++ b/NHSEnglandFHIRGenomicsImplementationGuide/backup/Task/Task-NonWGSRareDiseaseTestOrder-Example.json
@@ -1,30 +1,30 @@
{
- "resourceType": "Task",
- "id": "Task-NonWGSRareDiseaseTestOrder-Example",
- "status": "requested",
- "intent": "order",
- "priority": "routine",
- "code": {
- "coding": [
- {
- "system": "https://fhir.nhs.uk/CodeSystem/task-code-genomics",
- "code": "SampleManagement",
- "display": "Sample Management"
- }
- ]
- },
- "focus": {
- "reference": "ServiceRequest/ServiceRequest-SavedTestOrder-Example"
- },
- "for": {
- "reference": "Patient/Patient-MeirLieberman-Example",
- "identifier": {
- "system": "https://fhir.nhs.uk/Id/nhs-number",
- "value": "9449307873"
- }
- },
- "authoredOn": "2023-08-05",
- "requester": {
- "reference": "PractitionerRole/PractitionerRole-GeneSmithENT-Example"
- }
+ "resourceType": "Task",
+ "id": "Task-NonWGSRareDiseaseTestOrder-Example",
+ "status": "requested",
+ "intent": "order",
+ "priority": "routine",
+ "code": {
+ "coding": [
+ {
+ "system": "https://fhir.nhs.uk/CodeSystem/task-code-genomics",
+ "code": "ProcessGenomicTestRequest",
+ "display": "Process Genomic Test Request"
+ }
+ ]
+ },
+ "focus": {
+ "reference": "ServiceRequest/ServiceRequest-SavedTestOrder-Example"
+ },
+ "for": {
+ "reference": "Patient/Patient-MeirLieberman-Example",
+ "identifier": {
+ "system": "https://fhir.nhs.uk/Id/nhs-number",
+ "value": "9449307873"
+ }
+ },
+ "authoredOn": "2023-08-05",
+ "requester": {
+ "reference": "PractitionerRole/PractitionerRole-GeneSmithENT-Example"
+ }
}
diff --git a/NHSEnglandFHIRGenomicsImplementationGuide/backup/Task/Task-NonWGSRareDiseaseTestOrderAccepted-Example.json b/NHSEnglandFHIRGenomicsImplementationGuide/backup/Task/Task-NonWGSRareDiseaseTestOrderAccepted-Example.json
index 918e8b6d9..5bf65bcd6 100644
--- a/NHSEnglandFHIRGenomicsImplementationGuide/backup/Task/Task-NonWGSRareDiseaseTestOrderAccepted-Example.json
+++ b/NHSEnglandFHIRGenomicsImplementationGuide/backup/Task/Task-NonWGSRareDiseaseTestOrderAccepted-Example.json
@@ -1,52 +1,52 @@
{
- "resourceType": "Task",
- "id": "Task-NonWGSRareDiseaseTestOrderAccepted-Example",
- "status": "accepted",
- "businessStatus": {
- "coding": [
- {
- "system": "https://fhir.nhs.uk/CodeSystem/business-status-genomics",
- "code": "AwaitingSpecimen",
- "display": "Awaiting Specimen"
- }
- ]
- },
- "intent": "order",
- "priority": "routine",
- "code": {
- "coding": [
- {
- "system": "https://fhir.nhs.uk/CodeSystem/task-code-genomics",
- "code": "SampleManagement",
- "display": "Sample Management"
- }
- ]
- },
- "focus": {
- "reference": "ServiceRequest/ServiceRequest-SavedTestOrder-Example"
- },
- "for": {
- "reference": "Patient/Patient-MeirLieberman-Example",
- "identifier": {
- "system": "https://fhir.nhs.uk/Id/nhs-number",
- "value": "9449307873"
- }
- },
- "authoredOn": "2023-08-05",
- "lastModified": "2023-08-08",
- "requester": {
- "reference": "PractitionerRole/PractitionerRole-GeneSmithENT-Example"
- },
- "owner": {
- "identifier": {
- "system": "https://fhir.nhs.uk/Id/ods-organization-code",
- "value": "69010"
- },
- "display": "Pathology Lab - ADDENBROOKE'S HOSPITAL LABORATORY"
- },
- "note": [
- {
- "text": "Optional Free Text field to record any additional details"
- }
- ]
+ "resourceType": "Task",
+ "id": "Task-NonWGSRareDiseaseTestOrderAccepted-Example",
+ "status": "accepted",
+ "businessStatus": {
+ "coding": [
+ {
+ "system": "https://fhir.nhs.uk/CodeSystem/business-status-genomics",
+ "code": "AwaitingSpecimen",
+ "display": "Awaiting Specimen"
+ }
+ ]
+ },
+ "intent": "order",
+ "priority": "routine",
+ "code": {
+ "coding": [
+ {
+ "system": "https://fhir.nhs.uk/CodeSystem/task-code-genomics",
+ "code": "RequestSampleAlignment",
+ "display": "Request & Sample Alignment"
+ }
+ ]
+ },
+ "focus": {
+ "reference": "ServiceRequest/ServiceRequest-SavedTestOrder-Example"
+ },
+ "for": {
+ "reference": "Patient/Patient-MeirLieberman-Example",
+ "identifier": {
+ "system": "https://fhir.nhs.uk/Id/nhs-number",
+ "value": "9449307873"
+ }
+ },
+ "authoredOn": "2023-08-05",
+ "lastModified": "2023-08-08",
+ "requester": {
+ "reference": "PractitionerRole/PractitionerRole-GeneSmithENT-Example"
+ },
+ "owner": {
+ "identifier": {
+ "system": "https://fhir.nhs.uk/Id/ods-organization-code",
+ "value": "69010"
+ },
+ "display": "Pathology Lab - ADDENBROOKE'S HOSPITAL LABORATORY"
+ },
+ "note": [
+ {
+ "text": "Optional Free Text field to record any additional details"
+ }
+ ]
}
diff --git a/NHSEnglandFHIRGenomicsImplementationGuide/backup/Task/Task-NonWGSRareDiseaseTestOrderHold-Example.json b/NHSEnglandFHIRGenomicsImplementationGuide/backup/Task/Task-NonWGSRareDiseaseTestOrderHold-Example.json
index b4d3f3b89..1e4399d78 100644
--- a/NHSEnglandFHIRGenomicsImplementationGuide/backup/Task/Task-NonWGSRareDiseaseTestOrderHold-Example.json
+++ b/NHSEnglandFHIRGenomicsImplementationGuide/backup/Task/Task-NonWGSRareDiseaseTestOrderHold-Example.json
@@ -1,61 +1,61 @@
{
- "resourceType": "Task",
- "id": "Task-NonWGSRareDiseaseTestOrderHold-Example",
- "status": "on-hold",
- "statusReason": {
- "coding": [
- {
- "system": "https://fhir.nhs.uk/CodeSystem/task-status-reason-genomics",
- "code": "InsufficientSample",
- "display": "Insufficient Sample"
- }
- ]
- },
- "businessStatus": {
- "coding": [
- {
- "system": "https://fhir.nhs.uk/CodeSystem/business-status-genomics",
- "code": "AwaitingSpecimen",
- "display": "Awaiting Specimen"
- }
- ]
- },
- "intent": "order",
- "priority": "routine",
- "code": {
- "coding": [
- {
- "system": "https://fhir.nhs.uk/CodeSystem/task-code-genomics",
- "code": "SampleManagement",
- "display": "Sample Management"
- }
- ]
- },
- "focus": {
- "reference": "ServiceRequest/ServiceRequest-SavedTestOrder-Example"
- },
- "for": {
- "reference": "Patient/Patient-MeirLieberman-Example",
- "identifier": {
- "system": "https://fhir.nhs.uk/Id/nhs-number",
- "value": "9449307873"
- }
- },
- "authoredOn": "2023-08-05",
- "lastModified": "2023-08-08",
- "requester": {
- "reference": "PractitionerRole/PractitionerRole-GeneSmithENT-Example"
- },
- "owner": {
- "identifier": {
- "system": "https://fhir.nhs.uk/Id/ods-organization-code",
- "value": "69010"
- },
- "display": "Pathology Lab - ADDENBROOKE'S HOSPITAL LABORATORY"
- },
- "note": [
- {
- "text": "Please provide additional sample of X"
- }
- ]
+ "resourceType": "Task",
+ "id": "Task-NonWGSRareDiseaseTestOrderHold-Example",
+ "status": "on-hold",
+ "statusReason": {
+ "coding": [
+ {
+ "system": "https://fhir.nhs.uk/CodeSystem/task-statusReason-genomics",
+ "code": "TaskTimeExceeded",
+ "display": "Task Time Exceeded"
+ }
+ ]
+ },
+ "businessStatus": {
+ "coding": [
+ {
+ "system": "https://fhir.nhs.uk/CodeSystem/business-status-genomics",
+ "code": "AwaitingSpecimen",
+ "display": "Awaiting Specimen"
+ }
+ ]
+ },
+ "intent": "order",
+ "priority": "routine",
+ "code": {
+ "coding": [
+ {
+ "system": "https://fhir.nhs.uk/CodeSystem/task-code-genomics",
+ "code": "RequestSampleAlignment",
+ "display": "Request & Sample Alignment"
+ }
+ ]
+ },
+ "focus": {
+ "reference": "ServiceRequest/ServiceRequest-SavedTestOrder-Example"
+ },
+ "for": {
+ "reference": "Patient/Patient-MeirLieberman-Example",
+ "identifier": {
+ "system": "https://fhir.nhs.uk/Id/nhs-number",
+ "value": "9449307873"
+ }
+ },
+ "authoredOn": "2023-08-05",
+ "lastModified": "2023-08-08",
+ "requester": {
+ "reference": "PractitionerRole/PractitionerRole-GeneSmithENT-Example"
+ },
+ "owner": {
+ "identifier": {
+ "system": "https://fhir.nhs.uk/Id/ods-organization-code",
+ "value": "69010"
+ },
+ "display": "Pathology Lab - ADDENBROOKE'S HOSPITAL LABORATORY"
+ },
+ "note": [
+ {
+ "text": "Please provide additional sample of X"
+ }
+ ]
}
diff --git a/NHSEnglandFHIRGenomicsImplementationGuide/backup/Task/Task-NonWGSRareDiseaseTestOrderRejected-Example.json b/NHSEnglandFHIRGenomicsImplementationGuide/backup/Task/Task-NonWGSRareDiseaseTestOrderRejected-Example.json
index 411f5e70e..b5aba3d75 100644
--- a/NHSEnglandFHIRGenomicsImplementationGuide/backup/Task/Task-NonWGSRareDiseaseTestOrderRejected-Example.json
+++ b/NHSEnglandFHIRGenomicsImplementationGuide/backup/Task/Task-NonWGSRareDiseaseTestOrderRejected-Example.json
@@ -1,61 +1,52 @@
{
- "resourceType": "Task",
- "id": "Task-NonWGSRareDiseaseTestOrderRejected-Example",
- "status": "rejected",
- "statusReason": {
- "coding": [
- {
- "system": "https://fhir.nhs.uk/CodeSystem/task-status-reason-genomics",
- "code": "Inappropriate",
- "display": "Inappropriate for patient"
- }
- ]
- },
- "businessStatus": {
- "coding": [
- {
- "system": "https://fhir.nhs.uk/CodeSystem/business-status-genomics",
- "code": "InvalidRequest",
- "display": "Invalid Request"
- }
- ]
- },
- "intent": "order",
- "priority": "routine",
- "code": {
- "coding": [
- {
- "system": "https://fhir.nhs.uk/CodeSystem/task-code-genomics",
- "code": "SampleManagement",
- "display": "Sample Management"
- }
- ]
- },
- "focus": {
