Sample
Overview
Sample data model hosts information about any biological material, normally extracted from an Individual, that is used for a particular analysis. This is the main data model, it stores the most basic and important information.
Summary
id
uuid
source
processing
collection
qualityControl
creationDate
modificationDate
description
somatic
phenotypes
individualId
fileIds
cohortIds
status
attributes
release
version
internal
Data Model
Sample
You can find the Java code here.
id String
Sample data model hosts information about any biological material, normally extracted from an Individual, that is used for a particular analysis. This is the main data model, it stores the most basic and important information.
uuid String
Unique 32-character identifier assigned automatically by OpenCGA.
source ExternalSource since: 2.2
The external source from where the example was imported.
processing SampleProcessing since: 2.0
Describes how the sample was processed in the lab.
collection SampleCollection since: 2.0
Describes how the sample was collected.
qualityControl SampleQualityControl since: 2.0
Contains different metrics to evaluate the quality of the sample.
creationDate String since: 1.0
Autogenerated date following the format YYYYMMDDhhmmss containing the date when the entry was first registered.
modificationDate String since: 1.0
Autogenerated date following the format YYYYMMDDhhmmss containing the date when the entry was last modified.
description String
Users may provide a description for the entry.
somatic boolean
Describes if the sample is somatic or not .
phenotypes List<Phenotype>
List of phenotypes .
individualId String
Individual id of the sample.
fileIds List<String>
File ids of the sample.
cohortIds List<String>
Cohort ids of the sample.
status Status since: 2.0
Cohort ids of the sample.
attributes Map<String,Object> since: 1.0
You can use this field to store any other information, keep in mind this is not indexed so you cannot search by attributes.
release int
An integer describing the current data release.
version int
Autoincremental version assigned to the registered entry. By default, updates does not create new versions. To enable versioning, users must set the incVersion flag from the /update web service when updating the document.
internal SampleInternal since: 2.0
Sample internal information.
SampleCollection
You can find the Java code here.
from List<OntologyTermAnnotation>
OntologyTermAnnotation list.
type String
Type of the sample collection.
quantity String
Quantity collected for the sample.
method String
Describes which method was used to collect the sample.
date String
Date when the sample was collected.
attributes Map<String,Object>
Attributes of the sample collection.
Status
You can find the Java code here.
SampleProcessing
You can find the Java code here.
product OntologyTermAnnotation
Describes which product was used to process the sample in the lab.
preparationMethod String
Describes which preparation method was used to process the sample in the lab.
preparationMethod String
Describes which extraction method was used to process the samplein the lab.
labSampleId String
Original id has the sample in the lab.
quantity String
Number of process has done the sample.
date String
Date when the sample was processed in the lab.
attributes Map<String,Object>
Attributes of the processing.
SampleInternal
You can find the Java code here.
RgaIndex.rga RgaIndex
Rga index for Sample internal.
status InternalStatus
Status of the internal object.
registrationDate String
Registration date of the internal object.
lastModified String
Date of the last modification of the internal object.
SampleQualityControl
You can find the Java code here.
files List<String>
Files used for the quality control of the sample.
comments List<ClinicalComment>
Comments for the quality control of the sample.
Describes variant quality control.
Phenotype
You can find the Java code here.
id String
Id to identify the object
ageOfOnset String
Indicates the age of on set of the phenotype
status Status
Status of phenotype OBSERVED, NOT_OBSERVED, UNKNOWN
name String
Object name
description String
Users may provide a description for the entry.
source String
Ontology source
url String
Ontology url
attributes Map<String,String>
Dictionary that can be customised by users to store any additional information users may require..
ExternalSource
You can find the Java code here.
id String
Source ID...
name String
Source name...
description String
Source description...
source String
Source ...
url String
Source ID
ClinicalComment
You can find the Java code here.
author String
Clinical comment author
message String
Clinical comment message
tags List<String>
List of tags for the clinical comment
date String
Date of the clinical comment
RgaIndex
You can find the Java code here.
status Status
Status of the Rga index NOT_INDEXED, INDEXED, INVALID_PERMISSIONS, INVALID_METADATA, INVALID.
date String
Date of Rga index.
InternalStatus
You can find the Java code here.
OntologyTermAnnotation
You can find the Java code here.
id String
Id to identify the object
name String
Object name
description String
Users may provide a description for the entry.
source String
Ontology source
url String
Ontology url
attributes Map<String,String>
Dictionary that can be customised by users to store any additional information users may require..
SampleVariantQualityControlMetrics
You can find the Java code here.
variantStats List<SampleQcVariantStats>
Variant stats for the quality control of the sample.
signatures List<Signature>
Signature for the quality control of the sample.
genomePlot GenomePlot
Genome plot for the quality control of the sample.
files List<String>
File for the quality control metrics of the sample.
GenomePlot
You can find the Java code here.
id String
Id to identify the object
description String
Users may provide a description for the entry.
config GenomePlotConfig
Config of the genomePlot
file String
File of the genomePlot
SampleQcVariantStats
You can find the Java code here.
id String
Id to identify the object
description String
Users may provide a description for the entry.
query Map<String,String>
Map for query
stats SampleVariantStats
Stats result set
sampleId String
Stats result set
Signature
You can find the Java code here.
id String
Id to identify the object
description String
Users may provide a description for the entry.
query ObjectMap
Map for query
type String
Signature type SNV, INDEL...
counts List<GenomeContextCount>
List of GenomeContextCount
files List<String>
List of files of signature
fitting SignatureFitting
Signature fitting
GenomePlotConfig
You can find the Java code here.
title String
Title of the genome plot configuration
density String
Density of the genome plot configuration
generalQuery Map<String,String>
Map for the general query of the genome plot configuration
tracks List<GenomePlotTrack>
List of GenomePlotTrack
SignatureFitting
You can find the Java code here.
method String
Method used to fit the signature
signatureSource String
Source of the fitting signature
signatureVersion String
Signature version of the fitting signature
scores List<Score>
Scores of the fitting signature
coeff double
Coefficient of the fitting signature
file String
Files of the fitting signature
GenomeContextCount
You can find the Java code here.
context String
Genome context to count
total int
Counted integer
GenomePlotTrack
You can find the Java code here.
type String
Genome Plot Track Type
description String
Genome Plot Track description
query Map<String,String>
Genome Plot Track map for query
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