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IOPS-3719 Adding Community Cloud Assets #202
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0e98430
Create CommunityCloud-VCFDocumentReference-Example.json
omarisgreat 5a3ebfd
Create CommunityCloud-DNASpecimen-Example.json
omarisgreat b54e9c5
Create CommunityCloud-VariantCallerDevice-Example.json
omarisgreat 3dcc7f4
Create CommunityCloud-BioinformaticsPipelineDevice-Example.json
omarisgreat 75bcf30
Create CommunityCloud-SequencerDevice-Example.json
omarisgreat 29b7c2d
Create CommunityCloud-GenomicStudyAnalysis-Example.json
omarisgreat 7e18f8e
Create CommunityCloud-GenomicStudy-Example.json
omarisgreat 22c857d
Create CommunityCloud-Bundle-Example.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,320 @@ | ||
| { | ||
| "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" | ||
| } | ||
| }, | ||
| { | ||
| "extension" : [ | ||
| { | ||
| "url" : "device", | ||
| "valueReference" : { | ||
| "reference" : "urn:uuid:44ae1fac-d147-43fb-87ba-35f6bc056f51" | ||
|
Collaborator
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||
| } | ||
| }, | ||
| { | ||
| "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" | ||
|
Collaborator
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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" | ||
|
Collaborator
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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
15
Device/CommunityCloud-BioinformaticsPipelineDevice-Example.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,15 @@ | ||
| { | ||
| "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" | ||
| } | ||
| ] | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,23 @@ | ||
| { | ||
| "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" | ||
| } | ||
| ] | ||
| } | ||
| ] | ||
| } |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,15 @@ | ||
| { | ||
| "resourceType": "Device", | ||
| "id": "04a7b32d-2270-4e4e-a1bb-80f0eaa0c4cc", | ||
| "deviceName": [ | ||
| { | ||
| "type": "user-friendly-name", | ||
| "name": "Sentieon Haplotyper" | ||
| } | ||
| ], | ||
| "version": [ | ||
| { | ||
| "value": "202308.03" | ||
| } | ||
| ] | ||
| } |
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Expected logical reference; Specimen/b6c3ebd7-53e4-450b-b46f-0e9f83d995e6