- "reference": "ServiceRequest/ServiceRequest-SavedTestOrder-Example"
- },
- "for": {
- "reference": "Patient/Patient-MeirLieberman-Example",
- "identifier": {
- "system": "https://fhir.nhs.uk/Id/nhs-number",
- "value": "9449307873"
- }
- },
- "authoredOn": "2023-08-05",
- "lastModified": "2023-08-08",
- "requester": {
- "reference": "PractitionerRole/PractitionerRole-GeneSmithENT-Example"
- },
- "owner": {
- "identifier": {
- "system": "https://fhir.nhs.uk/Id/ods-organization-code",
- "value": "69010"
- },
- "display": "Pathology Lab - ADDENBROOKE'S HOSPITAL LABORATORY"
- },
- "note": [
- {
- "text": "Optional Free Text field to record any additional details"
- }
- ]
+ "resourceType": "Task",
+ "id": "Task-NonWGSRareDiseaseTestOrderRejected-Example",
+ "status": "rejected",
+ "statusReason": {
+ "coding": [
+ {
+ "system": "https://fhir.nhs.uk/CodeSystem/task-statusReason-genomics",
+ "code": "InvalidRequest",
+ "display": "Invalid Request"
+ }
+ ]
+ },
+ "intent": "order",
+ "priority": "routine",
+ "code": {
+ "coding": [
+ {
+ "system": "https://fhir.nhs.uk/CodeSystem/task-code-genomics",
+ "code": "ProcessGenomicTestRequest",
+ "display": "Process Genomic Test Request"
+ }
+ ]
+ },
+ "focus": {
+ "reference": "ServiceRequest/ServiceRequest-SavedTestOrder-Example"
+ },
+ "for": {
+ "reference": "Patient/Patient-MeirLieberman-Example",
+ "identifier": {
+ "system": "https://fhir.nhs.uk/Id/nhs-number",
+ "value": "9449307873"
+ }
+ },
+ "authoredOn": "2023-08-05",
+ "lastModified": "2023-08-08",
+ "requester": {
+ "reference": "PractitionerRole/PractitionerRole-GeneSmithENT-Example"
+ },
+ "owner": {
+ "identifier": {
+ "system": "https://fhir.nhs.uk/Id/ods-organization-code",
+ "value": "69010"
+ },
+ "display": "Pathology Lab - ADDENBROOKE'S HOSPITAL LABORATORY"
+ },
+ "note": [
+ {
+ "text": "Optional Free Text field to record any additional details"
+ }
+ ]
}
diff --git a/NHSEnglandFHIRGenomicsImplementationGuide/backup/Task/Task-WGSRareDiseaseTestOrder-Example.json b/NHSEnglandFHIRGenomicsImplementationGuide/backup/Task/Task-WGSRareDiseaseTestOrder-Example.json
index 2fe74605b..3813fa4a4 100644
--- a/NHSEnglandFHIRGenomicsImplementationGuide/backup/Task/Task-WGSRareDiseaseTestOrder-Example.json
+++ b/NHSEnglandFHIRGenomicsImplementationGuide/backup/Task/Task-WGSRareDiseaseTestOrder-Example.json
@@ -1,30 +1,30 @@
{
- "resourceType": "Task",
- "id": "Task-WGSRareDiseaseTestOrder-Example",
- "status": "requested",
- "intent": "order",
- "priority": "routine",
- "code": {
- "coding": [
- {
- "system": "https://fhir.nhs.uk/CodeSystem/task-code-genomics",
- "code": "SampleManagement",
- "display": "Sample Management"
- }
- ]
- },
- "focus": {
- "reference": "ServiceRequest/ServiceRequest-SavedTestOrder-Example"
- },
- "for": {
- "reference": "Patient/Patient-LindsaySorrell-Example",
- "identifier": {
- "system": "https://fhir.nhs.uk/Id/nhs-number",
- "value": "9449307946"
- }
- },
- "authoredOn": "2023-08-08",
- "requester": {
- "reference": "PractitionerRole/PractitionerRole-HazelSmithRenal-Example"
- }
+ "resourceType": "Task",
+ "id": "Task-WGSRareDiseaseTestOrder-Example",
+ "status": "requested",
+ "intent": "order",
+ "priority": "routine",
+ "code": {
+ "coding": [
+ {
+ "system": "https://fhir.nhs.uk/CodeSystem/task-code-genomics",
+ "code": "ProcessGenomicTestRequest",
+ "display": "Process Genomic Test Request"
+ }
+ ]
+ },
+ "focus": {
+ "reference": "ServiceRequest/ServiceRequest-SavedTestOrder-Example"
+ },
+ "for": {
+ "reference": "Patient/Patient-LindsaySorrell-Example",
+ "identifier": {
+ "system": "https://fhir.nhs.uk/Id/nhs-number",
+ "value": "9449307946"
+ }
+ },
+ "authoredOn": "2023-08-08",
+ "requester": {
+ "reference": "PractitionerRole/PractitionerRole-HazelSmithRenal-Example"
+ }
}
diff --git a/NHSEnglandFHIRGenomicsImplementationGuide/backup/Task/Task-WGSRareDiseaseTestOrderAccepted-Example.json b/NHSEnglandFHIRGenomicsImplementationGuide/backup/Task/Task-WGSRareDiseaseTestOrderAccepted-Example.json
index c38d17c4a..acc2d7dcd 100644
--- a/NHSEnglandFHIRGenomicsImplementationGuide/backup/Task/Task-WGSRareDiseaseTestOrderAccepted-Example.json
+++ b/NHSEnglandFHIRGenomicsImplementationGuide/backup/Task/Task-WGSRareDiseaseTestOrderAccepted-Example.json
@@ -1,47 +1,47 @@
{
- "resourceType": "Task",
- "id": "Task-WGSRareDiseaseTestOrderAccepted-Example",
- "status": "on-hold",
- "businessStatus": {
- "coding": [
- {
- "system": "https://fhir.nhs.uk/CodeSystem/business-status-genomics",
- "code": "AwaitingRoDAndSpecimen",
- "display": "Awaiting Record of Discussion and Specimen"
- }
- ]
- },
- "intent": "order",
- "priority": "routine",
- "code": {
- "coding": [
- {
- "system": "https://fhir.nhs.uk/CodeSystem/task-code-genomics",
- "code": "SampleManagement",
- "display": "Sample Management"
- }
- ]
- },
- "focus": {
- "reference": "ServiceRequest/ServiceRequest-SavedTestOrder-Example"
- },
- "for": {
- "reference": "Patient/Patient-LindsaySorrell-Example",
- "identifier": {
- "system": "https://fhir.nhs.uk/Id/nhs-number",
- "value": "9449307946"
- }
- },
- "authoredOn": "2023-08-08",
- "lastModified": "2023-08-09",
- "requester": {
- "reference": "PractitionerRole/PractitionerRole-HazelSmithRenal-Example"
- },
- "owner": {
- "identifier": {
- "system": "https://fhir.nhs.uk/Id/ods-organization-code",
- "value": "RJ1"
- },
- "display": "GUY'S AND ST THOMAS' NHS FOUNDATION TRUST"
- }
+ "resourceType": "Task",
+ "id": "Task-WGSRareDiseaseTestOrderAccepted-Example",
+ "status": "on-hold",
+ "businessStatus": {
+ "coding": [
+ {
+ "system": "https://fhir.nhs.uk/CodeSystem/business-status-genomics",
+ "code": "AwaitingRoDAndSpecimen",
+ "display": "Awaiting Record of Discussion and Specimen"
+ }
+ ]
+ },
+ "intent": "order",
+ "priority": "routine",
+ "code": {
+ "coding": [
+ {
+ "system": "https://fhir.nhs.uk/CodeSystem/task-code-genomics",
+ "code": "RequestSampleAlignment",
+ "display": "Request & Sample Alignment"
+ }
+ ]
+ },
+ "focus": {
+ "reference": "ServiceRequest/ServiceRequest-SavedTestOrder-Example"
+ },
+ "for": {
+ "reference": "Patient/Patient-LindsaySorrell-Example",
+ "identifier": {
+ "system": "https://fhir.nhs.uk/Id/nhs-number",
+ "value": "9449307946"
+ }
+ },
+ "authoredOn": "2023-08-08",
+ "lastModified": "2023-08-09",
+ "requester": {
+ "reference": "PractitionerRole/PractitionerRole-HazelSmithRenal-Example"
+ },
+ "owner": {
+ "identifier": {
+ "system": "https://fhir.nhs.uk/Id/ods-organization-code",
+ "value": "RJ1"
+ },
+ "display": "GUY'S AND ST THOMAS' NHS FOUNDATION TRUST"
+ }
}
diff --git a/NHSEnglandFHIRGenomicsImplementationGuide/backup/Task/Task-WGSRareDiseaseTestOrderForwarded-Example.json b/NHSEnglandFHIRGenomicsImplementationGuide/backup/Task/Task-WGSRareDiseaseTestOrderForwarded-Example.json
index 242c93d56..9b9af0b5b 100644
--- a/NHSEnglandFHIRGenomicsImplementationGuide/backup/Task/Task-WGSRareDiseaseTestOrderForwarded-Example.json
+++ b/NHSEnglandFHIRGenomicsImplementationGuide/backup/Task/Task-WGSRareDiseaseTestOrderForwarded-Example.json
@@ -1,47 +1,47 @@
{
- "resourceType": "Task",
- "id": "Task-WGSRareDiseaseTestOrderForwarded-Example",
- "status": "ready",
- "businessStatus": {
- "coding": [
- {
- "system": "https://fhir.nhs.uk/CodeSystem/business-status-genomics",
- "code": "SpecimenReceived",
- "display": "Specimen Received"
- }
- ]
- },
- "intent": "order",
- "priority": "routine",
- "code": {
- "coding": [
- {
- "system": "https://fhir.nhs.uk/CodeSystem/task-code-genomics",
- "code": "SampleManagement",
- "display": "Sample Management"
- }
- ]
- },
- "focus": {
- "reference": "ServiceRequest/ServiceRequest-SavedTestOrder-Example"
- },
- "for": {
- "reference": "Patient/Patient-LindsaySorrell-Example",
- "identifier": {
- "system": "https://fhir.nhs.uk/Id/nhs-number",
- "value": "9449307946"
- }
- },
- "authoredOn": "2023-08-08",
- "lastModified": "2023-08-10",
- "requester": {
- "reference": "PractitionerRole/PractitionerRole-HazelSmithRenal-Example"
- },
- "owner": {
- "identifier": {
- "system": "https://fhir.nhs.uk/Id/ods-organization-code",
- "value": "8J834"
- },
- "display": "GENOMICS ENGLAND"
- }
+ "resourceType": "Task",
+ "id": "Task-WGSRareDiseaseTestOrderForwarded-Example",
+ "status": "ready",
+ "businessStatus": {
+ "coding": [
+ {
+ "system": "https://fhir.nhs.uk/CodeSystem/business-status-genomics",
+ "code": "SpecimenReceived",
+ "display": "Specimen Received"
+ }
+ ]
+ },
+ "intent": "order",
+ "priority": "routine",
+ "code": {
+ "coding": [
+ {
+ "system": "https://fhir.nhs.uk/CodeSystem/task-code-genomics",
+ "code": "SamplePreparation",
+ "display": "Sample Preparation"
+ }
+ ]
+ },
+ "focus": {
+ "reference": "ServiceRequest/ServiceRequest-SavedTestOrder-Example"
+ },
+ "for": {
+ "reference": "Patient/Patient-LindsaySorrell-Example",
+ "identifier": {
+ "system": "https://fhir.nhs.uk/Id/nhs-number",
+ "value": "9449307946"
+ }
+ },
+ "authoredOn": "2023-08-08",
+ "lastModified": "2023-08-10",
+ "requester": {
