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
father Individual
mother Individual
location Location
qualityControl IndividualQualityControl
sex Sex
karyotypicSex KaryotypicSex
ethnicity String
population IndividualPopulation
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.
samples List<Sample>	A List with related samples.
parentalConsanguinity boolean
status CustomStatus
internal IndividualInternal
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
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.

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
status Status
rga RgaIndex

IndividualInternal

You can find the Java code here.

Field	Description
status Status

FileInternal

You can find the Java code here.

Field	Description
status FileStatus
index FileIndex
sampleMap Map<String>
missingSamples MissingSamples

JobInternal

You can find the Java code here.

Field	Description
status ExecutionStatus
webhook JobInternalWebhook
events List<Event>

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