diff --git a/Condition/Condition-AcuteMyeloidLeukaemia-Example.json b/Condition/Condition-AcuteMyeloidLeukaemia-Example.json new file mode 100644 index 0000000..8c90f87 --- /dev/null +++ b/Condition/Condition-AcuteMyeloidLeukaemia-Example.json @@ -0,0 +1,38 @@ +{ + "resourceType": "Condition", + "id": "Condition-AcuteMyeloidLeukaemia-Example", + "clinicalStatus": { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/condition-clinical", + "code": "active", + "display": "Active" + } + ] + }, + "verificationStatus": { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/condition-ver-status", + "code": "provisional", + "display": "Provisional" + } + ] + }, + "code": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "1162928000", + "display": "Acute myeloid leukemia (morphologic abnormality)" + } + ] + }, + "subject": { + "identifier": { + "system": "https://fhir.nhs.uk/Id/nhs-number", + "value": "9449307873" + } + }, + "recordedDate": "2023-09-05" +} \ No newline at end of file diff --git a/Observation/Observation-BlastPercentageWGSSample-Example.json b/Observation/Observation-BlastPercentageWGSSample-Example.json new file mode 100644 index 0000000..ecc9c32 --- /dev/null +++ b/Observation/Observation-BlastPercentageWGSSample-Example.json @@ -0,0 +1,40 @@ +{ + "resourceType": "Observation", + "id": "Observation-BlastPercentageWGSSample-Example", + "status": "final", + "code": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "1015521000000107", + "display": "Percentage blast cells (observable entity)" + } + ] + }, + "subject": { + "reference": "Patient/Patient-PatrickSammy-Example", + "identifier": { + "system": "https://fhir.nhs.uk/Id/nhs-number", + "value": "9449307873" + } + }, + "specimen": { + "identifier": { + "system": "urn:oid:2.16.840.1.113883.2.1.3.2.4.18.24", + "value": "RR81235", + "assigner": { + "identifier": { + "system": "https://fhir.nhs.uk/Id/ods-organization-code", + "value": "696B0" + } + } + } + }, + "valueQuantity": { + "value": 25, + "unit": "%", + "system": "http://unitsofmeasure.org", + "code": "%" + }, + "effectiveDateTime": "2023-08-05" +} \ No newline at end of file diff --git a/Observation/Observation-NucleatedCellCountWGSSample-Example.json b/Observation/Observation-NucleatedCellCountWGSSample-Example.json new file mode 100644 index 0000000..b2eaf2c --- /dev/null +++ b/Observation/Observation-NucleatedCellCountWGSSample-Example.json @@ -0,0 +1,40 @@ +{ + "resourceType": "Observation", + "id": "Observation-NucleatedCellCount-Example", + "status": "final", + "code": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "1022461000000100", + "display": "Nucleated red blood cell count" + } + ] + }, + "subject": { + "reference": "Patient/Patient-PatrickSammy-Example", + "identifier": { + "system": "https://fhir.nhs.uk/Id/nhs-number", + "value": "9449307873" + } + }, + "specimen": { + "identifier": { + "system": "urn:oid:2.16.840.1.113883.2.1.3.2.4.18.24", + "value": "RR81235", + "assigner": { + "identifier": { + "system": "https://fhir.nhs.uk/Id/ods-organization-code", + "value": "696B0" + } + } + } + }, + "valueQuantity": { + "value": 10, + "unit": "10^12/l", + "system": "http://unitsofmeasure.org", + "code": "10^12/L" + }, + "effectiveDateTime": "2023-09-05" +} \ No newline at end of file diff --git a/Observation/Observation-PatrickSammyNoBoneMarrowTransplant-Example.json b/Observation/Observation-PatrickSammyNoBoneMarrowTransplant-Example.json new file mode 100644 index 0000000..7449498 --- /dev/null +++ b/Observation/Observation-PatrickSammyNoBoneMarrowTransplant-Example.json @@ -0,0 +1,31 @@ +{ + "resourceType": "Observation", + "id": "Observation-PatrickSammyNoBoneMarrowTransplant-Example", + "status": "final", + "code": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "416128008", + "display": "No