+ "reference": "PractitionerRole/PractitionerRole-HazelSmithRenal-Example"
+ },
+ "owner": {
+ "identifier": {
+ "system": "https://fhir.nhs.uk/Id/ods-organization-code",
+ "value": "8J834"
+ },
+ "display": "GENOMICS ENGLAND"
+ }
}
diff --git a/NHSEnglandFHIRGenomicsImplementationGuide/backup/ValueSet/ValueSet-Genomics-business-status.json b/NHSEnglandFHIRGenomicsImplementationGuide/backup/ValueSet/ValueSet-Genomics-business-status.json
index 03a246855..2b2968e15 100644
--- a/NHSEnglandFHIRGenomicsImplementationGuide/backup/ValueSet/ValueSet-Genomics-business-status.json
+++ b/NHSEnglandFHIRGenomicsImplementationGuide/backup/ValueSet/ValueSet-Genomics-business-status.json
@@ -1,17 +1,17 @@
{
- "resourceType": "ValueSet",
- "id": "genomics-business-status",
- "url": "https://fhir.nhs.uk/ValueSet/genomics-business-status",
- "version": "0.1.0",
- "name": "GenomicsBusinessStatus",
- "status": "draft",
- "description": "A ValueSet to identify the business status for a Genomic Test Order filler Task",
- "compose": {
- "include": [
- {
- "system": "https://fhir.nhs.uk/CodeSystem/business-status-genomics",
- "version": "0.1.0"
- }
- ]
- }
+ "resourceType": "ValueSet",
+ "id": "genomics-business-status",
+ "url": "https://fhir.nhs.uk/ValueSet/genomics-business-status",
+ "version": "0.1.0",
+ "name": "GenomicsBusinessStatus",
+ "status": "draft",
+ "description": "A ValueSet to identify the business status for a Genomic Test Order filler Task",
+ "compose": {
+ "include": [
+ {
+ "system": "https://fhir.nhs.uk/CodeSystem/business-status-genomics",
+ "version": "0.2.0"
+ }
+ ]
+ }
}
\ No newline at end of file
diff --git a/NHSEnglandFHIRGenomicsImplementationGuide/backup/ValueSet/ValueSet-Genomics-task-code.json b/NHSEnglandFHIRGenomicsImplementationGuide/backup/ValueSet/ValueSet-Genomics-task-code.json
new file mode 100644
index 000000000..acce906aa
--- /dev/null
+++ b/NHSEnglandFHIRGenomicsImplementationGuide/backup/ValueSet/ValueSet-Genomics-task-code.json
@@ -0,0 +1,17 @@
+{
+ "resourceType": "ValueSet",
+ "id": "task-code-genomics",
+ "url": "https://fhir.nhs.uk/ValueSet/task-code-genomics",
+ "version": "0.1.0",
+ "name": "TaskCodeGenomics",
+ "status": "draft",
+ "description": "A ValueSet to identify the type of Task for Genomic Order Management",
+ "compose": {
+ "include": [
+ {
+ "system": "https://fhir.nhs.uk/CodeSystem/task-code-genomics",
+ "version": "0.1.0"
+ }
+ ]
+ }
+}
\ No newline at end of file
diff --git a/NHSEnglandFHIRGenomicsImplementationGuide/backup/ValueSet/ValueSet-Genomics-task-statusReason.json b/NHSEnglandFHIRGenomicsImplementationGuide/backup/ValueSet/ValueSet-Genomics-task-statusReason.json
new file mode 100644
index 000000000..9374a86ca
--- /dev/null
+++ b/NHSEnglandFHIRGenomicsImplementationGuide/backup/ValueSet/ValueSet-Genomics-task-statusReason.json
@@ -0,0 +1,17 @@
+{
+ "resourceType": "ValueSet",
+ "id": "task-statusReason-genomics",
+ "url": "https://fhir.nhs.uk/ValueSet/task-statusReason-genomics",
+ "version": "0.1.0",
+ "name": "TaskStatusReasonGenomics",
+ "status": "draft",
+ "description": "A ValueSet to identify the reasons for failure states of Tasks for Genomic Order Management",
+ "compose": {
+ "include": [
+ {
+ "system": "https://fhir.nhs.uk/CodeSystem/task-statusReason-genomics",
+ "version": "0.1.0"
+ }
+ ]
+ }
+}
\ No newline at end of file
diff --git a/NHSEnglandFHIRGenomicsImplementationGuide/backup/guides/FHIR-Genomics-Implementation-Guide/Home/Build/Authentication/Consent.page.md b/NHSEnglandFHIRGenomicsImplementationGuide/backup/guides/FHIR-Genomics-Implementation-Guide/Home/Build/Authentication/Consent.page.md
new file mode 100644
index 000000000..c590dff1f
--- /dev/null
+++ b/NHSEnglandFHIRGenomicsImplementationGuide/backup/guides/FHIR-Genomics-Implementation-Guide/Home/Build/Authentication/Consent.page.md
@@ -0,0 +1,15 @@
+## {{page-title}}
+
+Consent within Genomics can be split into two main categories:
+* General consent to having genetic/genomic testing performed, including consent obtained from family members for cascade testing
+* Consent allowing for storage and secondary use of data, e.g. for research. Most relevant to WGS test requests, allowing storage of data in the National Genomic Research Library.
+
+### Consent for Testing
+
+Consent for testing is assumed to have been taken when submitting a test request to the Genomic Medicine Service. As of publication, capturing of this consent information is not considered in scope for storage in the central broker, however, this information can be represented using FHIR Consent resources. Guidance on how this information should be captured if general consent is later deemed in scope for the GMS.
+
+### Consent for Research
+
+Currently, representation of Consent for Research within the Genomic Medicine Service is limited to the [Record of Discussion form](https://github.com/NHSDigital/NHSDigital-FHIR-Genomics-ImplementationGuide/blob/04ab4bc353a3c002613c422ecfc9aea6ab38c1c7/documents/nhs-genomic-medicine-service-record-of-discussion-form.pdf). Within GMS payloads this is modelled as a QuestionnaireResponse, based upon the {{pagelink:Questionnaire-Genomic-Testing}} FHIR Questionnaire resource.
+
+It is expected that this QuestionnaireResponse will be wrapped/referenced from a Consent resource to capture the status of the discussion and categorise the consent as consent for research.
\ No newline at end of file
diff --git a/NHSEnglandFHIRGenomicsImplementationGuide/backup/guides/FHIR-Genomics-Implementation-Guide/Home/Build/Authentication/toc.yaml b/NHSEnglandFHIRGenomicsImplementationGuide/backup/guides/FHIR-Genomics-Implementation-Guide/Home/Build/Authentication/toc.yaml
index 878279f49..eca729d0e 100644
--- a/NHSEnglandFHIRGenomicsImplementationGuide/backup/guides/FHIR-Genomics-Implementation-Guide/Home/Build/Authentication/toc.yaml
+++ b/NHSEnglandFHIRGenomicsImplementationGuide/backup/guides/FHIR-Genomics-Implementation-Guide/Home/Build/Authentication/toc.yaml
@@ -8,3 +8,5 @@
filename: Security.page.md
- name: Integration with SPINE
filename: IntegrationwithSPINE.page.md
+- name: Consent
+ filename: Consent.page.md
diff --git a/NHSEnglandFHIRGenomicsImplementationGuide/backup/guides/FHIR-Genomics-Implementation-Guide/Home/Build/Operationresponses.page.md b/NHSEnglandFHIRGenomicsImplementationGuide/backup/guides/FHIR-Genomics-Implementation-Guide/Home/Build/Operationresponses.page.md
index f354d621f..02873bc17 100644
--- a/NHSEnglandFHIRGenomicsImplementationGuide/backup/guides/FHIR-Genomics-Implementation-Guide/Home/Build/Operationresponses.page.md
+++ b/NHSEnglandFHIRGenomicsImplementationGuide/backup/guides/FHIR-Genomics-Implementation-Guide/Home/Build/Operationresponses.page.md
@@ -2,6 +2,6 @@
This page is used to describe the search operations supported by the API and their responses.
-No custom search parameters have been defined for use in Genomics as of publication, though these will be listed here if developed.
+No custom search parameters or operations have been defined for use in Genomics as of publication, though these will be listed here if developed.
The current list of supported search parameters by resource can be found on the {{pagelink:Home/FHIRAssets/CapabilityStatements/Instance.page.md}} CapabilityStatement page.
diff --git a/NHSEnglandFHIRGenomicsImplementationGuide/backup/guides/FHIR-Genomics-Implementation-Guide/Home/Build/Querytypes.page.md b/NHSEnglandFHIRGenomicsImplementationGuide/backup/guides/FHIR-Genomics-Implementation-Guide/Home/Build/Querytypes.page.md
deleted file mode 100644
index 07f9d5fd1..000000000
--- a/NHSEnglandFHIRGenomicsImplementationGuide/backup/guides/FHIR-Genomics-Implementation-Guide/Home/Build/Querytypes.page.md
+++ /dev/null
@@ -1,3 +0,0 @@
-## {{page-title}}
-
-Query types supported by the API are defined within the {{pagelink:Home/FHIRAssets/CapabilityStatements/Instance.page.md}} CapabilityStatement. From initial design work, it is expected the main use case will be labs and requesters polling the central service for test orders and reports, including associated clinical information, as well as polling the system for the current state of Tasks and Task update history, through associated AuditEvents and Provenance resources.
\ No newline at end of file
diff --git a/NHSEnglandFHIRGenomicsImplementationGuide/backup/guides/FHIR-Genomics-Implementation-Guide/Home/Build/Supported-CRUD-capability.page.md b/NHSEnglandFHIRGenomicsImplementationGuide/backup/guides/FHIR-Genomics-Implementation-Guide/Home/Build/Supported-CRUD-capability.page.md
new file mode 100644
index 000000000..9fafa7f51
--- /dev/null
+++ b/NHSEnglandFHIRGenomicsImplementationGuide/backup/guides/FHIR-Genomics-Implementation-Guide/Home/Build/Supported-CRUD-capability.page.md
@@ -0,0 +1,15 @@
+## {{page-title}}
+
+Interactions supported by the API are defined within the {{pagelink:Home/FHIRAssets/CapabilityStatements/Instance.page.md}} CapabilityStatement.
