Individual
Overview
Created by jacobo on 11/09/14.
Summary
Field
create
update
unique
required
id
name
father
mother
location
qualityControl
sex
karyotypicSex
ethnicity
population
dateOfBirth
lifeStatus
phenotypes
disorders
samples
parentalConsanguinity
status
internal
attributes
uuid
release
version
creationDate
modificationDate
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.Tags: required, immutable, unique
uuid String
Global unique ID at the whole OpenCGA installation. This is automatically created during the sample creation and cannot be changed.Tags: internal, unique, immutable
name String
father Individual
mother Individual
location Location
qualityControl IndividualQualityControl
sex Sex
karyotypicSex KaryotypicSex
ethnicity String
population IndividualPopulation
dateOfBirth String
release int
An integer describing the current data release.Tags: internal
version int
An integer describing the current version.Tags: internal
creationDate String
String representing when the sample was created, this is automatically set by OpenCGA.Tags: internal
modificationDate String
String representing when was the last time the sample was modified, this is automatically set by OpenCGA.Tags: internal
lifeStatus LifeStatus
phenotypes List<Phenotype>
A List with related phenotypes.
disorders List<Disorder>
A List with related disorders.
samples List<Sample>
A List with related samples.
parentalConsanguinity boolean
status CustomStatus
internal IndividualInternal
attributes Map<Object,String>
You can use this field to store any other information, keep in mind this is not indexed so you cannot search by attributes.
Sample
You can find the Java code here.
Field
Description
id String
Sample 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 sample, this ID cannot be changed at the moment.Tags: required, immutable, unique
uuid String
Global unique ID at the whole OpenCGA installation. This is automatically created during the sample creation and cannot be changed.Tags: internal, unique, immutable
processing SampleProcessing
Describes how the sample was processed in the lab.
collection SampleCollection since: 2.1
Describes how the sample was collected.Note: The sample collection is a list of samples
qualityControl SampleQualityControl since: 2.1
Contains different metrics to evaluate the quality of the sample.Note: The sample collection is a list of samples</br>More info at: ZetaGenomics
release int
An integer describing the current data release.Tags: internal
version int
An integer describing the current version.Tags: internal
creationDate String
String representing when the sample was created, this is automatically set by OpenCGA.Tags: internal
modificationDate String
String representing when was the last time the sample was modified, this is automatically set by OpenCGA.Tags: internal
description String
An string to describe the properties of the sample.
somatic boolean
Indicates if the sample is somatic or germline (default)
phenotypes List<Phenotype>
A List with related phenotypes.
individualId String
A reference to the Individual containing this sample. Notice that samples can exist without and Individual ID, this field is not mandatory..More info at: ZetaGenomics
fileIds List<String> Deprecated
List of File ID containing this sample, eg BAM, VCF, QC images, ...
status CustomStatus
An object describing the status of the Sample.
internal SampleInternal
An object describing the internal information of the Sample. This is managed by OpenCGA.Tags: internal
attributes Map<Object,String>
You can use this field to store any other information, keep in mind this is not indexed so you cannot search by attributes.
IndividualQualityControl
You can find the Java code here.
Field
Description
sampleId String
Sample ID, only germinal sample and indexed
inferredSexReports List<InferredSexReport>
List of inferred sex reports, it depends on the method (currently by coverage ratio)
mendelianErrorReport MendelianErrorReport
Mendelian errors
fileIds List<String>
File IDs related to the quality control
comments List<ClinicalComment>
Comments related to the quality control
IndividualPopulation
You can find the Java code here.
Field
Description
name String
subpopulation String
description String
Location
You can find the Java code here.
Field
Description
address String
postalCode String
city String
state String
country String
SampleInternal
You can find the Java code here.
IndividualInternal
You can find the Java code here.
Field
Description
status Status
FileInternal
You can find the Java code here.
Field
Description
status FileStatus
index FileIndex
sampleMap Map<String>
missingSamples MissingSamples
JobInternal
You can find the Java code here.
ProjectInternal
You can find the Java code here.
CohortInternal
You can find the Java code here.
Field
Description
status CohortStatus
StudyInternal
You can find the Java code here.
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