history of procedure (situation)" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "445715009", + "display": "Blood and marrow transplantation (qualifier value)" + } + ] + }, + "subject": { + "reference": "Patient/Patient-PatrickSammy-Example", + "identifier": { + "system": "https://fhir.nhs.uk/Id/nhs-number", + "value": "9449307873" + } + }, + "effectiveDateTime": "2023-09-05" +} \ No newline at end of file diff --git a/ServiceRequest/ServiceRequest-WGSTestOrderForm-CancerHaemOnc-Example.json b/ServiceRequest/ServiceRequest-WGSTestOrderForm-CancerHaemOnc-Example.json new file mode 100644 index 0000000..c257b7f --- /dev/null +++ b/ServiceRequest/ServiceRequest-WGSTestOrderForm-CancerHaemOnc-Example.json @@ -0,0 +1,106 @@ +{ + "resourceType": "ServiceRequest", + "id": "ServiceRequest-WGSTestOrderForm-CancerHaemOnc-Example", + "extension": [ + { + "url": "https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-Coverage", + "valueCodeableConcept": { + "coding": [ + { + "system": "https://fhir.hl7.org.uk/CodeSystem/UKCore-FundingCategory", + "code": "nhs-england", + "display": "NHS England" + } + ] + } + }, + { + "url": "https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-AdditionalContact", + "valueReference": { + "reference": "PractitionerRole/PractitionerRole-AnnaLaneKingstonPathology-Example" + } + } + ], + "status": "active", + "intent": "order", + "category": [ + { + "coding": [ + { + "system": "https://fhir.hl7.org.uk/CodeSystem/UKCore-GenomeSequencingCategory", + "code": "cancer-wgs", + "display": "Cancer - WGS" + } + ] + }, + { + "coding": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/reasonfortesting-genomics", + "code": "diagnostic", + "display": "Diagnostic" + } + ] + } + ], + "priority": "routine", + "code": { + "coding": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/England-GenomicTestDirectory", + "code": "M89.108", + "display": "Acute Leukaemia Other" + } + ] + }, + "subject": { + "reference": "Patient/Patient-DemeizaSeo-Example", + "identifier": { + "system": "https://fhir.nhs.uk/Id/nhs-number", + "value": "9449306559" + } + }, + "authoredOn": "2023-09-08", + "requester": { + "reference": "PractitionerRole/PractitionerRole-HazelSmithKingstonPathology-Example" + }, + "performer": [ + { + "identifier": { + "system": "https://fhir.nhs.uk/Id/ods-organization-code", + "value": "RJZ" + }, + "display": "KING'S COLLEGE HOSPITAL NHS FOUNDATION TRUST" + } + ], + "supportingInfo": [ + { + "reference": "Condition/Condition-AcuteMyeloidLeukaemia-Example" + }, + { + "reference": "Observation/Observation-BlastPercentage-Example" + }, + { + "reference": "Observation/Observation-NucleatedCellCount-Example" + }, + { + "reference": "Observation/Observation-PatrickSammyNoBoneMarrowTransplant-Example" + }, + { + "reference": "Consent/Consent-RoDToFollow-Example" + } + ], + "specimen": [ + { + "reference": "Specimen/Specimen-PatrickSammyBoneMarrowAspiration-Example" + } + ], + "note": [ + { + "text": "Relevant Family History" + }, + { + "text": "Other Additional Information" + } + ] +} \ No newline at end of file diff --git a/ServiceRequest/ServiceRequest-WGSTestOrderForm-GermlineLate-Example.json b/ServiceRequest/ServiceRequest-WGSTestOrderForm-GermlineLate-Example.json new file mode 100644 index 0000000..cb62a77 --- /dev/null +++ b/ServiceRequest/ServiceRequest-WGSTestOrderForm-GermlineLate-Example.json @@ -0,0 +1,94 @@ +{ + "resourceType": "ServiceRequest", + "id": "ServiceRequest-WGSTestOrderForm-GermlineLate-Example", + "basedOn": [ + { + "reference": "ServiceRequest/ServiceRequest-WGSTestOrderForm-CancerHaemOnc-Example" + } + ], + "extension": [ + { + "url": "https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-Coverage", + "valueCodeableConcept": { + "coding": [ + { + "system": "https://fhir.hl7.org.uk/CodeSystem/UKCore-FundingCategory", + "code": "nhs-england", + "display": "NHS England" + } + ] + } + }, + { + "url": "https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-AdditionalContact", + "valueReference": { + "reference": "PractitionerRole/PractitionerRole-AnnaLaneKingstonPathology-Example" + } + } + ], + "status": "active", + "intent": "order", + "category": [ + { + "coding": [ + { + "system": "https://fhir.hl7.org.uk/CodeSystem/UKCore-GenomeSequencingCategory", + "code": "cancer-wgs", + "display": "Cancer - WGS" + } + ] + }, + { + "coding": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/reasonfortesting-genomics", + "code": "diagnostic", + "display": "Diagnostic" + } + ] + } + ], + "priority": "routine", + "code": { + "coding": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/England-GenomicTestDirectory", + "code": "M89.109", + "display": "Acute Leukaemia Other" + } + ] + }, + "subject": { + "reference": "Patient/Patient-DemeizaSeo-Example", + "identifier": { + "system": "https://fhir.nhs.uk/Id/nhs-number", + "value": "9449306559" + } + }, + "authoredOn": "2023-09-08", + "requester": { + "reference": "PractitionerRole/PractitionerRole-HazelSmithKingstonPathology-Example" + }, + "performer": [ + { + "identifier": { + "system": "https://fhir.nhs.uk/Id/ods-organization-code", + "value": "RJZ" + }, + "display": "KING'S COLLEGE HOSPITAL NHS FOUNDATION TRUST" + } + ], + "specimen": [ + { + "reference": "Specimen/Specimen-PatrickSammyBloodEDTA-Example" + } + ], + "note": [ + { + "text": "Relevant Family History" + }, + { + "text": "Other Additional Information" + } + ] +} \ No newline at end of file diff --git a/Specimen/Specimen-BoneMarrowAspiration-Example.json b/Specimen/Specimen-BoneMarrowAspiration-Example.json index c598936..2788bd6 100644 --- a/Specimen/Specimen-BoneMarrowAspiration-Example.json +++ b/Specimen/Specimen-BoneMarrowAspiration-Example.json @@ -39,7 +39,7 @@ "receivedTime": "2023-08-29T11:00:00Z", "request": [ { - "reference": "ServiceRequest-NonWGSTestOrderForm-HaemOncology-Example" + "reference": "ServiceRequest/ServiceRequest-NonWGSTestOrderForm-HaemOncology-Example" } ] } \ No newline at end of file diff --git a/Specimen/Specimen-PatrickSammyBloodEDTA-Example.json b/Specimen/Specimen-PatrickSammyBloodEDTA-Example.json new file mode 100644 index 0000000..5749eeb --- /dev/null +++ b/Specimen/Specimen-PatrickSammyBloodEDTA-Example.json @@ -0,0 +1,54 @@ +{ + "resourceType": "Specimen", + "id": "Specimen-PatrickSammyBloodEDTA-Example", + "extension": [ + { + "url": "https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-SampleCategory", + "valueCodeableConcept": { + "coding": [ + { + "system": "https://fhir.hl7.org.uk/CodeSystem/UKCore-SampleCategory", + "code": "germline", + "display": "Germline" + } + ] + } + } + ], + "identifier": [ + { + "system": "https://fhir.add.nhs.uk/Id/specimenId", + "value": "RGT03135A" + } + ], + "status": "unavailable", + "type": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "445295009", + "display": "Blood specimen with EDTA" + } + ] + }, + "subject": { + "reference": "Patient/Patient-MeirLieberman-Example", + "identifier": { + "system": "https://fhir.nhs.uk/Id/nhs-number", + "value": "9449307873" + } + }, + "request": [ + { + "reference": "ServiceRequest/ServiceRequest-WGSTestOrderForm-CancerHaemOnc-Example" + } + ], + "collection": { + "collectedDateTime": "2023-09-11T09:00:00Z", + "quantity": { + "system": "http://unitsofmeasure.org", + "code": "mL", + "value": 2.5 + } + } +} \ No newline at end of file diff --git