+
+### Create
+The main create operations will be creation of the initial test request and associated clinical information; creation of interim data (either binary files or structured FHIR resources attached to Task.output; and creation of the resulting DiagnosticReport resources. Creation of ServiceRequest and DiagnosticReport resources will trigger the associated processes to kick-off or close down a test order fulfillment workflow.
+
+### Read
+From initial design work, it is expected the main use case will be labs and requesters polling the central service for test orders and reports, including associated clinical information, as well as polling the system for the current state of Tasks and Task update history, through associated AuditEvents and Provenance resources.
+
+### Update
+A large part of the interactions with the central service, over the course of order fulfillment, will be updates to Task resources, which constitute status updates. These events will be captured by the central broker through AuditEvent resources. Additionally, ServiceRequest and DiagnosticReport resources may be updated if tests need to be changed or new data added, captured through Provenance resources. The impact these updates have on work-in-progress will be defined within Business Rules on the central broker (including how cancellations are managed).
+
+### Delete
+It is not expected that delete operations will be supported by the central service for workflow based resources, e.g. if a service request or task was created in error. Cancellations or marking resources as entered in error SHOULD be represented using the associated status on the resources rather than deleting them from the central service to ensure auditability. However, if a clinical resource is no longer relevant, this may require a delete. Though additional logic will need to be added to the central service to ensure referential integrity and notifications if deletes constitute material changes affecting the processing of a test request. The Information Governance implications of limiting deletion of resources will be investigated within the Alpha phase of the project.
\ No newline at end of file
diff --git a/NHSEnglandFHIRGenomicsImplementationGuide/backup/guides/FHIR-Genomics-Implementation-Guide/Home/Build/toc.yaml b/NHSEnglandFHIRGenomicsImplementationGuide/backup/guides/FHIR-Genomics-Implementation-Guide/Home/Build/toc.yaml
index daae10032..3091becd4 100644
--- a/NHSEnglandFHIRGenomicsImplementationGuide/backup/guides/FHIR-Genomics-Implementation-Guide/Home/Build/toc.yaml
+++ b/NHSEnglandFHIRGenomicsImplementationGuide/backup/guides/FHIR-Genomics-Implementation-Guide/Home/Build/toc.yaml
@@ -10,7 +10,7 @@
filename: APIusage.page.md
- name: Error handling
filename: Errorhandling.page.md
-- name: Query types
- filename: Querytypes.page.md
+- name: Supported CRUD capability
+ filename: Supported-CRUD-capability.page.md
- name: Operation responses
filename: Operationresponses.page.md
diff --git a/NHSEnglandFHIRGenomicsImplementationGuide/backup/guides/FHIR-Genomics-Implementation-Guide/Home/Design/Clinicalheadings/Additional-Contact.page.md b/NHSEnglandFHIRGenomicsImplementationGuide/backup/guides/FHIR-Genomics-Implementation-Guide/Home/Design/Clinicalheadings/Additional-Contact.page.md
index 8a6b43f40..0093cae70 100644
--- a/NHSEnglandFHIRGenomicsImplementationGuide/backup/guides/FHIR-Genomics-Implementation-Guide/Home/Design/Clinicalheadings/Additional-Contact.page.md
+++ b/NHSEnglandFHIRGenomicsImplementationGuide/backup/guides/FHIR-Genomics-Implementation-Guide/Home/Design/Clinicalheadings/Additional-Contact.page.md
@@ -9,19 +9,19 @@ Mapped to an extension on the ServiceRequest, in review.
### Mapping
| Source Data item | Target FHIR Element | HL7v2.5.1 Mapping | Description
|--|--|
-|Additional contact - Full name|ServiceRequest.extension:additionalContact(PractitionerRole.practitioner(Practitioner.name))|Additional STF segment (STF-3), possibly referenced from the STF segment for the requester via STF-14|Additional contact's full name.|
-|Additional contact - Job Title|ServiceRequest.extension:additionalContact(PractitionerRole.code)|STF-18|Additional contact's job title.|
-|Additional contact - Current Specialty|ServiceRequest.extension:additionalContact(PractitionerRole.specialty)|PRA-5|Additional contact's current specialty.|
-|Additional contact - Phone|ServiceRequest.extension:additionalContact(PractitionerRole.telecom:system=phone)|STF-10|Additional contact's phone number.|
-|Additional contact - Email address|ServiceRequest.extension:additionalContact(PractitionerRole.telecom:system=email)|STF-15|Additional contact's email address.|
-|Additional contact - Organization name, address and ODS code.|ServiceRequest.extension:additionalContact(PractitionerRole.organization(Organization.name))|STF-9.2|Additional contact's organization name.|
-|Additional contact - Organization address.|ServiceRequest.extension:additionalContact(PractitionerRole.organization(Organization.address))|STF-11|Additional contact's organization address.|
-|Additional contact - Organization ODS code.|ServiceRequest.extension:additionalContact(PractitionerRole.organization(Organization.identifier))|STF-9.1|Additional contact's organization ODS code.|
-|Additional contact - Department name|ServiceRequest.extension:additionalContact(PractitionerRole.healthcareService(HealthcareService.name)), could alternatively use PractitionerRole.healthcareService.display to reduce resources in message|STF-8|Additional contact's department name.|
-|Additional contact - Professional registration number|ServiceRequest.extension:additionalContact(PractitionerRole.practitioner(Practitioner.identifier))|STF-2.1|Additional contact's professional registration number such as their GMC number.|
-|Additional contact - Professional registration number type|ServiceRequest.extension:additionalContact(PractitionerRole.practitioner(Practitioner.identifier.system))|STF-2.3|Additional contact's professional registration number type such GMC.|
-|Additional contact - Genomic report delivery method|ServiceRequest.requester(PractitionerRole.telecom.rank=1)|STF-16|Additional contact's report preferred delivery method.|
-|Additional contact - Central email for address and reporting (many)|Additional ServiceRequest.extension:additionalContact(PractitionerRole.telecom:system=email), may need to be additionally indicated in NEMS subscription|STF-15|Central email address provided by the additional contact.|
+|Additional contact - Full name|ServiceRequest.extension:additionalContact( PractitionerRole.practitioner( Practitioner.name ) )|Additional STF segment (STF-3), possibly referenced from the STF segment for the requester via STF-14|Additional contact's full name.|
+|Additional contact - Job Title|ServiceRequest.extension:additionalContact( PractitionerRole.code )|STF-18|Additional contact's job title.|
+|Additional contact - Current Specialty|ServiceRequest.extension:additionalContact( PractitionerRole.specialty )|PRA-5|Additional contact's current specialty.|
+|Additional contact - Phone|ServiceRequest.extension:additionalContact( PractitionerRole.telecom:system=phone )|STF-10|Additional contact's phone number.|
+|Additional contact - Email address|ServiceRequest.extension:additionalContact( PractitionerRole.telecom:system=email )|STF-15|Additional contact's email address.|
+|Additional contact - Organization name, address and ODS code.|ServiceRequest.extension:additionalContact( PractitionerRole.organization( Organization.name ) )|STF-9.2|Additional contact's organization name.|
+|Additional contact - Organization address.|ServiceRequest.extension:additionalContact( PractitionerRole.organization( Organization.address ) )|STF-11|Additional contact's organization address.|
+|Additional contact - Organization ODS code.|ServiceRequest.extension:additionalContact(PractitionerRole.organization( Organization.identifier ) )|STF-9.1|Additional contact's organization ODS code.|
+|Additional contact - Department name|ServiceRequest.extension:additionalContact(PractitionerRole.healthcareService( HealthcareService.name ) ), could alternatively use PractitionerRole.healthcareService.display to reduce resources in message|STF-8|Additional contact's department name.|
+|Additional contact - Professional registration number|ServiceRequest.extension:additionalContact(PractitionerRole.practitioner( Practitioner.identifier ) )|STF-2.1|Additional contact's professional registration number such as their GMC number.|
+|Additional contact - Professional registration number type|ServiceRequest.extension:additionalContact(PractitionerRole.practitioner( Practitioner.identifier.system ) )|STF-2.3|Additional contact's professional registration number type such GMC.|
+|Additional contact - Genomic report delivery method|ServiceRequest.requester( PractitionerRole.telecom.rank=1 )|STF-16|Additional contact's report preferred delivery method.|
+|Additional contact - Central email for address and reporting (many)|Additional ServiceRequest.extension:additionalContact( PractitionerRole.telecom:system=email ), may need to be additionally indicated in NEMS subscription|STF-15|Central email address provided by the additional contact.|
-
-{{index:current}}
\ No newline at end of file
+-->
\ No newline at end of file
diff --git a/NHSEnglandFHIRGenomicsImplementationGuide/backup/guides/FHIR-Genomics-Implementation-Guide/Home/FHIRAssets/Profiles/toc.yaml b/NHSEnglandFHIRGenomicsImplementationGuide/backup/guides/FHIR-Genomics-Implementation-Guide/Home/FHIRAssets/Profiles/toc.yaml
index 2f6081f59..10a540c90 100644
--- a/NHSEnglandFHIRGenomicsImplementationGuide/backup/guides/FHIR-Genomics-Implementation-Guide/Home/FHIRAssets/Profiles/toc.yaml
+++ b/NHSEnglandFHIRGenomicsImplementationGuide/backup/guides/FHIR-Genomics-Implementation-Guide/Home/FHIRAssets/Profiles/toc.yaml
@@ -1,52 +1,4 @@
- name: Index
filename: Index.page.md
-- name: Genomics-AuditEvent
- filename: Genomics-AuditEvent.page.md
-- name: Genomics-Condition
- filename: Genomics-Condition.page.md
-- name: Genomics-Consent
- filename: Genomics-Consent.page.md
-- name: Genomics-DiagnosticReport
- filename: Genomics-DiagnosticReport.page.md
-- name: Genomics-FamilyMemberHistory
- filename: Genomics-FamilyMemberHistory.page.md
