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

Field	create	update	unique	required
id
processing
collection
qualityControl
description
somatic
phenotypes
individualId
fileIds
status
attributes
uuid
release
version
creationDate
modificationDate
internal

Data Model

Sample

You can find the Java code here.

Field	Description
id String	Sample ID in the study, this must be unique in the study but can be repeated in different studies. This is a mandatory parameter when creating a new sample, this ID cannot be changed at the moment.Tags: required, immutable, unique
uuid String	Global unique ID at the whole OpenCGA installation. This is automatically created during the sample creation and cannot be changed.Tags: internal, unique, immutable
processing SampleProcessing	Describes how the sample was processed in the lab.
collection SampleCollection since: 2.1	Describes how the sample was collected.Note: The sample collection is a list of samples
qualityControl SampleQualityControl since: 2.1	Contains different metrics to evaluate the quality of the sample.Note: The sample collection is a list of samples</br>More info at: ZetaGenomics
release int	An integer describing the current data release.Tags: internal
version int	An integer describing the current version.Tags: internal
creationDate String	String representing when the sample was created, this is automatically set by OpenCGA.Tags: internal
modificationDate String	String representing when was the last time the sample was modified, this is automatically set by OpenCGA.Tags: internal
description String	An string to describe the properties of the sample.
somatic boolean	Indicates if the sample is somatic or germline (default)
phenotypes List<Phenotype>	A List with related phenotypes.
individualId String	A reference to the Individual containing this sample. Notice that samples can exist without and Individual ID, this field is not mandatory..More info at: ZetaGenomics
fileIds List<String> Deprecated	List of File ID containing this sample, eg BAM, VCF, QC images, ...
status CustomStatus	An object describing the status of the Sample.
internal SampleInternal	An object describing the internal information of the Sample. This is managed by OpenCGA.Tags: internal
attributes Map<Object,String>	You can use this field to store any other information, keep in mind this is not indexed so you cannot search by attributes.

SampleInternal

You can find the Java code here.

Field	Description
status Status
rga RgaIndex

ProjectInternal

You can find the Java code here.

Field	Description
datastores Datastores
cellbase CellBaseConfiguration
status Status

CohortInternal

You can find the Java code here.

Field	Description
status CohortStatus

StudyInternal

You can find the Java code here.

Field	Description
status Status
configuration StudyConfiguration

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: {}
    }
  }
}