Sample

Overview

Sample data model ...

Data Models

Sample

This is the main data model, it stores the most basic and important information. You can find the Java here.

SampleProcessing

This object describes how the sample was processed in the lab.

SampleCollection

SampleQualityControl

Example

This is a full JSON example:

{
    id: "ISDBM322015", 
    uuid: "eba13afe-0172-0004-0001-d4c92fd95e0a",
    individualId: "ISDBM322015",
    fileIds: [
        "data:quartet.variants.annotated.vcf.gz",
        "SonsAlignedBamFile.bam"
    ],
    annotationSets: [],
    description: "",
    somatic: false,
    qualityControl: {
        fileIds: [],
        comments: [],
        alignmentMetrics: [
            {
                bamFileId: SonsAlignedBamFile.bam,
                fastQc: {13 items},
                samtoolsFlagstats: {14 items},
                geneCoverageStats: [2 items]
            }
        ],
        variantMetrics: {
            variantStats: [1 item],
            signatures: [],
            vcfFileIds: []
        }
    },
    release: 1,
    version: 5,
    creationDate: "20200625131831",
    modificationDate: "20200709003738",
    phenotypes: [
        {
            id: "HP:0000545",
            name: "Myopia",
            source: "HPO"
        }
    ],
    status: {
        name: "",
        description: "",
        date: ""
    },
    internal: {
        status: {
            name: "READY",
            date: "20200625131831",
            description: ""
        }
    },
    attributes: {
        OPENCGA_INDIVIDUAL: {
            id: "ISDBM322015",
            name: "ISDBM322015",
            uuid: "eba13738-0172-0006-0001-283471b7ae69",
            father: {4 items},
            mother: {4 items},
            location: {},
            qualityControl: {4 items},
            sex: "MALE",
            karyotypicSex: "XY",
            ethnicity: "",
            population: {},
            release: 1,
            version: 6,
            creationDate: "20200625131830",
            modificationDate: "20201027004616",
            lifeStatus: "ALIVE",
            phenotypes: [2 items],
            disorders: [1 item],
            parentalConsanguinity: false,
            status: {3 items},
            internal: {1 item},
            attributes: {}
        }
    }
}

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