Study

Overview

Created by jacobo on 11/09/14.

Summary

Field	create	update	unique	required
id
name
alias
description
size
fqn
notification
groups
files
jobs
individuals
families
samples
cohorts
panels
clinicalAnalyses
variableSets
permissionRules
uri
release
status
attributes
uuid
creationDate
modificationDate
internal

Data Model

Study

You can find the Java code here.

Field	Description
id String	Study ID 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 study creation and cannot be changed.Tags: internal, unique, immutable
name String
alias String
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.
size long
fqn String
notification StudyNotification
groups List<Group>	A List with related groups.
files List<File>	A List with related files.
jobs List<Job>	A List with related jobs.
individuals List<Individual>	A List with related individuals.
families List<Family>	A List with related families.
samples List<Sample>	A List with related samples.
cohorts List<Cohort>	A List with related cohorts.
panels List<org.opencb.opencga.core.models.panel.Panel>	A List with related panels.
clinicalAnalyses List<ClinicalAnalysis>	A List with related clinicalAnalyses.
variableSets List<VariableSet>	A List with related variableSets.
permissionRules Map<ListPermissionRule,Enums.Entity>
uri URI
release int
status CustomStatus	An object describing the status of the Sample.
internal StudyInternal	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.

File

You can find the Java code here.

Field	Description
id String	File ID is a mandatory parameter when creating a new File, 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 File creation and cannot be changed.Tags: internal, unique, immutable
name String
type File.Type	Formats: file, folder, index.
format File.Format	Formats: txt, executable, image, ...
bioformat File.Bioformat	BAM, VCF, ...
checksum String
uri URI
path String
release int	An integer describing the current data release.Tags: internal
creationDate String	String representing when the File was created, this is automatically set by OpenCGA.Tags: internal
modificationDate String	String representing when was the last time the File was modified, this is automatically set by OpenCGA.Tags: internal
description String	An string to describe the properties of the File.
external boolean
size long
software Software
experiment FileExperiment
sampleIds List<String>
jobId String
tags List<String>
relatedFiles List<FileRelatedFile>
qualityControl FileQualityControl
stats Map<Object,String>
status CustomStatus	An object describing the status of the File.
internal FileInternal	An object describing the internal information of the File. 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.

VariableSet

You can find the Java code here.

Field	Description
id String
name String
unique boolean
confidential boolean
internal boolean
description String
variables Set<Variable>
entities List<AnnotableDataModels>
release int
attributes Map<Object,String>

Individual

You can find the Java code here.

Field	Description
id String	Individual 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 Individual, 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
name String
father Individual
mother Individual
location Location
qualityControl IndividualQualityControl
sex Sex
karyotypicSex KaryotypicSex
ethnicity String
population IndividualPopulation
dateOfBirth String
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
lifeStatus LifeStatus
phenotypes List<Phenotype>	A List with related phenotypes.
disorders List<Disorder>	A List with related disorders.
samples List<Sample>	A List with related samples.
parentalConsanguinity boolean
status CustomStatus
internal IndividualInternal
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.

Group

You can find the Java code here.

Field	Description
id String	Group id, unique in the belonging study.
userIds List<String>	Set of users belonging to this group.
syncedFrom Group.Sync	Group has been synchronised from an external authorization.

Job

You can find the Java code here.

Field	Description
id String	Job ID 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
description String	An string to describe the properties of the Job.
tool ToolInfo
userId String
commandLine String
params Map<Object,String>
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
priority Priority
internal JobInternal	An object describing the internal information of the Sample. This is managed by OpenCGA.Tags: internal
outDir File
input List<File>
output List<File>
tags List<String>
dependsOn List<Job>
execution ExecutionResult
stdout File
stderr File
visited boolean
OPENCGA_PARENTS String
release int	An integer describing the current data release.Tags: internal
study JobStudyParam
attributes Map<Object,String>

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.

ClinicalAnalysis

You can find the Java code here.

Field	Description
id String	ClinicalAnalysis ID is a mandatory parameter when creating a new ClinicalAnalysis, 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 ClinicalAnalysis creation and cannot be changed.Tags: internal, unique, immutable
description String	An string to describe the properties of the ClinicalAnalysis.
type ClinicalAnalysis.Type
disorder Disorder
files List<File>
proband Individual
family Family
panels List<Panel>
panelLock boolean
locked boolean
interpretation Interpretation
secondaryInterpretations List<Interpretation>
consent ClinicalConsentAnnotation
analyst ClinicalAnalyst
priority ClinicalPriorityAnnotation
flags List<FlagAnnotation>
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
dueDate String
release int	An integer describing the current data release.Tags: internal
qualityControl ClinicalAnalysisQualityControl
comments List<ClinicalComment>
audit List<ClinicalAudit>
internal ClinicalAnalysisInternal	An object describing the internal information of the ClinicalAnalysis. 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.
status Status	An object describing the status of the ClinicalAnalysis.

Family

You can find the Java code here.

Field	Description
id String	Family 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 Family creation and cannot be changed.Tags: internal, unique, immutable
name String
members List<Individual>
phenotypes List<Phenotype>
disorders List<Disorder>
qualityControl FamilyQualityControl
creationDate String	String representing when the Family was created, this is automatically set by OpenCGA.Tags: internal
modificationDate String	String representing when was the last time the Family was modified, this is automatically set by OpenCGA.Tags: internal
expectedSize int
description String	An string to describe the properties of the Family.
release int	An integer describing the current data release.Tags: internal
version int	An integer describing the current version.Tags: internal
status CustomStatus	An object describing the status of the Family.
internal FamilyInternal	An object describing the internal information of the Family. This is managed by OpenCGA.Tags: internal
roles Map<MapString,String,FamiliarRelationship>
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.

SampleInternal

You can find the Java code here.

Field	Description
status Status
rga RgaIndex

IndividualInternal

You can find the Java code here.

Field	Description
status Status

FamilyInternal

You can find the Java code here.

Field	Description
status FamilyStatus

FileInternal

You can find the Java code here.

Field	Description
status FileStatus
index FileIndex
sampleMap Map<String>
missingSamples MissingSamples

JobInternal

You can find the Java code here.

Field	Description
status ExecutionStatus
webhook JobInternalWebhook
events List<Event>

InterpretationInternal

You can find the Java code here.

Field	Description
status InterpretationStatus

ProjectInternal

You can find the Java code here.

Field	Description
datastores Datastores
cellbase CellBaseConfiguration
status Status

CohortInternal

You can find the Java code here.

Field	Description
status CohortStatus

ClinicalAnalysisInternal

You can find the Java code here.

Field	Description
status ClinicalAnalysisStatus

UserInternal

You can find the Java code here.

Field	Description
status UserStatus

StudyInternal

You can find the Java code here.

Field	Description
status Status
configuration StudyConfiguration