-- name: Genomics-MessageDefinition
- filename: Genomics-MessageDefinition.page.md
-- name: Genomics-MessageHeader
- filename: Genomics-MessageHeader.page.md
-- name: Genomics-Observation
- filename: Genomics-Observation.page.md
-- name: Genomics-Organization
- filename: Genomics-Organization.page.md
-- name: Genomics-Patient
- filename: Genomics-Patient.page.md
-- name: Genomics-Practitioner
- filename: Genomics-Practitioner.page.md
-- name: Genomics-PractitionerRole
- filename: Genomics-PractitionerRole.page.md
-- name: Genomics-Procedure
- filename: Genomics-Procedure.page.md
-- name: Genomics-Provenance
- filename: Genomics-Provenance.page.md
-- name: Genomics-RelatedPerson
- filename: Genomics-RelatedPerson.page.md
-- name: Genomics-ServiceRequest
- filename: Genomics-ServiceRequest.page.md
-- name: Genomics-Specimen
- filename: Genomics-Specimen.page.md
-- name: Genomics-Task
- filename: Genomics-Task.page.md
-- name: Genomics-BodyStructure
- filename: Genomics-BodyStructure.page.md
-- name: Genomics-Bundle
- filename: Genomics-Bundle.page.md
-- name: Genomics-OperationOutcome
- filename: Genomics-OperationOutcome.page.md
-- name: Genomics-Questionnaire
- filename: Genomics-Questionnaire.page.md
-- name: Genomics-QuestionnaireResponse
- filename: Genomics-QuestionnaireResponse.page.md
-- name: Genomics-ResearchSubject
- filename: Genomics-ResearchSubject.page.md
-- name: Genomics-Subscription
- filename: Genomics-Subscription.page.md
+- name: All Profiles
+ filename: All-Profiles
diff --git a/NHSEnglandFHIRGenomicsImplementationGuide/backup/guides/FHIR-Genomics-Implementation-Guide/Home/FHIRAssets/ValueSets/Genomic-Task-Code.page.md b/NHSEnglandFHIRGenomicsImplementationGuide/backup/guides/FHIR-Genomics-Implementation-Guide/Home/FHIRAssets/ValueSets/Genomic-Task-Code.page.md
new file mode 100644
index 000000000..0040ca462
--- /dev/null
+++ b/NHSEnglandFHIRGenomicsImplementationGuide/backup/guides/FHIR-Genomics-Implementation-Guide/Home/FHIRAssets/ValueSets/Genomic-Task-Code.page.md
@@ -0,0 +1,30 @@
+## {{page-title}}
+
+A ValueSet to identify the possible codes for a Genomic Test Order Task
+
+
+ HTML View
+ Table View
+ XML View
+ JSON View
+
+
+
+
HTML View
+{{render:https://fhir.nhs.uk/ValueSet/task-code-genomics}}
+
+
+
+
Table View
+{{table:https://fhir.nhs.uk/ValueSet/task-code-genomics}}
+
+
+
+
XML View
+{{xml:https://fhir.nhs.uk/ValueSet/task-code-genomics}}
+
+
+
+
JSON View
+{{json:https://fhir.nhs.uk/ValueSet/task-code-genomics}}
+
\ No newline at end of file
diff --git a/NHSEnglandFHIRGenomicsImplementationGuide/backup/guides/FHIR-Genomics-Implementation-Guide/Home/FHIRAssets/ValueSets/Genomic-Task-StatusReason.page.md b/NHSEnglandFHIRGenomicsImplementationGuide/backup/guides/FHIR-Genomics-Implementation-Guide/Home/FHIRAssets/ValueSets/Genomic-Task-StatusReason.page.md
new file mode 100644
index 000000000..776697ba2
--- /dev/null
+++ b/NHSEnglandFHIRGenomicsImplementationGuide/backup/guides/FHIR-Genomics-Implementation-Guide/Home/FHIRAssets/ValueSets/Genomic-Task-StatusReason.page.md
@@ -0,0 +1,30 @@
+## {{page-title}}
+
+A ValueSet to identify the possible codes for a Task statusReasons in Genomics
+
+
+ HTML View
+ Table View
+ XML View
+ JSON View
+
+
+
+
HTML View
+{{render:https://fhir.nhs.uk/ValueSet/task-statusReason-genomics}}
+
+
+
+
Table View
+{{table:https://fhir.nhs.uk/ValueSet/task-statusReason-genomics}}
+
+
+
+
XML View
+{{xml:https://fhir.nhs.uk/ValueSet/task-statusReason-genomics}}
+
+
+
+
JSON View
+{{json:https://fhir.nhs.uk/ValueSet/task-statusReason-genomics}}
+
\ No newline at end of file
diff --git a/NHSEnglandFHIRGenomicsImplementationGuide/backup/guides/FHIR-Genomics-Implementation-Guide/Home/FHIRAssets/ValueSets/toc.yaml b/NHSEnglandFHIRGenomicsImplementationGuide/backup/guides/FHIR-Genomics-Implementation-Guide/Home/FHIRAssets/ValueSets/toc.yaml
index 9555e03bd..34fe671af 100644
--- a/NHSEnglandFHIRGenomicsImplementationGuide/backup/guides/FHIR-Genomics-Implementation-Guide/Home/FHIRAssets/ValueSets/toc.yaml
+++ b/NHSEnglandFHIRGenomicsImplementationGuide/backup/guides/FHIR-Genomics-Implementation-Guide/Home/FHIRAssets/ValueSets/toc.yaml
@@ -2,6 +2,10 @@
filename: Index.page.md
- name: Genomic-Business-Status
filename: Genomic-Business-Status.page.md
+- name: Genomic-Task-Code
+ filename: Genomic-Task-Code.page.md
+- name: Genomic-Task-StatusReason
+ filename: Genomic-Task-StatusReason.page.md
- name: Genomic-Coverage
filename: Genomic-Coverage.page.md
- name: Genomic-Message-Events
diff --git a/NHSEnglandFHIRGenomicsImplementationGuide/backup/guides/FHIR-Genomics-Implementation-Guide/Home/Helpandsupport/Glossary.page.md b/NHSEnglandFHIRGenomicsImplementationGuide/backup/guides/FHIR-Genomics-Implementation-Guide/Home/Helpandsupport/Glossary.page.md
index 8939ee09f..65b13ed95 100644
--- a/NHSEnglandFHIRGenomicsImplementationGuide/backup/guides/FHIR-Genomics-Implementation-Guide/Home/Helpandsupport/Glossary.page.md
+++ b/NHSEnglandFHIRGenomicsImplementationGuide/backup/guides/FHIR-Genomics-Implementation-Guide/Home/Helpandsupport/Glossary.page.md
@@ -14,6 +14,8 @@ When describing genetic tests, different regions and professions sometimes use d
|CG WG|HL7 Clinical Genomics Working Group, responsible for the development of the Genomic Reporting Implementation Guide|
|CI/CITT|Clinical Indication (and Test ID/Target Gene), used within the Test Directory to uniquely identify test types|
|CIS2|NHS Care Identity Service 2, formerly known as NHS Identity, is a new, secure authentication service used by health and care professionals in England to access national clinical information systems.|
+|Consultand|Patient's/samples included as part of a test request in order to aid interpretation of the Proband's test results e.g. in the case of familial testing.|
+|CPGC|Cellular Pathology Genomic Centres, specialist labs set up to streamline the process of preparing samples for genetic testing.|
|DICOM|Digital Imaging and Communications in Medicine, the standard for the communication and management of medical imaging information and related data|
|DLP|Data Landing Portal, allows data to be transferred securely between organisations through a centrally managed system|
|DNA|Deoxyribonucleic acid, polymer composed of two polynucleotide chains that coil around each other to form a double helix|
@@ -54,6 +56,7 @@ When describing genetic tests, different regions and professions sometimes use d
|NGIS|National Genomic Information System, system used by Genomics Labs, commissioned by NHS England from Genomics England Ltd. Genomics England is a processor for the provision of the NGIS, acting on the instructions of NHS England for the Trusts that provide lab services.|
|NGTP|National Genomic Testing Process, process map developed by the NHS England Genomics Unit for defining the end-to-end genomic testing process|
|NHS|Tha National Health Service, the public body responsible for healthcare provision within the UK|
+|Non-WGS|Non-Whole Genome Sequencing, laboratory technique in which particular genes/gene panels are tested for variants.|
|NPEx|National Pathology Exchange, Labnostic exchange hub, connecting almost 200 diagnostic organisations worldwide.|
|NRL|National Record Locator, service which allows users to find and access patient information shared by other health and social care organisations, to support the direct care of a patient.|
|ODS|Organisation Data Service, manages and issues unique identification codes for NHS and affiliated organisations|
@@ -62,11 +65,13 @@ When describing genetic tests, different regions and professions sometimes use d
|PDF|Portable Document Format, the expected format for unstructured diagnostic reports in the first phases of the Genomic Order Management programme|
|PDS|Patient Demographics Service, the national electronic database of NHS patient demographic data, such as name, address, date of birth and NHS number, and associated API for querying and retrieving this information|
|PLCM|Patient Level Contract Monitoring, to enable the interchange, in a uniform format, of monthly patient level contract monitoring data between commissioners and providers of healthcare.|
+|Proband|The primary beneficiary of the genomic test, who the test order is for.|
|PRSB|Professional Records Standard Body, body responsible for setting records standards within the UK|
|RBAC|Role-Based Access Control, an approach to restricting system access to authorized users|
|READ|Coded thesaurus of clinical terms, superseded by SNOMED CT|
|RESTful|Representational State Transfer, a software architecture that imposes conditions on how an API should work.|
|RoD|Record of Discussion, form required to record consent discussion for use of WGS data/results in research|
+|Send-away|The process by which a test order is sent to another organization to perform part of the genomic testing, e.g. sample processing, interpretation etc. in order to fulfill the test order.|
|SET|IHE Specimen Event Tracking, defining Sample event tracking procedures|
|SNOMED CT|Systematized Nomenclature of Medicine - Clinical Terms, preferred ontology for coding clinical concepts in the UK, also referred to as SCT|
|SPINE|Spine supports the IT infrastructure for health and social care in England, joining together over 44,000 healthcare IT systems in 26,000 organisations|
diff --git a/NHSEnglandFHIRGenomicsImplementationGuide/backup/guides/FHIR-Genomics-Implementation-Guide/Home/Index.page.md b/NHSEnglandFHIRGenomicsImplementationGuide/backup/guides/FHIR-Genomics-Implementation-Guide/Home/Index.page.md
index 27b47e2a5..f53b19150 100644
--- a/NHSEnglandFHIRGenomicsImplementationGuide/backup/guides/FHIR-Genomics-Implementation-Guide/Home/Index.page.md
+++ b/NHSEnglandFHIRGenomicsImplementationGuide/backup/guides/FHIR-Genomics-Implementation-Guide/Home/Index.page.md
@@ -154,7 +154,7 @@ This section lists examples created to illustrate how to populate resources in c
+
+---
+
+Licence
+
+
+
+
+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.
+
+Developed and authored by NHS England Interoperability Team.
+
{{ guide-title }}
+
+
+
+
+
+
+ {{ dropdown-navigation }}
+
+
+
+
+
+
+
+
+
+
+
+
Notice
+
+ Important: This Implementation Guide is currently in Draft and SHOULD NOT be used for development or active implementation without express direction from the NHS England Genomics Unit.
