@startjson
#highlight "data" / "objectArray" / "0" / "minimalPublicAttributes" / "diseases" / "0" / "disease" / "termId"
#highlight "data" / "objectArray" / "0" / "minimalPublicAttributes" / "diseases" / "1" / "disease" / "termId"
#highlight "data" / "objectArray" / "0" / "minimalPublicAttributes" / "diseases" / "2" / "disease" / "termId"
#highlight "data" / "objectArray" / "0" / "minimalPublicAttributes" / "diseases" / "3" / "disease" / "termId"
#highlight "data" / "objectArray" / "0" / "minimalPublicAttributes" / "diseases" / "4" / "disease" / "termId"
#highlight "data" / "objectArray" / "0" / "organismDescriptor" / "organismTaxon" / "termId"
#highlight "data" / "objectArray" / "1" / "organismDescriptor" / "organismTaxon" / "termId"
#highlight "data" / "objectArray" / "1" / "sampleStatus" / "0" / "conditionUnderStudy" / "termId"
#highlight "data" / "objectArray" / "1" / "sampleCollection" / "samplingSite" / "termId"
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#highlight "data" / "objectArray" / "0" / "minimalPublicAttributes" / "diseases"
#highlight "data" / "objectArray" / "0" / "minimalPublicAttributes" / "diseases" / "0"
#highlight "data" / "objectArray" / "0" / "minimalPublicAttributes" / "diseases" / "0" / "disease"
#highlight "data" / "objectArray" / "0" / "minimalPublicAttributes" / "diseases" / "1"
#highlight "data" / "objectArray" / "0" / "minimalPublicAttributes" / "diseases" / "1" / "disease"
#highlight "data" / "objectArray" / "0" / "minimalPublicAttributes" / "diseases" / "2"
#highlight "data" / "objectArray" / "0" / "minimalPublicAttributes" / "diseases" / "2" / "disease"
#highlight "data" / "objectArray" / "0" / "minimalPublicAttributes" / "diseases" / "3"
#highlight "data" / "objectArray" / "0" / "minimalPublicAttributes" / "diseases" / "3" / "disease"
#highlight "data" / "objectArray" / "0" / "minimalPublicAttributes" / "diseases" / "4"
#highlight "data" / "objectArray" / "0" / "minimalPublicAttributes" / "diseases" / "4" / "disease"
#highlight "data" / "objectArray" / "0" / "organismDescriptor"
#highlight "data" / "objectArray" / "0" / "organismDescriptor" / "organismTaxon"
#highlight "data" / "objectArray" / "1"
#highlight "data" / "objectArray" / "1" / "organismDescriptor"
#highlight "data" / "objectArray" / "1" / "organismDescriptor" / "organismTaxon"
#highlight "data" / "objectArray" / "1" / "sampleStatus"
#highlight "data" / "objectArray" / "1" / "sampleStatus" / "0"
#highlight "data" / "objectArray" / "1" / "sampleStatus" / "0" / "conditionUnderStudy"
#highlight "data" / "objectArray" / "1" / "sampleCollection"
#highlight "data" / "objectArray" / "1" / "sampleCollection" / "samplingSite"

{
    "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 \\nsmall COVID-19 submission that may differ from other types of submissions: an \\nindividual, samples, and the study encompassing all. There are many other \\nobjects one would submit for a full COVID-19 submission: a policy, DAC and \\ndataset to specify the reusability of the data; experiments and assays \\ncontaining the raw data; analyses containing the bioinformatics investigations; \\nprotocols describing each of the procedures performed; and finally a submission \\nwhich would be referenced by all objects. This COVID-19 example is **inspired** \\non the COVID-19 example of Phenopackets \\n(https://phenopacket-schema.readthedocs.io/en/latest/covid19-example.html) and \\nthe published case report it is based on \\n(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 \\nLVAD Support",
                "objectDescription": "As health systems worldwide grapple with the coronavirus disease-2019 (COVID-19) \\npandemic, patients with durable LVAD support represent a unique population at \\nrisk for the disease. This paper outlines the case of such a patient who \\ndeveloped COVID-19 complicated by a \u201ccytokine storm\u201d with severe acute \\nrespiratory distress syndrome and myocardial injury and describes the challenges \\nthat 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://github.com/EbiEga/ega-metadata-schema/tree/main/schemas/EGA.object-set.json",
            "objectSchemaVersion": "0.0.0",
            "objectType": "object-set"
        }
    }
}
@endjson