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320 changes: 320 additions & 0 deletions Bundle/CommunityCloud-Bundle-Example.json
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{
"resourceType": "Bundle",
"type": "transaction",
"entry": [
{
"fullUrl": "urn:uuid:1e6aef26-d201-43d1-b54c-087cd4ee5c24",
"resource": {
"resourceType": "DocumentReference",
"id": "1e6aef26-d201-43d1-b54c-087cd4ee5c24",
"meta" : {
"profile" : [
"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-data-file"
]
},
"status": "current",
"subject": {
"identifier": {
"system": "urn:oid:2.16.840.1.113883.2.1.3.2.4.18.24",
"value": "SomePatientIdentifier"
}
},
"author": [
{
"identifier": {
"system": "https://fhir.nhs.uk/Id/ods-organization-code",
"value": "699M0"
},
"display": "NHS EAST GENOMIC LABORATORY HUB"
}
],
"content": [
{
"attachment": {
"contentType": "application/gzip",
"url": "https://002-cen.s3.eu-west-2.amazonaws.com/grch38/haplotyper_normalised_v0.3/140103896-25301R0078-25NGCEN64-9527-F-99347387_markdup_recalibrated_Haplotyper.vcf.gz",
"title": "140103896-25301R0078-25NGCEN64-9527-F-99347387_markdup_recalibrated_Haplotyper.vcf.gz"
}
}
]
},
"request": {
"method": "POST",
"url": "DocumentReference"
}
},
{
"fullUrl": "urn:uuid:b6c3ebd7-53e4-450b-b46f-0e9f83d995e6",
"resource": {
"resourceType": "Specimen",
"id": "b6c3ebd7-53e4-450b-b46f-0e9f83d995e6",
"identifier": [
{
"system": "urn:oid:2.16.840.1.113883.2.1.3.2.4.18.19",
"value": "140103896-25301R0078"
}
],
"type": {
"coding": [
{
"system": "http://snomed.info/sct",
"code": "24851008",
"display": "Deoxyribonucleic acid"
}
]
}
},
"request": {
"method": "POST",
"url": "Specimen"
}
},
{
"fullUrl": "urn:uuid:04a7b32d-2270-4e4e-a1bb-80f0eaa0c4cc",
"resource": {
"resourceType": "Device",
"id": "04a7b32d-2270-4e4e-a1bb-80f0eaa0c4cc",
"deviceName": [
{
"type": "user-friendly-name",
"name": "Sentieon Haplotyper"
}
],
"version": [
{
"value": "202308.03"
}
]
},
"request": {
"method": "POST",
"url": "Device"
}
},
{
"fullUrl": "urn:uuid:1e73bfaf-b851-463f-98df-c2b6582a948e",
"resource": {
"resourceType": "Device",
"id": "1e73bfaf-b851-463f-98df-c2b6582a948e",
"deviceName": [
{
"type": "user-friendly-name",
"name": "Dias"
}
],
"version": [
{
"value": "eggd_conductor_dias_CEN_config_v2.5.2"
}
]
},
"request": {
"method": "POST",
"url": "Device"
}
},
{
"fullUrl": "urn:uuid:44ae1fac-d147-43fb-87ba-35f6bc056f51",
"resource": {
"resourceType": "Device",
"id": "44ae1fac-d147-43fb-87ba-35f6bc056f51",
"manufacturer": "Illumina",
"deviceName": [
{
"type": "user-friendly-name",
"name": "Novaseq 6000"
}
],
"property": [
{
"type": {
"text": "Sequencing assay name"
},
"valueCode": [
{
"text": "CEN"
}
]
}
]
},
"request": {
"method": "POST",
"url": "Device"
}
},
{
"fullUrl": "urn:uuid:9bc12bd5-8e06-4f10-949e-512bb623552e",
"resource": {
"resourceType" : "Procedure",
"id" : "9bc12bd5-8e06-4f10-949e-512bb623552e",
"meta" : {
"profile" : [
"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis"
]
},
"extension" : [
{
"url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-specimen",
"valueReference" : {
"reference" : "urn:uuid:b6c3ebd7-53e4-450b-b46f-0e9f83d995e6"
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Expected logical reference; Specimen/b6c3ebd7-53e4-450b-b46f-0e9f83d995e6