+
+
+
+
+
+ {{ page-with-children }}
+
+ back to top
+
+
+
+
+
+
+ Powered by SIMPLIFIER.NET
+ IG © 2023+ NHS England
+ Version: {{ guide-version }}FHIR Version: {{ guide-fhir-version }} Packages are based on: FHIR UK Core STU3 0.0.6
+
+ Released: 12/12/2023Links: | | |
+
+
+
+
+
+
+
+
+
+
+
+
\ No newline at end of file
diff --git a/NHSEnglandFHIRGenomicsImplementationGuide/backup/guides/FHIR-Genomics-Implementation-Guide/styles/ukcore/settings.style b/NHSEnglandFHIRGenomicsImplementationGuide/backup/guides/FHIR-Genomics-Implementation-Guide/styles/ukcore/settings.style
new file mode 100644
index 000000000..b27b84cdb
--- /dev/null
+++ b/NHSEnglandFHIRGenomicsImplementationGuide/backup/guides/FHIR-Genomics-Implementation-Guide/styles/ukcore/settings.style
@@ -0,0 +1,7 @@
+{
+ "Name": "ukcore",
+ "Include": [
+ "styles/common",
+ "styles/ballotable"
+ ]
+}
\ No newline at end of file
diff --git a/NHSEnglandFHIRGenomicsImplementationGuide/backup/guides/FHIR-Genomics-Implementation-Guide/styles/ukcore/style.css b/NHSEnglandFHIRGenomicsImplementationGuide/backup/guides/FHIR-Genomics-Implementation-Guide/styles/ukcore/style.css
new file mode 100644
index 000000000..e72c9862d
--- /dev/null
+++ b/NHSEnglandFHIRGenomicsImplementationGuide/backup/guides/FHIR-Genomics-Implementation-Guide/styles/ukcore/style.css
@@ -0,0 +1,525 @@
+html, body {
+ padding: 0;
+ margin: 0;
+}
+ body {
+ position: relative;
+ height: 100%;
+}
+ body header {
+ background-color: #f5f5f5;
+}
+ body header .title {
+ font-size: 24px;
+ font-weight: 700;
+ padding-top: 23px;
+}
+ body header .title a {
+ color: #222;
+ text-decoration: none;
+}
+ body header h3 {
+ text-align: center;
+}
+ body header h5 {
+ text-align: center;
+}
+ body header .hl7-fhir-logo-lhs {
+ text-align: left;
+ margin-top: 7px;
+ margin-bottom: 5px;
+}
+ body header .hl7-logo {
+ text-align: right;
+ float: left;
+}
+ body header .guide-title {
+ font-size: 18px;
+ margin-top: 18px;
+}
+ body .content {
+ overflow: hidden;
+ min-height: 70%;
+ position: relative;
+ height: auto !important;
+ margin-bottom: -105px;
+ padding-bottom: 105px;
+}
+ body footer {
+ background-color: #dde1e4;
+ color: #222;
+ height: 105px;
+ position: relative;
+ padding-top: 40px;
+}
+ body .logos {
+ display: block;
+ margin-left: auto;
+ margin-right: auto;
+ width: 50%;
+}
+ .logocolumn {
+ float: left;
+ width: 33.33%;
+ padding: 5px;
+}
+ .logorow::after {
+ content: "";
+ clear: both;
+ display: table;
+}
+
+hr {
+ height: 1px;
+ background-color:#0072ce !important;
+}
+hr.thickline{
+ height: 2px;
+ background-color:#003087;
+}
+
+.tab {
+ overflow: hidden;
+ border: 1px solid #dde1e4;
+ background-color: #dde1e4;
+}
+/* Style the buttons inside the tab */
+.tab button {
+ background-color: inherit;
+ float: left;
+ border: none;
+ outline: none;
+ cursor: pointer;
+ padding: 14px 16px;
+ transition: 0.3s;
+ font-size: 14px;
+}
+/* Change background color of buttons on hover */
+ .tab button:hover {
+ background-color: #919ea8;
+}
+/* Create an active/current tablink class */
+ .tab button.active {
+ background-color: #005eb8;
+ color: #fff;
+}
+/* Style the tab content */
+ .tabcontent {
+ display: none;
+ padding: 6px 12px;
+ border: 1px solid #dde1e4;
+ border-top: none;
+}
+
+.tab button.feedback {
+ float: right;
+}
+
+/* css for simplifier diff/hybrid/snap buttons */
+.treetable-buttons {
+ padding-bottom: 5px !important
+}
+.tree-control button {
+ background-color: #dde1e4 !important;
+ float: left;
+ border: none;
+ outline: none;
+ cursor: pointer;
+ transition: 0.3s;
+ font-size: 14px;
+ color: #425563 !important;
+}
+/* Change background color of buttons on hover */
+.tree-control button:hover {
+ background-color: #919ea8 !important;
+}
+/* Create an active/current tablink class */
+.tree-control button.active {
+ background-color: #005eb8 !important;
+ color: #fff !important;
+}
+
+/* css for simplifier tabs */
+.cool-tabs .nav-tabs {
+ overflow: hidden;
+ border: 1px solid #dde1e4;
+ background-color: #dde1e4;
+}
+.cool-tabs .nav-tabs>li>a {
+ color: #425563;
+ background-color: inherit;
+ float: left;
+ border: none;
+ outline: none;
+ cursor: pointer;
+ padding: 14px 16px;
+ transition: 0.3s;
+ font-size: 14px;
+}
+.cool-tabs .nav-tabs>li>a:focus,.cool-tabs .nav-tabs>li>a:hover {
+ background-color: #919ea8;
+}
+.cool-tabs .nav-tabs>li.active>a,.cool-tabs .nav-tabs>li.active>a:focus,.cool-tabs .nav-tabs>li.active>a:hover {
+ color: #fff;
+ background-color: #005eb8;
+ border-radius: 0;
+ border: 1px solid transparent;
+ border-bottom-color: transparent;
+}
+.cool-tabs .tab-content {
+ padding: 6px 12px !important;
+ color: #425563 !important;
+ border: 1px solid #dde1e4;
+ border-top: none
+}
+.cool-tabs .tab-content .tab-pane {
+ padding-bottom: 0
+}
+
+/*core UKCore table style*/
+table.assets {
+ font-family: Arial, Helvetica, sans-serif !important;
+ border-collapse: collapse !important;
+ width: 100% !important;
+}
+table.assets td, table.assets th {
+ border: 1px solid #dde1e4 !important;
+ padding: 8px !important;
+}
+ table.assets tr:nth-child(odd){
+ background-color: #fff;
+}
+ table.assets tr:nth-child(even){
+ background-color: #dde1e4;
+}
+ table.assets tr:hover {
+ background-color: #919ea8 !important;
+}
+table.assets tr.balloted {
+ background-color:#dff0d8 !important;
+}
+table.assets tr td.balloted {
+ background-color:#dff0d8 !important;
+}
+ table.assets th {
+ padding-top: 12px !important;
+ padding-bottom: 12px !important;
+ text-align: left !important;
+ background-color: #005eb8 !important;
+ color: white !important;
+}
+ table.assets th a{
+ color: white !important;
+}
+
+
+ tr.wordBreak, td.wordBreak {
+ overflow-wrap: break-word !important;
+}
+
+ th.width5 { width: 5%; overflow-wrap: anywhere; }
+ th.width05 { width: 5%; overflow-wrap: anywhere; }
+ th.width10 { width: 10%; overflow-wrap: anywhere; }
+ th.width15 { width: 15%; overflow-wrap: anywhere; }
+ th.width20 { width: 20%; overflow-wrap: anywhere; }
+ th.width25 { width: 25%; overflow-wrap: anywhere; }
+ th.width30 { width: 30%; overflow-wrap: anywhere; }
+ th.width33 { width: 33%; overflow-wrap: anywhere; }
+ th.width35 { width: 35%; overflow-wrap: anywhere; }
+ th.width40 { width: 40%; overflow-wrap: anywhere; }
+ th.width45 { width: 45%; overflow-wrap: anywhere; }
+ th.width50 { width: 50%; overflow-wrap: anywhere; }
+ th.width55 { width: 55%; overflow-wrap: anywhere; }
+ th.width60 { width: 60%; overflow-wrap: anywhere; }
+ th.width65 { width: 65%; overflow-wrap: anywhere; }
+ th.width70 { width: 70%; overflow-wrap: anywhere; }
+ th.width75 { width: 75%; overflow-wrap: anywhere; }
+
+ td.width20 { width: 20%; overflow-wrap: anywhere; }
+ td.width25 { width: 25%; overflow-wrap: anywhere; }
+ td.width30 { width: 30%; overflow-wrap: anywhere; }
+ td.width35 { width: 35%; overflow-wrap: anywhere; }
+ td.width40 { width: 40%; overflow-wrap: anywhere; }
+
+ th.comparison-fhir { width: 22%; overflow-wrap: anywhere; }
+ th.comparison-note { width: 34%; overflow-wrap: anywhere; }
+ td.comparison-fhir { width: 22%; overflow-wrap: anywhere; }
+ td.comparison-note { width: 34%; overflow-wrap: anywhere; }
+
+ .underconstruction {
+ display: grid;
+ background-color: rgb(255, 208, 0);
+ border: 3px solid black;
+ padding-left: 50px;
+ padding-right: 50px;
+ font-size: 20px;
+ text-align: center;
+}
+
+ #valuesetlist {
+ font-family: Arial, Helvetica, sans-serif;
+ border-collapse: collapse;
+ width: 100%;
+}
+ #valuesetlist td, #valuesetlist th {
+ border: 1px solid #919ea8;
+ padding: 8px;
+}
+ #valuesetlist tr:nth-child{
+ background-color: #dde1e4;
+}
+ #valuesetlist tr:hover {
+ background-color: #919ea8;
+}
+
+ #valuesetlist tr.balloted {
+ background-color:#dff0d8 !important;
+}
+ #valuesetlist th {
+ padding-top: 12px;
+ padding-bottom: 12px;
+ text-align: left;
+ background-color: #005eb8;
+ color: white;
+}
+/* back to top button - renders when scrolling */
+ #back-to-top {
+ position: fixed;
+ bottom: 20px;
+ right: 30px;
+ z-index: 99;
+ display: none;
+}
+/* remove the padding on pages under the header */
+ #preview-content {
+ padding-top: 0px !important;
+}
+/* bootstrap overrides */
+ .btn-fhir {
+ background: #005eb8;
+ color: #fff;
+}
+
+/* Firely Simplifier base style overrides */
+ .navbar-nav>li>a:hover,
+ .navbar-nav>li>a:active,
+ .navbar-nav>li>a:focus {
+ background-color: #919ea8 !important;
+ color: #005eb8 !important;
+}
+ .container-fluid>.navbar-collapse,
+ .container-fluid>.navbar-header,
+ .container>.navbar-collapse,
+ .container>.navbar-header {
+ margin-right: -15px !important;
+ margin-left: -15px !important;
+}
+
+ div>pre {
+ border: 1px solid #919ea8 !important;
+ background-color: #f9f9f9 !important;
+ }
+
+ .submenu-list{
+ display:none;
+ width:max-content;
+}
+
+.submenu-parent:hover > ul {
+ display:block;
+}
+
+.submenu-list>li>a {
+ font-weight: 400;
+ color: #333;
+ display: block;
+ padding: 3px 20px;
+ line-height: 1.42857;
+ white-space: nowrap;
+}
+
+.forceWhite {
+ background-color: #fff;
+}
+.forceGreen {
+ background-color: #dff0d8;
+ padding-top: 5px;
+ padding-bottom: 5px;
+ margin-top: 5px;
