Individual
Overview
Individual data model hosts information about any indvidual.
Summary
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.
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 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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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