# 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](https://github.com/opencb/opencga/blob/master/opencga-core/src/main/java/org/opencb/opencga/core/models/cohort/Cohort.java).
| 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](https://github.com/opencb/opencga/blob/master/opencga-core/src/main/java/org/opencb/opencga/core/models/sample/Sample.java).
| 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*\*More info at*: [ZetaGenomics](https://www.zettagenomics.com) |
| 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](https://github.com/opencb/opencga/blob/master/opencga-core/src/main/java/org/opencb/opencga/core/models/common/Enums/CohortType.java).
| 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](https://github.com/opencb/opencga/blob/master/opencga-core/src/main/java/org/opencb/opencga/core/models/common/CustomStatus.java).
| 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](https://github.com/opencb/opencga/blob/master/opencga-core/src/main/java/org/opencb/opencga/core/models/sample/SampleInternal.java).
| Field | Description |
| ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ----------- |
| status
Status
| |
| rga
RgaIndex
| |
### CohortInternal
You can find the Java code [here](https://github.com/opencb/opencga/blob/master/opencga-core/src/main/java/org/opencb/opencga/core/models/cohort/CohortInternal.java).
| Field | Description |
| --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ----------- |
| status
CohortStatus
| |
---
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