From 0e98430fbcd487b0cacb183aff2a32e0c933496c Mon Sep 17 00:00:00 2001 From: Omar Khan <41755223+omarisgreat@users.noreply.github.com> Date: Tue, 10 Feb 2026 15:57:04 +0000 Subject: [PATCH 1/8] Create CommunityCloud-VCFDocumentReference-Example.json --- ...ityCloud-VCFDocumentReference-Example.json | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 DocumentReference/CommunityCloud-VCFDocumentReference-Example.json diff --git a/DocumentReference/CommunityCloud-VCFDocumentReference-Example.json b/DocumentReference/CommunityCloud-VCFDocumentReference-Example.json new file mode 100644 index 0000000..40f7491 --- /dev/null +++ b/DocumentReference/CommunityCloud-VCFDocumentReference-Example.json @@ -0,0 +1,34 @@ +{ + "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" + } + } + ] +} From 5a3ebfd1af7c0c99b185f37cd32fdfb97b25b921 Mon Sep 17 00:00:00 2001 From: Omar Khan <41755223+omarisgreat@users.noreply.github.com> Date: Tue, 10 Feb 2026 16:00:50 +0000 Subject: [PATCH 2/8] Create CommunityCloud-DNASpecimen-Example.json --- .../CommunityCloud-DNASpecimen-Example.json | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 Specimen/CommunityCloud-DNASpecimen-Example.json diff --git a/Specimen/CommunityCloud-DNASpecimen-Example.json b/Specimen/CommunityCloud-DNASpecimen-Example.json new file mode 100644 index 0000000..62db41c --- /dev/null +++ b/Specimen/CommunityCloud-DNASpecimen-Example.json @@ -0,0 +1,19 @@ +{ + "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" + } + ] + } +} From b54e9c5c7b84968f18df66bb921b025bd9c8a474 Mon Sep 17 00:00:00 2001 From: Omar Khan <41755223+omarisgreat@users.noreply.github.com> Date: Tue, 10 Feb 2026 16:02:53 +0000 Subject: [PATCH 3/8] Create CommunityCloud-VariantCallerDevice-Example.json --- ...ommunityCloud-VariantCallerDevice-Example.json | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 Device/CommunityCloud-VariantCallerDevice-Example.json diff --git a/Device/CommunityCloud-VariantCallerDevice-Example.json b/Device/CommunityCloud-VariantCallerDevice-Example.json new file mode 100644 index 0000000..ba5e52d --- /dev/null +++ b/Device/CommunityCloud-VariantCallerDevice-Example.json @@ -0,0 +1,15 @@ +{ + "resourceType": "Device", + "id": "04a7b32d-2270-4e4e-a1bb-80f0eaa0c4cc", + "deviceName": [ + { + "type": "user-friendly-name", + "name": "Sentieon Haplotyper" + } + ], + "version": [ + { + "value": "202308.03" + } + ] +} From 3dcc7f492852557af007726bb1537ecd2fc1c586 Mon Sep 17 00:00:00 2001 From: Omar Khan <41755223+omarisgreat@users.noreply.github.com> Date: Tue, 10 Feb 2026 16:03:42 +0000 Subject: [PATCH 4/8] Create CommunityCloud-BioinformaticsPipelineDevice-Example.json --- ...loud-BioinformaticsPipelineDevice-Example.json | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 Device/CommunityCloud-BioinformaticsPipelineDevice-Example.json diff --git a/Device/CommunityCloud-BioinformaticsPipelineDevice-Example.json b/Device/CommunityCloud-BioinformaticsPipelineDevice-Example.json new file mode 100644 index 0000000..7c05a3b --- /dev/null +++ b/Device/CommunityCloud-BioinformaticsPipelineDevice-Example.json @@ -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" + } + ] +} From 75bcf302d555ef3d9e1ef647c173548b9bd4477c Mon Sep 17 00:00:00 2001 From: Omar Khan <41755223+omarisgreat@users.noreply.github.com> Date: Tue, 10 Feb 2026 16:04:14 +0000 Subject: [PATCH 