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Update to Task codes
Including associated updated businessStatuses, statusReasons and necessary updates to tasks
1 parent f915553 commit 38f1243

13 files changed

Lines changed: 296 additions & 89 deletions

‎CodeSystem/CodeSystem-Genomics-business-status.json‎

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"value": "business-status-genomics"
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}
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],
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"version": "0.1.0",
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"version": "0.2.0",
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"name": "BusinessStatusGenomics",
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"title": "Business Status Genomics",
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"status": "draft",
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"caseSensitive": true,
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"content": "complete",
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"concept": [
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{
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"code": "InvalidRequest",
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"display": "Invalid Request"
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},
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{
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"code": "UnsatisfiedCondition",
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"display": "Unsatisfied Condition"
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},
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{
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"code": "TimeframeExceeded",
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"display": "Timeframe Exceeded"
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},
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{
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"code": "AwaitingSpecimen",
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"display": "Awaiting Specimen"
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"code": "SpecimenReceived",
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"display": "Specimen Received"
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},
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{
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"code": "SpecimenQualityNotOk",
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"display": "Specimen Quality Not OK"
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},
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{
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"code": "SpecimenProcessingInProgress",
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"display": "Specimen Processing In Progress"
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},
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{
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"code": "SpecimenProcessed",
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"display": "Specimen Processed"
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},
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{
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"code": "RemoteProcessingRequired",
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"display": "Remote Processing Required"
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},
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{
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"code": "SpecimenProcessingUnsuccessful",
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"display": "Specimen Processing Unsuccessful"
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},
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{
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"code": "SequencingCompleted",
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"display": "Sequencing Completed"
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},
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{
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"code": "RepeatSequencing",
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"display": "Repeat Sequencing"
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},
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{
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"code": "AlignSequencing",
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"display": "Align Sequencing"
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},
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{
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"code": "GeneticDataProcessingInProgress",
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"display": "Genetic Data Processing In Progress"
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},
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{
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"code": "RemoteGeneticDataProcessingRequired",
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"display": "Remote Genetic Data Processing Required"
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"code": "VariantsIdentified",
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"display": "Variants Identified"
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},
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{
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"code": "InterpretationInProgress",
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"display": "Interpretation In Progress"
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},
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{
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"code": "RemoteInterpretationRequired",
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"display": "Remote Interpretation Required"
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},
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{
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"code": "InterpretationCompleted",
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"display": "Interpretation Completed"
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},
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{
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"code": "InterpretationUnsuccessful",
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"display": "Interpretation Unsuccessful"
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},
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{
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"code": "FurtherClinicalDetailsRequired",
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"display": "Further Clinical Details Required"
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{
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"code": "ReflexTestComplete",
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"display": "Reflex Test Complete"
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},
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{
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"code": "DraftingReport",
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"display": "Drafting Report"
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},
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{
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"code": "ReportCompleted",
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"display": "ReportCompleted"
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}
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]
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}

