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.

Field	Description
id String	Unique Sample ID in the study, this can be repeated across different studies. This is a mandatory parameter in the creation and cannot be changed at the moment. Constraints: Mandatory, Unique, Immutable
uuid String	Global unique ID in any study of any OpenCGA installation. This is created during the sample creation and cannot be changed. Constraints: Internal, Unique, Immutable
individualId String	A reference to the Individual containing this sample. Notice that samples can exist without and Individual ID, this field is not mandatory.
fileIds List<String>	List of File ID containing this sample, eg BAM, VCF, QC images, ...
processing SampleProcessing	An object describing how to sample was processed.
collection SampleCollection	An object describing how the sample was collected.
somatic Boolean
annotationSets List<AnnotationSet>
qualityControl SampleQualityControl
release Integer
version Integer
creationDate String	A string representing the creation date in format YYYYMMDDHHmmss
modificationDate String	A string representing the modification date in format YYYYMMDDHHmmss
description String
phenotypes List<Phenotype>
status CustomStatus
internal SampleInternal
attributes Map

SampleProcessing

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

Field	Description
product String	Type of product sequenced, this can be DNA or RNA for instance
preparationMethod String
extractionMethod String
labSampleId String
quantity String
date String

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: {}
        }
    }
}