}
},
{
"extension" : [
{
"url" : "device",
"valueReference" : {
"reference" : "urn:uuid:44ae1fac-d147-43fb-87ba-35f6bc056f51"
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As above

}
},
{
"url" : "function",
"valueCodeableConcept" : {
"text" : "Sequencing platform"
}
}
],
"url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-device"
},
{
"extension" : [
{
"url" : "device",
"valueReference" : {
"reference" : "urn:uuid:1e73bfaf-b851-463f-98df-c2b6582a948e"
}
},
{
"url" : "function",
"valueCodeableConcept" : {
"text" : "Bioinformatics Pipeline"
}
}
],
"url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-device"
},
{
"extension" : [
{
"url" : "device",
"valueReference" : {
"reference" : "urn:uuid:04a7b32d-2270-4e4e-a1bb-80f0eaa0c4cc"
}
},
{
"url" : "function",
"valueCodeableConcept" : {
"text" : "Bioinformatics Variant Caller"
}
}
],
"url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-device"
},
{
"extension" : [
{
"url" : "type",
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs",
"code" : "vcf",
"display" : "VCF"
}
]
}
},
{
"url" : "file",
"valueReference" : {
"reference" : "urn:uuid:1e6aef26-d201-43d1-b54c-087cd4ee5c24"
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?

}
}
],
"url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-output"
}
],
"status" : "completed",
"category" : {
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/observation-category",
"code" : "laboratory"
}
]
},
"subject" : {
"identifier" : {
"system": "urn:oid:2.16.840.1.113883.2.1.3.2.4.18.24",
"value": "SomePatientIdentifier"
}
},
"performedDateTime" : "2025-11-25T17:49:00Z"
},
"request": {
"method": "POST",
"url": "Procedure"
}
},
{
"fullUrl": "urn:uuid:fc708a88-9a59-4efd-9ff7-c028cf2b9491",
"resource": {
"resourceType" : "Procedure",
"id" : "fc708a88-9a59-4efd-9ff7-c028cf2b9491",
"meta" : {
"profile" : [
"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study"
]
},
"extension" : [
{
"url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-ext",
"valueReference" : {
"reference" : "urn:uuid:9bc12bd5-8e06-4f10-949e-512bb623552e"
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?

}
}
],
"status" : "completed",
"category" : {
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/observation-category",
"code" : "laboratory"
}
]
},
"code" : {
"text": "Small"
},
"subject" : {
"identifier" : {
"system": "urn:oid:2.16.840.1.113883.2.1.3.2.4.18.24",
"value": "SomePatientIdentifier"
}
},
"performedDateTime" : "2025-11-25T17:49:00Z",
"reasonCode" : [
{
"coding" : [
{
"system" : "https://fhir.nhs.uk/CodeSystem/England-GenomicTestDirectory",
"code" : "R134",
"display" : "Familial Hypercholesterolaemia"
}
]
}
],
"note" : [
{
"text" : "Rare Disease"
}
]
},
"request": {
"method": "POST",
"url": "Procedure"
}
}
]
}
15 changes: 15 additions & 0 deletions Device/CommunityCloud-BioinformaticsPipelineDevice-Example.json
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{
"resourceType": "Device",
"id": "1e73bfaf-b851-463f-98df-c2b6582a948e",
"deviceName": [
{
"type": "user-friendly-name",
"name": "Dias"
}
],
"version": [
{
"value": "eggd_conductor_dias_CEN_config_v2.5.2"
}
]
}
23 changes: 23 additions & 0 deletions Device/CommunityCloud-SequencerDevice-Example.json
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{
"resourceType": "Device",
"id": "44ae1fac-d147-43fb-87ba-35f6bc056f51",
"manufacturer": "Illumina",
"deviceName": [
{
"type": "user-friendly-name",
"name": "Novaseq 6000"
}
],
"property": [
{
"type": {
"text": "Sequencing assay name"
},
"valueCode": [
{
"text": "CEN"
}
]
}
]
}
15 changes: 15 additions & 0 deletions Device/CommunityCloud-VariantCallerDevice-Example.json
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{
"resourceType": "Device",
"id": "04a7b32d-2270-4e4e-a1bb-80f0eaa0c4cc",
"deviceName": [
{
"type": "user-friendly-name",
"name": "Sentieon Haplotyper"
}
],
"version": [
{
"value": "202308.03"
}
]
}
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