Family
Overview
Family data model hosts information about any family.
Summary
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.
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.
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.
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.
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.
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.
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.
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
Last updated
