Family

Overview

Family data model hosts information about any family.

Summary

Field	Create	Update	Unique	Required
id
uuid
name
members
phenotypes
disorders
qualityControl
creationDate
modificationDate
expectedSize
description
status
internal
roles
attributes
release
version

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.
uuid String	Unique 32-character identifier assigned automatically by OpenCGA.
name String	Family name.
members List<Individual>	List of individuals who are family members.
phenotypes List<Phenotype>	List of phenotypes .
disorders List<Disorder>	Family disorders.
qualityControl FamilyQualityControl	Contains different metrics to evaluate the quality of the individual.
creationDate String since: 1.0	Autogenerated date following the format YYYYMMDDhhmmss containing the date when the entry was first registered.
modificationDate String since: 1.0	Autogenerated date following the format YYYYMMDDhhmmss containing the date when the entry was last modified.
expectedSize int	Family expected size.
description String	Users may provide a description for the entry.
status Status since: 2.0	Object to set a custom status.
internal FamilyInternal since: 2.0	Internal field for manage the object.
roles Map<String,Map<String,FamiliarRelationship>	Map of members ids and enum of roles (FATHER, MOTHER, IDENTICAL_TWIN, SON, UNCLE, PATERNAL_GRANDFATHER.) .
attributes Map<String,Object> since: 1.0	You can use this field to store any other information, keep in mind this is not indexed so you cannot search by attributes.
release int	An integer describing the current data release.
version int	Autoincremental version assigned to the registered entry. By default, updates does not create new versions. To enable versioning, users must set the incVersion flag from the /update web service when updating the document.

Status

You can find the Java code here.

FamilyInternal

You can find the Java code here.

Field	Description
status InternalStatus	Status of the internal object.
registrationDate String	Registration date of the internal object.
lastModified String	Date of the last modification of the internal object.

Phenotype

You can find the Java code here.

Field	Description
id String	Id to identify the object
ageOfOnset String	Indicates the age of on set of the phenotype
status Status	Status of phenotype OBSERVED, NOT_OBSERVED, UNKNOWN
name String	Object name
description String	Users may provide a description for the entry.
source String	Ontology source
url String	Ontology url
attributes Map<String,String>	Dictionary that can be customised by users to store any additional information users may require..

FamilyQualityControl

You can find the Java code here.

Field	Description
relatedness List<RelatednessReport>	Reports of family relationship.
files List<String>	File IDs related to the quality control.
comments List<ClinicalComment>	Comments related to the quality control.

Disorder

You can find the Java code here.

Field	Description
id String	Id to identify the object
name String	Object name
description String	Users may provide a description for the entry.
source String	Ontology source
url String	Ontology url
attributes Map<String,String>	Dictionary that can be customised by users to store any additional information users may require..

RelatednessReport

You can find the Java code here.

Field	Description
method String	Method of the relatedness report
maf String	Minor allele frequency to filter variants, e.g.: 1kg_phase3:CEU>0.35, cohort:ALL>0.05
scores List<RelatednessScore>	Relatedness scores for pair of samples
files List<String>	List of files of Relatedness Report

InternalStatus

You can find the Java code here.

ClinicalComment

You can find the Java code here.

Field	Description
author String	Clinical comment author
message String	Clinical comment message
tags List<String>	List of tags for the clinical comment
date String	Date of the clinical comment