Individual

Overview

Individual data model hosts information about any indvidual.

Summary

Field	Create	Update	Unique	Required
id
uuid
name
father
mother
familyIds
location
qualityControl
sex
karyotypicSex
ethnicity
ethnicity
dateOfBirth
creationDate
modificationDate
lifeStatus
phenotypes
disorders
samples
parentalConsanguinity
status
internal
attributes
release
version

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.
uuid String	Unique 32-character identifier assigned automatically by OpenCGA.
name String	Name of the individual.
father Individual	Father of the individual.
mother Individual	Mother of the individual.
familyIds List<String>	List of ids of the family members.
location Location	Location of the individual.
qualityControl IndividualQualityControl	Contains different metrics to evaluate the quality of the individual.
sex SexOntologyTermAnnotation	Sex of the individual.
karyotypicSex KaryotypicSex	Karyotypic sex of the individual.
ethnicity OntologyTermAnnotation	Ethnicity of the individual.
ethnicity IndividualPopulation	Ethnicity of the individual.
dateOfBirth String	Date of birth 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.
lifeStatus LifeStatus	Life status of the of the individual ALIVE, ABORTED, DECEASED, UNBORN, STILLBORN, MISCARRIAGE, UNKNOWN.
phenotypes List<Phenotype>	List of phenotypes .
disorders List<Disorder>	List of the individual disorders.
samples List<Sample>	List of the individual samples.
parentalConsanguinity boolean	Indicates the parental consanguinity is true or false.
status Status since: 2.0	Object to set a custom status.
internal IndividualInternal since: 2.0	Internal field for manage the object.
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.

Location

You can find the Java code here.

Field	Description
address String	Location address.
postalCode String	Location postal code.
city String	Location city.
state String	Location state.
country String	Location country.

Status

You can find the Java code here.

SexOntologyTermAnnotation

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..

OntologyTermAnnotation

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..

IndividualPopulation

You can find the Java code here.

Field	Description
name String	Name of the individual population.
subpopulation String	Subpopulation of the individual population.
description String	Description of the individual population.

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..

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..

IndividualQualityControl

You can find the Java code here.

Field	Description
inferredSexReports List<InferredSexReport>	List of inferred sex reports, it depends on the method (currently by coverage ratio).
sampleRelatednessReport SampleRelatednessReport	Reports of samples relatedness.
mendelianErrorReports List<MendelianErrorReport>	Mendelian errors.
files List<String>	File IDs related to the quality control.
author List<ClinicalComment>	Comments related to the quality control.

IndividualInternal

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.

SampleRelatednessReport

You can find the Java code here.

MendelianErrorReport

You can find the Java code here.

InferredSexReport

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

InternalStatus

You can find the Java code here.