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Specimen extensions and codesystems
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‎CodeSystem/CodeSystem-Genomics-sample-state.json‎

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{
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"resourceType": "CodeSystem",
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"url": "https://fhir.nhs.uk/CodeSystem/sample-state-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": "sample-state-genomics"
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}
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],
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"version": "0.1.0",
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"name": "SampleStateGenomics",
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"title": "Sample State Genomics",
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"status": "draft",
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"date": "2022-12-05",
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"publisher": "NHS Digital",
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"contact": [
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{
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"name": "NHS Digital",
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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": "The type of sample, for use in Specimen resources in genomics",
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"copyright": "Copyright © 2022 NHS Digital",
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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": "ST",
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"display": "Solid tumour sample"
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},
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{
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"code": "LT",
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"display": "Liquid tumour sample"
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},
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{
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"code": "N",
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"display": "Normal"
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},
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{
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"code": "G",
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"display": "Germline sample"
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}
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]
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}

‎StructureDefinition/Extension-Genomics-Morphology.StructureDefinition.json‎

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{
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"resourceType": "StructureDefinition",
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"id": "genomics-histology-morphology-behavior",
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"url": "https://fhir.nhs.uk/StructureDefinition/mcode-histology-morphology-behavior",
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"version": "2.0.0",
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"name": "HistologyMorphologyBehavior",
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"title": "Histology-Morphology-Behavior Extension",
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"status": "active",
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"date": "2022-01-18T03:26:29+00:00",
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"publisher": "HL7 International Clinical Interoperability Council",
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"contact": [
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{
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"name": "HL7 International Clinical Interoperability Council",
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"telecom": [
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{
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"system": "url",
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"value": "http://www.hl7.org/Special/committees/cic"
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},
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{
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"system": "email",
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"value": "ciclist@lists.HL7.org"
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}
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]
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}
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],
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"description": "An extension describing the morphologic and behavioral characteristics of the cancer.",
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"fhirVersion": "4.0.1",
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"mapping": [
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{
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"identity": "rim",
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"uri": "http://hl7.org/v3",
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"name": "RIM Mapping"
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}
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],
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"kind": "complex-type",
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"abstract": false,
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"context": [
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{
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"type": "element",
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"expression": "Specimen"
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}
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],
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"type": "Extension",
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"baseDefinition": "http://hl7.org/fhir/StructureDefinition/Extension",
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"derivation": "constraint",
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"differential": {
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"element": [
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{
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"id": "Extension",
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"path": "Extension",
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"short": "Histology-Morphology-Behavior Extension",
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"definition": "An extension describing the morphologic and behavioral characteristics of the cancer."
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},
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{
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"id": "Extension.extension",
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"path": "Extension.extension",
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"max": "0"
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},
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{
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"id": "Extension.url",
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"path": "Extension.url",
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"fixedUri": "https://fhir.nhs.uk/StructureDefinition/mcode-histology-morphology-behavior"
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},
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{
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"id": "Extension.value[x]",
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"path": "Extension.value[x]",
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"min": 1,
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"type": [
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{
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"code": "CodeableConcept"
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}
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],
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"binding": {
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"strength": "extensible",
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"valueSet": "https://fhir.nhs.uk/ValueSet/mcode-histology-morphology-behavior-vs"
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}
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}
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]
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}
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}

‎StructureDefinition/Extension-Genomics-SampleState.StructureDefinition.json‎

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{
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"resourceType": "StructureDefinition",
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"url": "https://fhir.nhs.uk/StructureDefinition/Extension-Genomics-SampleState",
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"version": "0.1.0",
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"name": "GenomicsSampleState",
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"status": "draft",
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"date": "2022-12-05",
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"fhirVersion": "4.0.1",
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"kind": "complex-type",
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"abstract": false,
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"context": [
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{
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"type": "element",
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"expression": "Specimen"
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}
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],
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"type": "Extension",
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"baseDefinition": "http://hl7.org/fhir/StructureDefinition/Extension",
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"derivation": "constraint",
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"differential": {
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"element": [
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{
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"id": "Extension",
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"path": "Extension",
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"short": "Sample/Biopsy State",
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"definition": "One of: Solid tumour sample, Liquid tumour sample, Normal or germline sample"
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},
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{
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"id": "Extension.url",
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"path": "Extension.url",
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"fixedUri": "https://fhir.nhs.uk/StructureDefinition/Extension-Genomics-SampleState"
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},
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{
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"id": "Extension.value[x]",
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"path": "Extension.value[x]",
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"type": [
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{
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"code": "Coding"
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}
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],
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"binding": {
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"strength": "extensible",
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"valueSet": "https://fhir.nhs.uk/ValueSet/genomics-sample-state"
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}
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}
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]
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}
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}