+}
+
+p.balloted {
+ background-color: #dff0d8;
+ padding: 5px 10px;
+}
+
+li.balloted {
+ background-color: #dff0d8;
+}
+
+tr.a-to-z {
+ vertical-align: top;
+}
+
+tr.frm-group {
+ border-right: 1px solid black;
+ border-left: 1px solid black;
+ border-top: 1px solid black;
+ border-bottom: 0px none black;
+ font-weight: bold;
+}
+
+tr.frm-group-n {
+ border: 1px solid black;
+ font-weight: bold;
+}
+
+tr.frm-contents {
+ border-right: 1px solid black;
+ border-left: 1px solid black;
+ padding-bottom: 3px;
+ border-bottom: 1px solid black;
+ vertical-align: top;
+}
+
+td.frm-category {
+ border-left: 1px solid #eeeeee;
+ font-weight: bold;
+ text-align: center;
+}
+
+td.frm-group {
+ background: #f4f4f4;
+ font-weight: bold;
+}
+
+
+td.frm-set {
+ border-left: 1px solid #eeeeee;
+}
+
+.rotate {
+ text-align: center;
+ vertical-align: middle;
+ width: 1.5em;
+}
+.rotate div {
+ -moz-transform: rotate(-90.0deg); /* FF3.5+ */
+ -o-transform: rotate(-90.0deg); /* Opera 10.5 */
+ -webkit-transform: rotate(-90.0deg); /* Saf3.1+, Chrome */
+ filter: progid:DXImageTransform.Microsoft.BasicImage(rotation=0.083); /* IE6,IE7 */
+ -ms-filter: "progid:DXImageTransform.Microsoft.BasicImage(rotation=0.083)"; /* IE8 */
+ margin-left: -4em;
+ margin-right: -10em;
+ min-height:100px;
+}
+
+
+/*recreating base simplifier table.regular class to enable display override for showing/hiding */
+#preview-content table.codes {
+ border: 1px solid #e0e0e0;
+ border-right: 1px solid #e0e0e0;
+ width: 100%;
+ position: relative;
+ display: table;
+ font-family: "Open Sans","Helvetica Neue",Helvetica,Arial,sans-serif;
+ font-size: 14px;
+ line-height: 1.42857;
+ margin-bottom: 10px;
+}
+
+#preview-content table.codes tbody,#preview-content table.codes tfoot,#preview-content table.codes thead {
+ width: 100%;
+ border-color: #e0e0e0
+}
+
+#preview-content table.codes thead,#preview-content table.codes tr:not(:last-child) {
+ border-bottom: 1px solid #e0e0e0
+}
+
+#preview-content table.codes thead th {
+ background-color: #f9f9f9
+}
+
+#preview-content table.codes tbody td {
+ background-color: #fff
+}
+
+#preview-content table.codes td,#preview-content table.codes th{
+ padding: 5px;
+ color: #425563;
+ border-color: #e0e0e0
+}
+
+#preview-content table.codes td:not(:last-child),#preview-content table.codes th:not(:last-child) {
+ border-right: 1px solid #e0e0e0;
+}
+
+
+/* styling for nhse style sort buttons */
+.sort-icon {
+ display: inline-block;
+ position: relative;
+ margin-left: 5px;
+ width: 16px;
+ height: 16px;
+}
+
+.sort-icon,
+.sort-icon:after,
+.sort-icon:before {
+ box-sizing: border-box;
+}
+
+.sort-icon>img,
+.sort-icon>svg {
+ display: block;
+ position: relative;
+ width: 100%;
+ height: 100%;
+}
+
+.sort-icon>img {
+ position: absolute;
+ top: 50%;
+ left: 50%;
+ transform: translate(-50%,-50%);
+}
+
+.sort-icon>svg+img {
+ width: 50%;
+ height: 50%;
+}
+
+/* additional styling on headers for nhse style sort buttons */
+table.codes thead tr:first-child td.orderable button,
+table.codes thead tr:first-child th.orderable button {
+ display: flex;
+ width: 100%;
+ height: 100%;
+ margin-bottom: 3px;
+ padding: .5555555556rem;
+ border: 0;
+ color: inherit;
+ background: 0 0;
+ font: inherit;
+ text-align: inherit;
+ cursor: pointer;
+ align-items: center;
+}
+
+table.codes thead tr:first-child td.orderable button:hover .sort-icon,
+table.codes thead tr:first-child th.orderable button:hover .sort-icon {
+ margin-bottom: 0;
+ border-bottom: 3px solid #231f20;
+ color: #231f20;
+ background-color: #919ea8;
+}
+
+/* this part adds an icon after external links, using FontAwesome*/
+a.external:after {
+ font-family: 'Font Awesome 5 Free';
+ font-weight: 900;
+ content: "\f35d";
+ padding-left: 5px;
+}
\ No newline at end of file
diff --git a/NHSEnglandFHIRGenomicsImplementationGuide/backup/package.json b/NHSEnglandFHIRGenomicsImplementationGuide/backup/package.json
index 82c6526c0..6510e157f 100644
--- a/NHSEnglandFHIRGenomicsImplementationGuide/backup/package.json
+++ b/NHSEnglandFHIRGenomicsImplementationGuide/backup/package.json
@@ -1,8 +1,7 @@
{
- "name": "uk.nhsengland.genomics.r4",
- "version": "0.2.0-prerelease",
- "description": "FHIR Genomics Implementation Guide FHIR Assets",
- "author": "NHS England",
+ "name": "uk.nhsdigital.r4.genomics",
+ "description": "FHIR Genomics Implementation Guide",
+ "author": "nhsdigital",
"fhirVersions": [
"4.0.1"
],
diff --git a/NHSEnglandFHIRGenomicsImplementationGuide/backup/project/guides/FHIR-Genomics-Implementation-Guide/styles/ukcore/master.html b/NHSEnglandFHIRGenomicsImplementationGuide/backup/project/guides/FHIR-Genomics-Implementation-Guide/styles/ukcore/master.html
new file mode 100644
index 000000000..6eb8a1fbc
--- /dev/null
+++ b/NHSEnglandFHIRGenomicsImplementationGuide/backup/project/guides/FHIR-Genomics-Implementation-Guide/styles/ukcore/master.html
@@ -0,0 +1,775 @@
+
+
+
+
+
+ {{ guide-title }}
+
+
+
+
+
+
+ {{ dropdown-navigation }}
+
+
+
+
+
+
+
+
+
+
+
+ {{ page-with-children }}
+
+
+
+
+ back to top
+
+
+
+
+
+
+ Powered by SIMPLIFIER.NET
+ IG © 2023+ NHS England
+ Version: {{ guide-version }}FHIR Version: {{ guide-fhir-version }} Packages are based on: FHIR UK Core STU3 0.0.6
+
+ Released: 07/12/2023Links: | | |
+
+
+
+
+
+
+
+
+
+
+
+
\ No newline at end of file
diff --git a/NHSEnglandFHIRGenomicsImplementationGuide/backup/project/guides/FHIR-Genomics-Implementation-Guide/styles/ukcore/settings.style b/NHSEnglandFHIRGenomicsImplementationGuide/backup/project/guides/FHIR-Genomics-Implementation-Guide/styles/ukcore/settings.style
new file mode 100644
index 000000000..b27b84cdb
--- /dev/null
+++ b/NHSEnglandFHIRGenomicsImplementationGuide/backup/project/guides/FHIR-Genomics-Implementation-Guide/styles/ukcore/settings.style
@@ -0,0 +1,7 @@
+{
+ "Name": "ukcore",
+ "Include": [
+ "styles/common",
+ "styles/ballotable"
+ ]
+}
\ No newline at end of file
diff --git a/NHSEnglandFHIRGenomicsImplementationGuide/backup/project/guides/FHIR-Genomics-Implementation-Guide/styles/ukcore/style.css b/NHSEnglandFHIRGenomicsImplementationGuide/backup/project/guides/FHIR-Genomics-Implementation-Guide/styles/ukcore/style.css
new file mode 100644
index 000000000..e72c9862d
--- /dev/null
+++ b/NHSEnglandFHIRGenomicsImplementationGuide/backup/project/guides/FHIR-Genomics-Implementation-Guide/styles/ukcore/style.css
@@ -0,0 +1,525 @@
+html, body {
+ padding: 0;
+ margin: 0;
+}
+ body {
+ position: relative;
+ height: 100%;
+}
+ body header {
+ background-color: #f5f5f5;
+}
+ body header .title {
+ font-size: 24px;
+ font-weight: 700;
+ padding-top: 23px;
+}
+ body header .title a {
+ color: #222;
+ text-decoration: none;
+}
+ body header h3 {
+ text-align: center;
+}
+ body header h5 {
+ text-align: center;
+}
+ body header .hl7-fhir-logo-lhs {
+ text-align: left;
+ margin-top: 7px;
+ margin-bottom: 5px;
+}
+ body header .hl7-logo {
+ text-align: right;
+ float: left;
+}
+ body header .guide-title {
+ font-size: 18px;
+ margin-top: 18px;
+}
+ body .content {
+ overflow: hidden;
+ min-height: 70%;
+ position: relative;
+ height: auto !important;
+ margin-bottom: -105px;
+ padding-bottom: 105px;
+}
+ body footer {
+ background-color: #dde1e4;
+ color: #222;
+ height: 105px;
+ position: relative;
+ padding-top: 40px;
+}
+ body .logos {
+ display: block;
+ margin-left: auto;
+ margin-right: auto;
+ width: 50%;
+}
+ .logocolumn {
+ float: left;
+ width: 33.33%;
+ padding: 5px;
+}
+ .logorow::after {
+ content: "";
+ clear: both;
+ display: table;
+}
+
+hr {
+ height: 1px;
+ background-color:#0072ce !important;
+}
+hr.thickline{
+ height: 2px;
+ background-color:#003087;
+}
+
+.tab {
+ overflow: hidden;
+ border: 1px solid #dde1e4;
+ background-color: #dde1e4;
+}
+/* Style the buttons inside the tab */
+.tab button {
+ background-color: inherit;
+ float: left;
+ border: none;
+ outline: none;
+ cursor: pointer;
+ padding: 14px 16px;
+ transition: 0.3s;
+ font-size: 14px;
+}
+/* Change background color of buttons on hover */
+ .tab button:hover {
+ background-color: #919ea8;
+}
+/* Create an active/current tablink class */
+ .tab button.active {
+ background-color: #005eb8;
+ color: #fff;
+}
+/* Style the tab content */
+ .tabcontent {
+ display: none;
+ padding: 6px 12px;
+ border: 1px solid #dde1e4;
+ border-top: none;
+}
+
+.tab button.feedback {
+ float: right;
+}
+
+/* css for simplifier diff/hybrid/snap buttons */
+.treetable-buttons {
+ padding-bottom: 5px !important
+}
+.tree-control button {
+ background-color: #dde1e4 !important;
+ float: left;
+ border: none;
+ outline: none;
+ cursor: pointer;
+ transition: 0.3s;
+ font-size: 14px;
+ color: #425563 !important;
+}
+/* Change background color of buttons on hover */
+.tree-control button:hover {
+ background-color: #919ea8 !important;
+}
+/* Create an active/current tablink class */
+.tree-control button.active {
+ background-color: #005eb8 !important;
+ color: #fff !important;
+}
+
+/* css for simplifier tabs */
+.cool-tabs .nav-tabs {
+ overflow: hidden;
+ border: 1px solid #dde1e4;
+ background-color: #dde1e4;
+}
+.cool-tabs .nav-tabs>li>a {
+ color: #425563;
