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 of the individual.

karyotypicSex KaryotypicSex

Karyotypic sex of the individual.

Ethnicity of the individual.

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 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.

Last updated