Family

Overview

Created by pfurio on 02/05/17.

Summary

Field	create	update	unique	required
id
name
members
phenotypes
disorders
qualityControl
expectedSize
description
status
roles
attributes
uuid
creationDate
modificationDate
release
version
internal

Data Model

Family

You can find the Java code here.

Field	Description
id String	Family 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 Family creation and cannot be changed.Tags: internal, unique, immutable
name String
members List<Individual>
phenotypes List<Phenotype>
disorders List<Disorder>
qualityControl FamilyQualityControl
creationDate String	String representing when the Family was created, this is automatically set by OpenCGA.Tags: internal
modificationDate String	String representing when was the last time the Family was modified, this is automatically set by OpenCGA.Tags: internal
expectedSize int
description String	An string to describe the properties of the Family.
release int	An integer describing the current data release.Tags: internal
version int	An integer describing the current version.Tags: internal
status CustomStatus	An object describing the status of the Family.
internal FamilyInternal	An object describing the internal information of the Family. This is managed by OpenCGA.Tags: internal
roles Map<MapString,String,FamiliarRelationship>
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.

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.

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

FamilyInternal

You can find the Java code here.

Field	Description
status FamilyStatus

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>

InterpretationInternal

You can find the Java code here.

Field	Description
status InterpretationStatus

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

ClinicalAnalysisInternal

You can find the Java code here.

Field	Description
status ClinicalAnalysisStatus

UserInternal

You can find the Java code here.

Field	Description
status UserStatus

StudyInternal

You can find the Java code here.

Field	Description
status Status
configuration StudyConfiguration