‎CodeSystem/CodeSystem-Genomics-task-code.json‎

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{
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"resourceType": "CodeSystem",
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"url": "https://fhir.nhs.uk/CodeSystem/task-code-genomics",
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"identifier": [
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{
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"system": "https://fhir.nhs.uk/identifier/CodeSystem",
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"value": "task-code-genomics"
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}
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],
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"version": "0.1.0",
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"name": "TaskCodeGenomics",
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"title": "Task Code Genomics",
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"status": "draft",
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"date": "2023-12-06T10:54:00+00:00",
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"publisher": "NHS England",
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"contact": [
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{
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"name": "NHS England",
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"telecom": [
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{
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"system": "email",
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"value": "interoperabilityteam@nhs.net",
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"use": "work"
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}
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]
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}
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],
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"description": "A set of codes use to identify the type of task for Genomic Order Management",
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"copyright": "Copyright © 2023 NHS England",
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"caseSensitive": true,
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"content": "complete",
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"concept": [
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{
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"code": "RequestGenomicTest",
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"display": "RequestGenomicTest",
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"designation": [
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{
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"use": {
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"system": "http://snomed.info/sct",
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"code": "900000000000013009",
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"display": "Synonym"
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}
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"value": "10.00"
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}
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]
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},
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{
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"code": "ProcessGenomicTestRequest",
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"display": "Process Genomic Test Request",
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"designation": [
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{
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"use": {
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"system": "http://snomed.info/sct",
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"code": "900000000000013009",
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"display": "Synonym"
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}
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"value": "50.00"
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}
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]
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},
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{
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"code": "RequestSampleAlignment",
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"display": "Request & Sample Alignment",
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"designation": [
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{
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"use": {
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"system": "http://snomed.info/sct",
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"code": "900000000000013009",
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"display": "Synonym"
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}
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"value": "100.00"
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}
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]
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},
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{
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"code": "SamplePreparation",
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"display": "Sample Preparation",
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"designation": [
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{
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"use": {
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"system": "http://snomed.info/sct",
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"code": "900000000000013009",
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"display": "Synonym"
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}
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"value": "150.00"
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}
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]
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},
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{
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"code": "SampleProcessing",
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"display": "SampleProcessing",
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"designation": [
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{
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"use": {
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"system": "http://snomed.info/sct",
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"code": "900000000000013009",
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"display": "Synonym"
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}
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"value": "200.00"
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}
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]
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},
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{
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"code": "GeneticGenomicDataProcessing",
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"display": "Genetic/Genomic Data Processing",
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"designation": [
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{
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"use": {
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"system": "http://snomed.info/sct",
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"code": "900000000000013009",
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"display": "Synonym"
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}
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"value": "250.00"
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}
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]
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},
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{
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"code": "Interpretation",
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"display": "Interpretation",
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"designation": [
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{
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"use": {
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"system": "http://snomed.info/sct",
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"code": "900000000000013009",
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"display": "Synonym"
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}
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"value": "300.00"
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}
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]
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},
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{
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"code": "ProduceInterimReport",
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"display": "Produce Interim Report",
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"designation": [
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{
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"use": {
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"system": "http://snomed.info/sct",
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"code": "900000000000013009",
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"display": "Synonym"
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}
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"value": "350.00"
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}
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]
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},
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{
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"code": "Genomic MDT",
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"display": "GenomicMDT",
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"designation": [
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{
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"use": {
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"system": "http://snomed.info/sct",
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"code": "900000000000013009",
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"display": "Synonym"
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}
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"value": "400.00"
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}
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]
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},
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{
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"code": "ProduceFinalReport",
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"display": "Produce Final Report",
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"designation": [
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{
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"use": {
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"system": "http://snomed.info/sct",
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"code": "900000000000013009",
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"display": "Synonym"
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}
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"value": "450.00"
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}
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]
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},
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{
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"code": "DistributeReport",
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"display": "Distribute Report",
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"designation": [
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{
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"use": {
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"system": "http://snomed.info/sct",
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"code": "900000000000013009",
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"display": "Synonym"
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}
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"value": "500.00"
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}
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]
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}
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]
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}

‎CodeSystem/CodeSystem-Genomics-task-statusReason.json‎

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{
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"resourceType": "CodeSystem",
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"url": "https://fhir.nhs.uk/CodeSystem/task-statusReason-genomics",
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"identifier": [
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{
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"system": "https://fhir.nhs.uk/identifier/CodeSystem",
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"value": "task-statusReason-genomics"
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}
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],
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"version": "0.1.0",
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"name": "TaskStatusReasonGenomics",
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"title": "Task StatusReason Genomics",
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"status": "draft",
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"date": "2023-12-06",
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"publisher": "NHS England",
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"contact": [
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{
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"name": "NHS England",
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"telecom": [
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{
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"system": "email",
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"value": "interoperabilityteam@nhs.net",
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"use": "work"
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}
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]
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}
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],
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"description": "Status reasons for Tasks in genomics",
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"copyright": "Copyright © 2023 NHS England",
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"caseSensitive": true,
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"content": "complete",
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"concept": [
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{
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"code": "InvalidRequest",
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"display": "Invalid Request"
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},
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{
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"code": "PipelineActivityFailure",
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"display": "Pipeline Activity Failure"
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},
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{
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"code": "Task Time Exceeded",
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"display": "Task Time Exceeded"
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},
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{
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"code": "UnableToInterpret",
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"display": "Unable To Interpret"
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},
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{
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"code": "SpecimenQualityNotOK",
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"display": "Specimen Quality Not OK"
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}
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]
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}

‎Task/Task-NonWGSRareDiseaseTestOrder-Example.json‎

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"coding": [
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{
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"system": "https://fhir.nhs.uk/CodeSystem/task-code-genomics",
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"code": "SampleManagement",
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"display": "Sample Management"
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"code": "ProcessGenomicTestRequest",
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"display": "Process Genomic Test Request"
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}
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]
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},

‎Task/Task-NonWGSRareDiseaseTestOrderAccepted-Example.json‎

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"coding": [
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{
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"system": "https://fhir.nhs.uk/CodeSystem/task-code-genomics",
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"code": "SampleManagement",
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"display": "Sample Management"
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"code": "RequestSampleAlignment",
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"display": "Request & Sample Alignment"
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}
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]
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},

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