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object-set_Covid19.json
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{
"schema": {
"$ref": "https://raw.githubusercontent.com/EbiEga/ega-metadata-schema/main/schemas/EGA.object-set.json"
},
"data": {
"objectTitle": "Example of a COVID19 small submission",
"objectDescription": "This object-set constitutes an example of some objects one would expect in a small COVID-19 submission that may differ from other types of submissions: an individual, samples, and the study encompassing all. There are many other objects one would submit for a full COVID-19 submission: a policy, DAC and dataset to specify the reusability of the data; experiments and assays containing the raw data; analyses containing the bioinformatics investigations; protocols describing each of the procedures performed; and finally a submission which would be referenced by all objects. This COVID-19 example is **inspired** on the COVID-19 example of Phenopackets (https://phenopacket-schema.readthedocs.io/en/latest/covid19-example.html) and the published case report it is based on (https://www.jacc.org/doi/10.1016/j.jaccas.2020.04.001).",
"objectArray": [
{
"objectId": {
"alias": "P123542",
"centerName": "EBI-TEST"
},
"minimalPublicAttributes": {
"subjectId": "P123542",
"biologicalSex": "male",
"diseases": [
{
"disease": {
"termId": "MONDO:0100096",
"termLabel": "COVID-19"
}
},
{
"disease": {
"termId": "EFO:0000400",
"termLabel": "Diabetes Mellitus"
}
},
{
"disease": {
"termId": "EFO:0000318",
"termLabel": "Cardiomyopathy"
}
},
{
"disease": {
"termId": "EFO:0009909",
"termLabel": "Chronic Kidney Disease"
}
},
{
"disease": {
"termId": "EFO:0001073",
"termLabel": "Obesity"
}
}
]
},
"organismDescriptor": {
"organismTaxon": {
"termId": "NCBITaxon:9606",
"termLabel": "homo sapiens"
},
"commonName": "human"
},
"individualAttributes": [
{
"tag": "vitalStatus",
"value": "DECEASED"
}
],
"individualRelationships": [
{
"rSource": {
"objectId": {
"externalAccessions": [
{
"objectExternalAccessionURI": "https://www.jacc.org/doi/10.1016/j.jaccas.2020.04.001"
}
]
},
"objectType": "externalAccession"
},
"rType": "referencedBy"
},
{
"rSource": {
"objectId": {
"egaAccession": "EGAB00000000001"
},
"objectType": "submission"
},
"rType": "referencedBy"
}
],
"schemaDescriptor": {
"commonSchemaVersion": "0.0.0",
"describedBySchemaUri": "https://github.com/EbiEga/ega-metadata-schema/tree/main/schemas/EGA.individual.json",
"objectSchemaVersion": "0.0.0",
"objectType": "individual"
}
},
{
"objectId": {
"alias": "P123542 - Lung swab",
"centerName": "EBI-TEST"
},
"objectTitle": "P123542 - Lung swab",
"organismDescriptor": {
"organismTaxon": {
"termId": "NCBITaxon:9606",
"termLabel": "homo sapiens"
},
"commonName": "human"
},
"sampleStatus": [
{
"caseVsControl": "case",
"conditionUnderStudy": {
"termId": "MONDO:0100096",
"termLabel": "COVID-19"
}
}
],
"sampleTypes": [
"biofilm",
"RNA"
],
"sampleCollection": {
"ageAtCollection": {
"age": "P70Y"
},
"sampleCollectionDate": "2020-03-28T00:00:00Z",
"samplingSite": {
"termId": "UBERON:0007196",
"termLabel": "tracheobronchial tree"
}
},
"sampleRelationships": [
{
"rSource": {
"objectId": {
"alias": "P123542",
"centerName": "EBI-TEST"
},
"objectType": "individual"
},
"rType": "referencedBy"
},
{
"rSource": {
"objectId": {
"alias": "Lung swab collection",
"centerName": "EBI-TEST"
},
"objectType": "protocol"
},
"rType": "referencedBy"
},
{
"rSource": {
"objectId": {
"egaAccession": "EGAB00000000001"
},
"objectType": "submission"
},
"rType": "referencedBy"
}
],
"schemaDescriptor": {
"commonSchemaVersion": "0.0.0",
"describedBySchemaUri": "https://github.com/EbiEga/ega-metadata-schema/tree/main/schemas/EGA.sample.json",
"objectSchemaVersion": "0.0.0",
"objectType": "sample"
}
},
{
"objectId": {
"alias": "COVID19 Study",
"centerName": "EBI-TEST"
},
"objectTitle": "The Imperfect Cytokine Storm: Severe COVID-19 With ARDS in a Patient on Durable LVAD Support",
"objectDescription": "As health systems worldwide grapple with the coronavirus disease-2019 (COVID-19) pandemic, patients with durable LVAD support represent a unique population at risk for the disease. This paper outlines the case of such a patient who developed COVID-19 complicated by a \u201ccytokine storm\u201d with severe acute respiratory distress syndrome and myocardial injury and describes the challenges that arose during management.",
"studyDesigns": [
"clinical history design"
],
"studyTypes": [
"COVID-19"
],
"studyRelationships": [
{
"rSource": {
"objectId": {
"externalAccessions": [
{
"objectExternalAccessionURI": "https://www.jacc.org/doi/10.1016/j.jaccas.2020.04.001"
}
]
},
"objectType": "externalAccession"
},
"rType": "referencedBy"
},
{
"rSource": {
"objectId": {
"egaAccession": "EGAB00000000001"
},
"objectType": "submission"
},
"rType": "referencedBy"
}
],
"schemaDescriptor": {
"commonSchemaVersion": "0.0.0",
"describedBySchemaUri": "https://github.com/EbiEga/ega-metadata-schema/tree/main/schemas/EGA.study.json",
"objectSchemaVersion": "0.0.0",
"objectType": "study"
}
}
],
"schemaDescriptor": {
"commonSchemaVersion": "0.0.0",
"describedBySchemaUri": "https://raw.githubusercontent.com/EbiEga/ega-metadata-schema/main/schemas/EGA.object-set.json",
"objectSchemaVersion": "0.0.0",
"objectType": "object-set"
}
}
}