+ background-color: inherit;
+ float: left;
+ border: none;
+ outline: none;
+ cursor: pointer;
+ padding: 14px 16px;
+ transition: 0.3s;
+ font-size: 14px;
+}
+.cool-tabs .nav-tabs>li>a:focus,.cool-tabs .nav-tabs>li>a:hover {
+ background-color: #919ea8;
+}
+.cool-tabs .nav-tabs>li.active>a,.cool-tabs .nav-tabs>li.active>a:focus,.cool-tabs .nav-tabs>li.active>a:hover {
+ color: #fff;
+ background-color: #005eb8;
+ border-radius: 0;
+ border: 1px solid transparent;
+ border-bottom-color: transparent;
+}
+.cool-tabs .tab-content {
+ padding: 6px 12px !important;
+ color: #425563 !important;
+ border: 1px solid #dde1e4;
+ border-top: none
+}
+.cool-tabs .tab-content .tab-pane {
+ padding-bottom: 0
+}
+
+/*core UKCore table style*/
+table.assets {
+ font-family: Arial, Helvetica, sans-serif !important;
+ border-collapse: collapse !important;
+ width: 100% !important;
+}
+table.assets td, table.assets th {
+ border: 1px solid #dde1e4 !important;
+ padding: 8px !important;
+}
+ table.assets tr:nth-child(odd){
+ background-color: #fff;
+}
+ table.assets tr:nth-child(even){
+ background-color: #dde1e4;
+}
+ table.assets tr:hover {
+ background-color: #919ea8 !important;
+}
+table.assets tr.balloted {
+ background-color:#dff0d8 !important;
+}
+table.assets tr td.balloted {
+ background-color:#dff0d8 !important;
+}
+ table.assets th {
+ padding-top: 12px !important;
+ padding-bottom: 12px !important;
+ text-align: left !important;
+ background-color: #005eb8 !important;
+ color: white !important;
+}
+ table.assets th a{
+ color: white !important;
+}
+
+
+ tr.wordBreak, td.wordBreak {
+ overflow-wrap: break-word !important;
+}
+
+ th.width5 { width: 5%; overflow-wrap: anywhere; }
+ th.width05 { width: 5%; overflow-wrap: anywhere; }
+ th.width10 { width: 10%; overflow-wrap: anywhere; }
+ th.width15 { width: 15%; overflow-wrap: anywhere; }
+ th.width20 { width: 20%; overflow-wrap: anywhere; }
+ th.width25 { width: 25%; overflow-wrap: anywhere; }
+ th.width30 { width: 30%; overflow-wrap: anywhere; }
+ th.width33 { width: 33%; overflow-wrap: anywhere; }
+ th.width35 { width: 35%; overflow-wrap: anywhere; }
+ th.width40 { width: 40%; overflow-wrap: anywhere; }
+ th.width45 { width: 45%; overflow-wrap: anywhere; }
+ th.width50 { width: 50%; overflow-wrap: anywhere; }
+ th.width55 { width: 55%; overflow-wrap: anywhere; }
+ th.width60 { width: 60%; overflow-wrap: anywhere; }
+ th.width65 { width: 65%; overflow-wrap: anywhere; }
+ th.width70 { width: 70%; overflow-wrap: anywhere; }
+ th.width75 { width: 75%; overflow-wrap: anywhere; }
+
+ td.width20 { width: 20%; overflow-wrap: anywhere; }
+ td.width25 { width: 25%; overflow-wrap: anywhere; }
+ td.width30 { width: 30%; overflow-wrap: anywhere; }
+ td.width35 { width: 35%; overflow-wrap: anywhere; }
+ td.width40 { width: 40%; overflow-wrap: anywhere; }
+
+ th.comparison-fhir { width: 22%; overflow-wrap: anywhere; }
+ th.comparison-note { width: 34%; overflow-wrap: anywhere; }
+ td.comparison-fhir { width: 22%; overflow-wrap: anywhere; }
+ td.comparison-note { width: 34%; overflow-wrap: anywhere; }
+
+ .underconstruction {
+ display: grid;
+ background-color: rgb(255, 208, 0);
+ border: 3px solid black;
+ padding-left: 50px;
+ padding-right: 50px;
+ font-size: 20px;
+ text-align: center;
+}
+
+ #valuesetlist {
+ font-family: Arial, Helvetica, sans-serif;
+ border-collapse: collapse;
+ width: 100%;
+}
+ #valuesetlist td, #valuesetlist th {
+ border: 1px solid #919ea8;
+ padding: 8px;
+}
+ #valuesetlist tr:nth-child{
+ background-color: #dde1e4;
+}
+ #valuesetlist tr:hover {
+ background-color: #919ea8;
+}
+
+ #valuesetlist tr.balloted {
+ background-color:#dff0d8 !important;
+}
+ #valuesetlist th {
+ padding-top: 12px;
+ padding-bottom: 12px;
+ text-align: left;
+ background-color: #005eb8;
+ color: white;
+}
+/* back to top button - renders when scrolling */
+ #back-to-top {
+ position: fixed;
+ bottom: 20px;
+ right: 30px;
+ z-index: 99;
+ display: none;
+}
+/* remove the padding on pages under the header */
+ #preview-content {
+ padding-top: 0px !important;
+}
+/* bootstrap overrides */
+ .btn-fhir {
+ background: #005eb8;
+ color: #fff;
+}
+
+/* Firely Simplifier base style overrides */
+ .navbar-nav>li>a:hover,
+ .navbar-nav>li>a:active,
+ .navbar-nav>li>a:focus {
+ background-color: #919ea8 !important;
+ color: #005eb8 !important;
+}
+ .container-fluid>.navbar-collapse,
+ .container-fluid>.navbar-header,
+ .container>.navbar-collapse,
+ .container>.navbar-header {
+ margin-right: -15px !important;
+ margin-left: -15px !important;
+}
+
+ div>pre {
+ border: 1px solid #919ea8 !important;
+ background-color: #f9f9f9 !important;
+ }
+
+ .submenu-list{
+ display:none;
+ width:max-content;
+}
+
+.submenu-parent:hover > ul {
+ display:block;
+}
+
+.submenu-list>li>a {
+ font-weight: 400;
+ color: #333;
+ display: block;
+ padding: 3px 20px;
+ line-height: 1.42857;
+ white-space: nowrap;
+}
+
+.forceWhite {
+ background-color: #fff;
+}
+.forceGreen {
+ background-color: #dff0d8;
+ padding-top: 5px;
+ padding-bottom: 5px;
+ margin-top: 5px;
+}
+
+p.balloted {
+ background-color: #dff0d8;
+ padding: 5px 10px;
+}
+
+li.balloted {
+ background-color: #dff0d8;
+}
+
+tr.a-to-z {
+ vertical-align: top;
+}
+
+tr.frm-group {
+ border-right: 1px solid black;
+ border-left: 1px solid black;
+ border-top: 1px solid black;
+ border-bottom: 0px none black;
+ font-weight: bold;
+}
+
+tr.frm-group-n {
+ border: 1px solid black;
+ font-weight: bold;
+}
+
+tr.frm-contents {
+ border-right: 1px solid black;
+ border-left: 1px solid black;
+ padding-bottom: 3px;
+ border-bottom: 1px solid black;
+ vertical-align: top;
+}
+
+td.frm-category {
+ border-left: 1px solid #eeeeee;
+ font-weight: bold;
+ text-align: center;
+}
+
+td.frm-group {
+ background: #f4f4f4;
+ font-weight: bold;
+}
+
+
+td.frm-set {
+ border-left: 1px solid #eeeeee;
+}
+
+.rotate {
+ text-align: center;
+ vertical-align: middle;
+ width: 1.5em;
+}
+.rotate div {
+ -moz-transform: rotate(-90.0deg); /* FF3.5+ */
+ -o-transform: rotate(-90.0deg); /* Opera 10.5 */
+ -webkit-transform: rotate(-90.0deg); /* Saf3.1+, Chrome */
+ filter: progid:DXImageTransform.Microsoft.BasicImage(rotation=0.083); /* IE6,IE7 */
+ -ms-filter: "progid:DXImageTransform.Microsoft.BasicImage(rotation=0.083)"; /* IE8 */
+ margin-left: -4em;
+ margin-right: -10em;
+ min-height:100px;
+}
+
+
+/*recreating base simplifier table.regular class to enable display override for showing/hiding */
+#preview-content table.codes {
+ border: 1px solid #e0e0e0;
+ border-right: 1px solid #e0e0e0;
+ width: 100%;
+ position: relative;
+ display: table;
+ font-family: "Open Sans","Helvetica Neue",Helvetica,Arial,sans-serif;
+ font-size: 14px;
+ line-height: 1.42857;
+ margin-bottom: 10px;
+}
+
+#preview-content table.codes tbody,#preview-content table.codes tfoot,#preview-content table.codes thead {
+ width: 100%;
+ border-color: #e0e0e0
+}
+
+#preview-content table.codes thead,#preview-content table.codes tr:not(:last-child) {
+ border-bottom: 1px solid #e0e0e0
+}
+
+#preview-content table.codes thead th {
+ background-color: #f9f9f9
+}
+
+#preview-content table.codes tbody td {
+ background-color: #fff
+}
+
+#preview-content table.codes td,#preview-content table.codes th{
+ padding: 5px;
+ color: #425563;
+ border-color: #e0e0e0
+}
+
+#preview-content table.codes td:not(:last-child),#preview-content table.codes th:not(:last-child) {
+ border-right: 1px solid #e0e0e0;
+}
+
+
+/* styling for nhse style sort buttons */
+.sort-icon {
+ display: inline-block;
+ position: relative;
+ margin-left: 5px;
+ width: 16px;
+ height: 16px;
+}
+
+.sort-icon,
+.sort-icon:after,
+.sort-icon:before {
+ box-sizing: border-box;
+}
+
+.sort-icon>img,
+.sort-icon>svg {
+ display: block;
+ position: relative;
+ width: 100%;
+ height: 100%;
+}
+
+.sort-icon>img {
+ position: absolute;
+ top: 50%;
+ left: 50%;
+ transform: translate(-50%,-50%);
+}
+
+.sort-icon>svg+img {
+ width: 50%;
+ height: 50%;
+}
+
+/* additional styling on headers for nhse style sort buttons */
+table.codes thead tr:first-child td.orderable button,
+table.codes thead tr:first-child th.orderable button {
+ display: flex;
+ width: 100%;
+ height: 100%;
+ margin-bottom: 3px;
+ padding: .5555555556rem;
+ border: 0;
+ color: inherit;
+ background: 0 0;
+ font: inherit;
+ text-align: inherit;
+ cursor: pointer;
+ align-items: center;
+}
+
+table.codes thead tr:first-child td.orderable button:hover .sort-icon,
+table.codes thead tr:first-child th.orderable button:hover .sort-icon {
+ margin-bottom: 0;
+ border-bottom: 3px solid #231f20;
+ color: #231f20;
+ background-color: #919ea8;
+}
+
+/* this part adds an icon after external links, using FontAwesome*/
+a.external:after {
+ font-family: 'Font Awesome 5 Free';
+ font-weight: 900;
+ content: "\f35d";
+ padding-left: 5px;
+}
\ No newline at end of file
diff --git a/NHSEnglandFHIRGenomicsImplementationGuide/export.zip b/NHSEnglandFHIRGenomicsImplementationGuide/export.zip
index b30139385..37bf06da8 100644
Binary files a/NHSEnglandFHIRGenomicsImplementationGuide/export.zip and b/NHSEnglandFHIRGenomicsImplementationGuide/export.zip differ
+ 
+