Cohort
Overview
Summary
Field
create
update
unique
required
id
type
description
samples
numSamples
status
attributes
uuid
creationDate
modificationDate
release
internal
Data Model
Cohort
You can find the Java code here.
Field
Description
id String
Cohort ID is a mandatory parameter when creating a new Cohort, 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 Cohort creation and cannot be changed.Tags: internal, unique, immutable
type CohortType
creationDate String
String representing when the Cohort was created, this is automatically set by OpenCGA.Tags: internal
modificationDate String
String representing when was the last time the Cohort was modified, this is automatically set by OpenCGA.Tags: internal
description String
An string to describe the properties of the Cohort.
samples List<Sample>
numSamples int
release int
An integer describing the current data release.Tags: internal
status CustomStatus
An object describing the status of the Sample.
internal CohortInternal
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.
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.
Enum Enums.CohortType
Enumeration class. You can find the Java code here.
Field
Description
CASE_CONTROL
CASE_SET
CONTROL_SET
PAIRED
PAIRED_TUMOR
AGGREGATE
TIME_SERIES
FAMILY
TRIO
COLLECTION
CustomStatus
You can find the Java code here.
Field
Description
name String
Lorem ipsum dolor sit amet, consectetur adipiscing elit. Sed vestibulum aliquet lobortis. Pellentesque venenatis lacus quis nibh interdum finibus.Tags: required, immutable
description String
Proin aliquam ante in ligula tincidunt, cursus volutpat urna suscipit. Phasellus interdum, libero at posuere blandit, felis dui dignissim leo, quis ullamcorper felis elit a augue.Tags: required
date String
Nullam commodo tortor nec lectus cursus finibus. Sed quis orci fringilla, cursus diam quis, vehicula sapien. Etiam bibendum dapibus lectus, ut ultrices nunc vulputate ac.Tags: internal, unique, immutable
SampleInternal
You can find the Java code here.
CohortInternal
You can find the Java code here.
Field
Description
status CohortStatus
Last updated
