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liberaliscomputing/00-Specimen-parental.json

Last active August 15, 2022 19:09
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INCLUDE/KF GenomicWorkflow Proposal 1A
Raw
00-Specimen-parental.json
{
"resourceType": "Specimen",
"id": "267782",
"meta": {
"versionId": "1",
"lastUpdated": "2022-03-11T19:23:28.018+00:00",
"source": "#3JFyWT9UTXBaF1xT",
"profile": [
"http://hl7.org/fhir/StructureDefinition/Specimen"
],
"tag": [
{
"code": "DS360-CHD"
}
]
},
"identifier": [
{
"use": "official",
"value": "BS_RVNCBGV8_Peripheral Whole Blood"
},
{
"system": "https://kf-api-dataservice.kidsfirstdrc.org/biospecimens/",
"value": "BS_RVNCBGV8"
},
{
"value": "SSH3962900"
}
],
"status": "unavailable",
"type": {
"coding": [
{
"system": "http://purl.obolibrary.org/obo/ncit.owl",
"code": "C17610",
"display": "Blood Sample"
}
],
"text": "Peripheral Whole Blood"
},
"subject": {
"reference": "Patient/262192"
}
}
Raw
01-Specimen-children.json
{
"resourceType": "Specimen",
"id": "268973",
"meta": {
"versionId": "1",
"lastUpdated": "2022-03-11T19:26:41.035+00:00",
"source": "#szdqQdlLmM9VVvYF",
"profile": [
"http://hl7.org/fhir/StructureDefinition/Specimen"
],
"tag": [
{
"code": "DS360-CHD"
}
]
},
"identifier": [
{
"use": "official",
"value": "BS_RVNCBGV8_DNA"
},
{
"system": "https://kf-api-dataservice.kidsfirstdrc.org/biospecimens/",
"value": "BS_RVNCBGV8"
},
{
"value": "SSH3962900"
}
],
"status": "unavailable",
"type": {
"coding": [
{
"system": "http://purl.obolibrary.org/obo/obi.owl",
"code": "OBI:0001051",
"display": "DNA extract"
}
],
"text": "DNA"
},
"subject": {
"reference": "Patient/262192"
},
"parent": [
{
"reference": "Specimen/267782"
}
]
}
Raw
02-DocumentReference-sequencing.json
{
"resourceType": "DocumentReference",
"id": "275231",
"meta": {
"versionId": "3",
"lastUpdated": "2022-03-15T20:13:48.611+00:00",
"source": "#0BPvNho16f7HJCEk",
"profile": [
"https://ncpi-fhir.github.io/ncpi-fhir-ig/StructureDefinition/ncpi-drs-document-reference"
],
"tag": [
{
"code": "DS360-CHD"
}
]
},
"identifier": [
{
"use": "official",
"system": "https://kf-api-dataservice.kidsfirstdrc.org/genomic-files/",
"value": "GF_K4GYZMM2"
}
],
"status": "current",
"docStatus": "final",
"type": {
"coding": [
{
"system": "https://includedcc.org/fhir/code-systems/data_types",
"code": "Aligned-Reads",
"display": "Aligned Reads"
}
],
"text": "Aligned Reads"
},
"category": [
{
"coding": [
{
"system": "https://includedcc.org/fhir/code-systems/experimental_strategies",
"code": "WGS",
"display": "Whole Genome Sequencing"
}
],
"text": "WGS"
},
{
"coding": [
{
"system": "https://includedcc.org/fhir/code-systems/data_categories",
"code": "Genomic",
"display": "Genomic"
}
],
"text": "WGS"
}
],
"subject": {
"reference": "Patient/262192"
},
"securityLabel": [
{
"coding": [
{
"system": "https://includedcc.org/fhir/code-systems/data_access_types",
"code": "controlled",
"display": "Controlled"
}
],
"text": "true"
},
{
"coding": [
{
"code": "c1"
}
],
"text": "phs002330.c1"
},
{
"coding": [
{
"code": "c999"
}
],
"text": "phs002330.c999"
},
{
"text": "SD_Z6MWD3H0"
}
],
"content": [
{
"attachment": {
"extension": [
{
"url": "https://nih-ncpi.github.io/ncpi-fhir-ig/StructureDefinition/file-size",
"valueDecimal": 18683181069
},
{
"url": "https://nih-ncpi.github.io/ncpi-fhir-ig/StructureDefinition/hashes",
"valueCodeableConcept": {
"coding": [
{
"display": "md5"
}
],
"text": "c4882ba91935a14a3e2bb0c28eb4724a"
}
},
{
"url": "https://nih-ncpi.github.io/ncpi-fhir-ig/StructureDefinition/hashes",
"valueCodeableConcept": {
"coding": [
{
"display": "sha256"
}
],
"text": "0d1c7d19ce4715f2c2c1caf15afc6f3d3b9e217210faf1f50f1ce99e0ae7a9a9"
}
}
],
"url": "drs://data.kidsfirstdrc.org/e993cef6-31d8-4a05-8a9f-83b5288b8541",
"title": "SSH3962900.cram"
},
"format": {
"display": "cram"
}
}
],
"context": {
"related": [
{
"reference": "Specimen/268973"
}
]
}
}
Raw
