Sample
Last updated
Last updated
Sample data model ...
This is the main data model, it stores the most basic and important information. You can find the Java here.
This object describes how the sample was processed in the lab.
This is a full JSON example:
Field
Description
id
String
Unique Sample ID in the study, this can be repeated across different studies. This is a mandatory parameter in the creation and cannot be changed at the moment.
Constraints: Mandatory, Unique, Immutable
uuid
String
Global unique ID in any study of any OpenCGA installation. This is created during the sample creation and cannot be changed.
Constraints: Internal, Unique, Immutable
individualId
String
A reference to the Individual containing this sample. Notice that samples can exist without and Individual ID, this field is not mandatory.
fileIds
List<String>
List of File ID containing this sample, eg BAM, VCF, QC images, ...
processing
<em></em>SampleProcessing<em></em>
An object describing how to sample was processed.
collection
<em></em>SampleCollection<em></em>
An object describing how the sample was collected.
somatic
Boolean
annotationSets
List<AnnotationSet>
qualityControl
<em></em>SampleQualityControl<em></em>
release
Integer
version
Integer
creationDate
String
A string representing the creation date in format YYYYMMDDHHmmss
modificationDate
String
A string representing the modification date in format YYYYMMDDHHmmss
description
String
phenotypes
List<Phenotype>
status
<em></em>CustomStatus<em></em>
internal
SampleInternal
attributes
Map
Field
Description
product
String
Type of product sequenced, this can be DNA or RNA for instance
preparationMethod
String
extractionMethod
String
labSampleId
String
quantity
String
date
String