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