5/8] Create CommunityCloud-SequencerDevice-Example.json --- ...ommunityCloud-SequencerDevice-Example.json | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 Device/CommunityCloud-SequencerDevice-Example.json diff --git a/Device/CommunityCloud-SequencerDevice-Example.json b/Device/CommunityCloud-SequencerDevice-Example.json new file mode 100644 index 0000000..12a90be --- /dev/null +++ b/Device/CommunityCloud-SequencerDevice-Example.json @@ -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" + } + ] + } + ] +} From 29b7c2db934a5b37db10c8427e9d93f9d4ebe417 Mon Sep 17 00:00:00 2001 From: Omar Khan <41755223+omarisgreat@users.noreply.github.com> Date: Tue, 10 Feb 2026 16:04:47 +0000 Subject: [PATCH 6/8] Create CommunityCloud-GenomicStudyAnalysis-Example.json --- ...ityCloud-GenomicStudyAnalysis-Example.json | 107 ++++++++++++++++++ 1 file changed, 107 insertions(+) create mode 100644 Procedure/CommunityCloud-GenomicStudyAnalysis-Example.json diff --git a/Procedure/CommunityCloud-GenomicStudyAnalysis-Example.json b/Procedure/CommunityCloud-GenomicStudyAnalysis-Example.json new file mode 100644 index 0000000..e9466b9 --- /dev/null +++ b/Procedure/CommunityCloud-GenomicStudyAnalysis-Example.json @@ -0,0 +1,107 @@ +{ + "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" : "Specimen/b6c3ebd7-53e4-450b-b46f-0e9f83d995e6" + } + }, + { + "extension" : [ + { + "url" : "device", + "valueReference" : { + "reference" : "Device/44ae1fac-d147-43fb-87ba-35f6bc056f51" + } + }, + { + "url" : "function", + "valueCodeableConcept" : { + "text" : "Sequencing platform" + } + } + ], + "url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-device" + }, + { + "extension" : [ + { + "url" : "device", + "valueReference" : { + "reference" : "Device/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" : "Device/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" : "DocumentReference/1e6aef26-d201-43d1-b54c-087cd4ee5c24" + } + } + ], + "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" +} From 7e18f8eabfd6cd09f5b2448f1e9d88e13b0dd9f9 Mon Sep 17 00:00:00 2001 From: Omar Khan <41755223+omarisgreat@users.noreply.github.com> Date: Tue, 10 Feb 2026 16:05:12 +0000 Subject: [PATCH 7/8] Create CommunityCloud-GenomicStudy-Example.json --- .../CommunityCloud-GenomicStudy-Example.json | 52 +++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 Procedure/CommunityCloud-GenomicStudy-Example.json diff --git a/Procedure/CommunityCloud-GenomicStudy-Example.json b/Procedure/CommunityCloud-GenomicStudy-Example.json new file mode 100644 index 0000000..3fb3298 --- /dev/null +++ b/Procedure/CommunityCloud-GenomicStudy-Example.json @@ -0,0 +1,52 @@ +{ + "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" : "Procedure/9bc12bd5-8e06-4f10-949e-512bb623552e" + } + } + ], + "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" + } + ] +} From 22c857df1377ce28300b0f17f8aabc53ff5b1785 Mon Sep 17 00:00:00 2001 From: Omar Khan <41755223+omarisgreat@users.noreply.github.com> Date: Tue, 10 Feb 2026 16:05:46 +0000 Subject: [PATCH 8/8] Create CommunityCloud-Bundle-Example.json --- Bundle/CommunityCloud-Bundle-Example.json | 320 ++++++++++++++++++++++ 1 file changed, 320 insertions(+) create mode 100644 Bundle/CommunityCloud-Bundle-Example.json diff --git a/Bundle/CommunityCloud-Bundle-Example.json 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