Individual

Overview

Created by jacobo on 11/09/14.

Summary

Field

create

update

unique

required

id

name

father

mother

location

qualityControl

sex

karyotypicSex

ethnicity

population

dateOfBirth

lifeStatus

phenotypes

disorders

samples

parentalConsanguinity

status

internal

attributes

uuid

release

version

creationDate

modificationDate

Data Model

Individual

You can find the Java code here.

Field

Description

id String

Individual 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 Individual, 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

name String

sex Sex

karyotypicSex KaryotypicSex

ethnicity String

dateOfBirth String

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

lifeStatus LifeStatus

phenotypes List<Phenotype>

A List with related phenotypes.

disorders List<Disorder>

A List with related disorders.

A List with related samples.

parentalConsanguinity boolean

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.

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

Describes how the sample was processed in the lab.

Describes how the sample was collected.Note: The sample collection is a list of samples

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

fileIds List<String> Deprecated

List of File ID containing this sample, eg BAM, VCF, QC images, ...

An object describing the status of the Sample.

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.

IndividualQualityControl

You can find the Java code here.

Field

Description

sampleId String

Sample ID, only germinal sample and indexed

inferredSexReports List<InferredSexReport>

List of inferred sex reports, it depends on the method (currently by coverage ratio)

mendelianErrorReport MendelianErrorReport

Mendelian errors

fileIds List<String>

File IDs related to the quality control

comments List<ClinicalComment>

Comments related to the quality control

IndividualPopulation

You can find the Java code here.

Field

Description

name String

subpopulation String

description String

Location

You can find the Java code here.

Field

Description

address String

postalCode String

city String

state String

country String

SampleInternal

You can find the Java code here.

Field

Description

IndividualInternal

You can find the Java code here.

Field

Description

FileInternal

You can find the Java code here.

Field

Description

sampleMap Map<String>

JobInternal

You can find the Java code here.

Field

Description

events List<Event>

ProjectInternal

You can find the Java code here.

Field

Description

CohortInternal

You can find the Java code here.

Field

Description

StudyInternal

You can find the Java code here.

Field

Description

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