03-DocumentReference-downstream.json
{
"resourceType": "DocumentReference",
"id": "275225",
"meta": {
"versionId": "3",
"lastUpdated": "2022-03-15T20:13:47.862+00:00",
"source": "#OA8N7hbZ569SiQgS",
"profile": [
"https://ncpi-fhir.github.io/ncpi-fhir-ig/StructureDefinition/ncpi-drs-document-reference"
],
"tag": [
{
"code": "DS360-CHD"
}
]
},
"identifier": [
{
"use": "official",
"system": "https://kf-api-dataservice.kidsfirstdrc.org/genomic-files/",
"value": "GF_0TRGJNAS"
}
],
"status": "current",
"docStatus": "final",
"type": {
"coding": [
{
"system": "https://includedcc.org/fhir/code-systems/data_types",
"code": "gVCF",
"display": "gVCF"
}
],
"text": "gVCF"
},
"category": [
{
"coding": [
{
"system": "https://includedcc.org/fhir/code-systems/experimental_strategies",
"code": "WGS",
"display": "Whole Genome Sequencing"
}
],
"text": "WGS"
},
{
"coding": [
{
"system": "https://includedcc.org/fhir/code-systems/data_categories",
"code": "Genomic",
"display": "Genomic"
}
],
"text": "WGS"
}
],
"subject": {
"reference": "Patient/262192"
},
"securityLabel": [
{
"coding": [
{
"system": "https://includedcc.org/fhir/code-systems/data_access_types",
"code": "controlled",
"display": "Controlled"
}
],
"text": "true"
},
{
"coding": [
{
"code": "c1"
}
],
"text": "phs002330.c1"
},
{
"coding": [
{
"code": "c999"
}
],
"text": "phs002330.c999"
},
{
"text": "SD_Z6MWD3H0"
}
],
"content": [
{
"attachment": {
"extension": [
{
"url": "https://nih-ncpi.github.io/ncpi-fhir-ig/StructureDefinition/file-size",
"valueDecimal": 3023663038
},
{
"url": "https://nih-ncpi.github.io/ncpi-fhir-ig/StructureDefinition/hashes",
"valueCodeableConcept": {
"coding": [
{
"display": "md5"
}
],
"text": "3d522c2ea12d19178cc97811a5811baf"
}
},
{
"url": "https://nih-ncpi.github.io/ncpi-fhir-ig/StructureDefinition/hashes",
"valueCodeableConcept": {
"coding": [
{
"display": "sha256"
}
],
"text": "cddc1812119c86de21408d0b42c1c002422e7d04d8ae3c16f23dcafab4a26374"
}
}
],
"url": "drs://data.kidsfirstdrc.org/661cc942-efa3-4a3d-83ee-11d86375c1cb",
"title": "651efbfc-8579-469c-bb23-f37b7da0927c.g.vcf.gz"
},
"format": {
"display": "gvcf"
}
}
],
"context": {
"related": [
{
"reference": "Specimen/268973"
}
]
}
}
Raw
04-Task-workflow.json
{
"resourceType": "Task",
"id": "task-workflow",
"meta": {
"profile": [
"http://hl7.org/fhir/StructureDefinition/Task"
],
"tag": [
{
"code": "DS360-CHD"
}
]
},
"identifier": [
{
"use": "official",
"system": "https://kf-api-dataservice.kidsfirstdrc.org/sequencing-experiments/",
"value": "SE_SM0PKR3V"
}
],
"status": "completed",
"intent": "order",
"input": [
{
"type": {
"text": "biospecimen"
},
"valueReference": {
"reference": "Specimen/268973"
}
},
{
"type": {
"text": "experiment_strategy"
},
"valueCodeableConcept": {
"text": "WGS"
}
},
{
"type": {
"text": "is_paired_end"
},
"valueBoolean": false
},
{
"type": {
"text": "instrument"
},
"valueCodeableConcept": {
"text": "HiSeq X Ten"
}
},
{
"type": {
"text": "library_name"
},
"valueString": "SSH3962900"
},
{
"type": {
"text": "library_prep"
},
"valueCodeableConcept": {
"text": "Reported Unknown"
}
},
{
"type": {
"text": "library_selection"
},
"valueCodeableConcept": {
"text": "Hybrid Selection"
}
},
{
"type": {
"text": "library_strand"
},
"valueCodeableConcept": {
"text": "Unstranded"
}
},
{
"type": {
"text": "platform"
},
"valueCodeableConcept": {
"text": "Illumina"
}
}
],
"output": [
{
"type": {
"text": "genomic_file"
},
"valueReference": {
"reference": "DocumentReference/275231"
}
},
{
"type": {
"text": "genomic_file"
},
"valueReference": {
"reference": "DocumentReference/275225"
}
},
{
"type": {
"text": "max_insert_size"
},
"valueDecimal": 999
},
{
"type": {
"text": "mean_depth"
},
"valueDecimal": 104
},
{
"type": {
"text": "mean_insert_size"
},
"valueDecimal": 105
},
{
"type": {
"text": "mean_read_length"
},
"valueDecimal": 107
},
{
"type": {
"text": "total_reads"
},
"valueDecimal": 99
}
]
}
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