a/Specimen/Specimen-PatrickSammyBoneMarrowAspiration-Example.json b/Specimen/Specimen-PatrickSammyBoneMarrowAspiration-Example.json new file mode 100644 index 0000000..21060e2 --- /dev/null +++ b/Specimen/Specimen-PatrickSammyBoneMarrowAspiration-Example.json @@ -0,0 +1,70 @@ +{ + "resourceType": "Specimen", + "id": "Specimen-PatrickSammyBoneMarrowAspiration-Example", + "extension": [ + { + "url": "https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-SampleCategory", + "valueCodeableConcept": { + "coding": [ + { + "system": "https://fhir.hl7.org.uk/CodeSystem/UKCore-SampleCategory", + "code": "liquid-tumour", + "display": "Liquid Tumour" + } + ] + } + } + ], + "identifier": [ + { + "system": "urn:oid:2.16.840.1.113883.2.1.3.2.4.18.24", + "value": "RR81235", + "assigner": { + "identifier": { + "system": "https://fhir.nhs.uk/Id/ods-organization-code", + "value": "696B0" + } + } + } + ], + "accessionIdentifier": { + "system": "https://www.leedsth.nhs.uk/path", + "value": "RR8123745", + "assigner": { + "identifier": { + "system": "https://fhir.nhs.uk/Id/ods-organization-code", + "value": "RR8" + } + } + }, + "status": "available", + "type": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "396997002", + "display": "Specimen from bone marrow obtained by aspiration" + } + ] + }, + "subject": { + "reference": "Patient/Patient-PatrickSammy-Example" + }, + "receivedTime": "2023-09-11T11:00:00Z", + "condition": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/v2-0493", + "code": "FROZ", + "display": "Frozen" + } + ] + } + ], + "request": [ + { + "reference": "ServiceRequest/ServiceRequest-WGSTestOrderForm-CancerHaemOnc-Example" + } + ] +} \ No newline at end of file diff --git a/Specimen/Specimen-SolidTumor-Example.json b/Specimen/Specimen-SolidTumor-Example.json index 8e28a56..bea94e0 100644 --- a/Specimen/Specimen-SolidTumor-Example.json +++ b/Specimen/Specimen-SolidTumor-Example.json @@ -48,9 +48,9 @@ { "coding": [ { - "system": "https://fhir.hl7.org.uk/CodeSystem/UKCore-BiopsyState", - "code": "fresh-unfixed", - "display": "Fresh Unfixed" + "system": "https://fhir.hl7.org.uk/CodeSystem/UKCore-PrimarySampleState", + "code": "fresh", + "display": "Fresh" } ] } diff --git a/Specimen/Specimen-TissueResection-Example.json b/Specimen/Specimen-TissueResection-Example.json index 7332521..413d249 100644 --- a/Specimen/Specimen-TissueResection-Example.json +++ b/Specimen/Specimen-TissueResection-Example.json @@ -48,9 +48,9 @@ { "coding": [ { - "system": "https://fhir.hl7.org.uk/CodeSystem/UKCore-BiopsyState", - "code": "fresh-unfixed", - "display": "Fresh Unfixed" + "system": "https://fhir.hl7.org.uk/CodeSystem/UKCore-PrimarySampleState", + "code": "fresh", + "display": "Fresh" } ] } diff --git a/Task/Task-WGSCancerTestOrder-HaemOnc-Example.json b/Task/Task-WGSCancerTestOrder-HaemOnc-Example.json new file mode 100644 index 0000000..20ade6a --- /dev/null +++ b/Task/Task-WGSCancerTestOrder-HaemOnc-Example.json @@ -0,0 +1,30 @@ +{ + "resourceType": "Task", + "id": "Task-WGSCancerTestOrder-HaemOnc-Example", + "status": "requested", + "intent": "order", + "priority": "routine", + "code": { + "coding": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/task-code-genomics", + "code": "process-genomic-test-request", + "display": "Process Genomic Test Request" + } + ] + }, + "focus": { + "reference": "ServiceRequest/ServiceRequest-WGSTestOrderForm-CancerHaemOnc-Example" + }, + "for": { + "reference": "Patient/Patient-PatrickSammy-Example", + "identifier": { + "system": "https://fhir.nhs.uk/Id/nhs-number", + "value": "9449307873" + } + }, + "authoredOn": "2023-09-28", + "requester": { + "reference": "PractitionerRole/PractitionerRole-HazelSmithKingstonPathology-Example" + } +}