object-set_RareDisease.json

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    "data": {
        "objectTitle": "Example of a Rare Disease small submission",
        "objectDescription": "This object-set constitutes an example of some objects one would expect in a small Rare Disease submission that may differ from other types of submissions: an affected individual and his unaffected mother, a sample and the study encompassing all. There are many other objects one could submit for a full Rare Disease 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 Rare Disease example is inspired on the Rare Disease example of Phenopackets (https://phenopacket-schema.readthedocs.io/en/latest/rd-example.html) and the article it is based on (https://pubmed.ncbi.nlm.nih.gov/30808312/).",
        "objectArray": [
            {
                "objectId": {
                    "alias": "14 year-old boy",
                    "centerName": "EBI-TEST"
                },
                "minimalPublicAttributes": {
                    "subjectId": "Affected_proband_14y",
                    "biologicalSex": "male",
                    "phenotypicAbnormalities": [
                        {
                            "phenotypicAbnormality": {
                                "termId": "HP:0001558",
                                "termLabel": "Decreased fetal movement"
                            }
                        },
                        {
                            "phenotypicAbnormality": {
                                "termId": "HP:0031910",
                                "termLabel": "Abnormal cranial nerve physiology"
                            }
                        },
                        {
                            "phenotypicAbnormality": {
                                "termId": "HP:0012587",
                                "termLabel": "Macroscopic hematuria"
                            }
                        },
                        {
                            "phenotypicAbnormality": {
                                "termId": "HP:0001270",
                                "termLabel": "Motor delay"
                            }
                        }
                    ],
                    "diseases": [
                        {
                            "disease": {
                                "termId": "MONDO:0008029",
                                "termLabel": "Bethlem myopathy"
                            }
                        }
                    ]
                },
                "organismDescriptor": {
                    "organismTaxon": {
                        "termId": "NCBITaxon:9606",
                        "termLabel": "homo sapiens"
                    },
                    "commonName": "human"
                },
                "individualRelationships": [
                    {
                        "rTarget": {
                            "objectId": {
                                "alias": "Unaffected mother",
                                "centerName": "EBI-TEST"
                            },
                            "objectType": "individual"
                        },
                        "rType": "childOf"
                    },
                    {
                        "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": "Unaffected mother",
                    "centerName": "EBI-TEST"
                },
                "minimalPublicAttributes": {
                    "subjectId": "Unaffected mother",
                    "biologicalSex": "female",
                    "phenotypicAbnormalities": [
                        {
                            "phenotypicAbnormality": {
                                "termId": "NCIT:C94232",
                                "termLabel": "Unaffected"
                            }
                        }
                    ]
                },
                "organismDescriptor": {
                    "organismTaxon": {
                        "termId": "NCBITaxon:9606",
                        "termLabel": "homo sapiens"
                    },
                    "commonName": "human"
                },
                "individualRelationships": [
                    {
                        "rSource": {
                            "objectId": {
                                "alias": "14 year-old boy",
                                "centerName": "EBI-TEST"
                            },
                            "objectType": "individual"
                        },
                        "rType": "childOf"
                    },
                    {
                        "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": "Blood sample - 14y Proband",
                    "centerName": "EBI-TEST"
                },
                "objectTitle": "Blood sample of the 14y affected proband",
                "organismDescriptor": {
                    "organismTaxon": {
                        "termId": "NCBITaxon:9606",
                        "termLabel": "homo sapiens"
                    },
                    "commonName": "human"
                },
                "sampleStatus": [
                    {
                        "caseVsControl": "not applicable",
                        "conditionUnderStudy": {
                            "termId": "MONDO:0008029",
                            "termLabel": "Bethlem myopathy"
                        }
                    }
                ],
                "sampleTypes": [
                    "DNA"
                ],
                "sampleCollection": {
                    "ageAtCollection": {
                        "age": "P14Y"
                    },
                    "samplingSite": {
                        "termId": "UBERON:0001414",
                        "termLabel": "median basilic vein"
                    }
                },
                "sampleRelationships": [
                    {
                        "rSource": {
                            "objectId": {
                                "alias": "14 year-old boy",
                                "centerName": "EBI-TEST"
                            },
                            "objectType": "individual"
                        },
                        "rType": "referencedBy"
                    },
                    {
                        "rSource": {
                            "objectId": {
                                "alias": "Blood drawn protocol",
                                "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": "14Y COL6A1 mutation - Bethlem myopathy",
                    "centerName": "EBI-TEST"
                },
                "objectTitle": "COL6A1 mutation leading to Bethlem myopathy with recurrent hematuria",
                "objectDescription": "Study of a 14-year-old boy presenting with muscle weakness from 3 years of age without any family history. Six months before admission, he developed recurrent gross hematuria, three bouts in total, with the presence of blood clots in the urine. Next-generation sequencing of his whole-exome was performed. The result of sequencing revealed a de novo heterozygous G-to-A nucleotide substitution at position 877 in exon 10 of the COL6A1 gene. After treatment, the hematuria healed, but the muscle weakness failed to improve.",
                "studyDesigns": [
                    "clinical history design",
                    "family based design",
                    "genotyping design"
                ],
                "studyTypes": [
                    "whole genome sequencing"
                ],
                "studyRelationships": [
                    {
                        "rSource": {
                            "objectId": {
                                "externalAccessions": [
                                    {
                                        "objectExternalAccessionURI": "https://pubmed.ncbi.nlm.nih.gov/30808312/"
                                    }
                                ]
                            },
                            "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"
                }
            }
        ],
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            "commonSchemaVersion": "0.0.0",
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            "objectSchemaVersion": "0.0.0",
            "objectType": "object-set"
        }
    }
}