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

Field	Create	Update	Unique	Required
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.

Field	Description
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.

Field	Description
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.

Field	Description
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.

Field	Description
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.

Field	Description
files List<String>	Files used for the quality control of the sample.
comments List<ClinicalComment>	Comments for the quality control of the sample.
variant SampleVariantQualityControlMetrics	Describes variant quality control.

Phenotype

You can find the Java code here.

Field	Description
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.

Field	Description
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.

Field	Description
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.

Field	Description
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.

Field	Description
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.

Field	Description
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.

Field	Description
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.

Field	Description
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.

Field	Description
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.

Field	Description
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.

Field	Description
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.

Field	Description
context String	Genome context to count
total int	Counted integer

GenomePlotTrack

You can find the Java code here.

Field	Description
type String	Genome Plot Track Type
description String	Genome Plot Track description
query Map<String,String>	Genome Plot Track map for query