‎StructureDefinition/Extension-Genomics-Topology.StructureDefinition.json‎

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{
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"resourceType" : "StructureDefinition",
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"id" : "genomics-body-location-qualifier",
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"url" : "https://fhir.nhs.uk/StructureDefinition/mcode-body-location-qualifier",
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"version" : "2.0.0",
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"name" : "BodyLocationQualifier",
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"title" : "Body Location Qualifier Extension",
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"status" : "active",
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"date" : "2022-01-18T03:26:29+00:00",
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"publisher" : "HL7 International Clinical Interoperability Council",
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"contact" : [
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{
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"name" : "HL7 International Clinical Interoperability Council",
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"telecom" : [
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{
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"system" : "url",
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"value" : "http://www.hl7.org/Special/committees/cic"
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},
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{
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"system" : "email",
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"value" : "ciclist@lists.HL7.org"
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}
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]
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}
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],
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"description" : "Qualifier to refine an body location. These include qualifiers for relative location, directionality, number, and plane, and exclude qualifiers for laterality.",
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"fhirVersion" : "4.0.1",
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"mapping" : [
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{
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"identity" : "rim",
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"uri" : "http://hl7.org/v3",
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"name" : "RIM Mapping"
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}
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],
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"kind" : "complex-type",
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"abstract" : false,
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"context" : [
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{
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"type" : "element",
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"expression" : "Specimen"
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}
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],
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"type" : "Extension",
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"baseDefinition" : "http://hl7.org/fhir/StructureDefinition/Extension",
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"derivation" : "constraint",
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"differential" : {
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"element" : [
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{
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"id" : "Extension",
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"path" : "Extension",
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"short" : "Body Location Qualifier Extension",
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"definition" : "Qualifier to refine an body location. These include qualifiers for relative location, directionality, number, and plane, and exclude qualifiers for laterality."
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},
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{
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"id" : "Extension.extension",
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"path" : "Extension.extension",
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"max" : "0"
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},
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{
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"id" : "Extension.url",
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"path" : "Extension.url",
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"fixedUri" : "https://fhir.nhs.uk/StructureDefinition/mcode-body-location-qualifier"
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},
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{
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"id" : "Extension.value[x]",
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"path" : "Extension.value[x]",
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"min" : 1,
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"type" : [
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{
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"code" : "CodeableConcept"
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}
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],
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"binding" : {
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"strength" : "required",
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"valueSet" : "https://fhir.nhs.uk/ValueSet/mcode-body-location-qualifier-vs"
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}
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}
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]
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}
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}

‎StructureDefinition/NHSDigital-Specimen-Genomics.StructureDefinition.json‎

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}
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]
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},
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{
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"id": "Specimen.extension",
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"path": "Specimen.extension",
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"slicing": {
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"discriminator": [
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{
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"type": "value",
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"path": "url"
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}
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],
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"rules": "open"
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},
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"min": 0
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},
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{
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"id": "Specimen.extension:state",
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"path": "Specimen.extension",
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"sliceName": "state",
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"min": 0,
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"max": "1",
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"type": [
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{
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"code": "Extension",
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"profile": [
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"https://fhir.nhs.uk/StructureDefinition/Extension-Genomics-SampleState"
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]
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}
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],
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"isModifier": false
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},
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{
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"id": "Specimen.extension:topology",
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"path": "Specimen.extension",
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"sliceName": "topology",
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"min": 0,
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"max": "1",
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"type": [
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{
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"code": "Extension",
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"profile": [
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"https://fhir.nhs.uk/StructureDefinition/mcode-body-location-qualifier"
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]
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}
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],
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"isModifier": false
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},
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{
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"id": "Specimen.extension:morphology",
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"path": "Specimen.extension",
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"sliceName": "morphology",
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"min": 0,
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"max": "1",
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"type": [
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{
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"code": "Extension",
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"profile": [
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"https://fhir.nhs.uk/StructureDefinition/mcode-histology-morphology-behavior"
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]
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}
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],
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"isModifier": false
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},
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{
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"id": "Specimen.identifier.assigner",
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"path": "Specimen.identifier.assigner",
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"type": [
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{
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"code": "Reference",
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"targetProfile": [
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"https://fhir.nhs.uk/StructureDefinition/NHSDigital-Organization-Genomics"
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]
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}
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]
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},
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{
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"id": "Specimen.accessionIdentifier",
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"path": "Specimen.accessionIdentifier",

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