Sample

Overview

Sample data model hosts information about any biological material, normally extracted from an Individual, that is used for a particular analysis. This is the main data model, it stores the most basic and important information.

Summary

Data Model

Sample

You can find the Java code here.

SampleInternal

You can find the Java code here.

ProjectInternal

You can find the Java code here.

CohortInternal

You can find the Java code here.

StudyInternal

You can find the Java code here.

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: {}
    }
  }
}

Last updated