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
A List with related groups.
A List with related files.
A List with related jobs.
A List with related individuals.
A List with related families.
A List with related samples.
A List with related cohorts.
panels List<org.opencb.opencga.core.models.panel.Panel>
A List with related panels.
A List with related clinicalAnalyses.
A List with related variableSets.
permissionRules Map<ListPermissionRule,Enums.Entity>
uri URI
release int
An object describing the status of the Sample.
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
Formats: file, folder, index.
Formats: txt, executable, image, ...
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
sampleIds List<String>
jobId String
tags List<String>
stats Map<Object,String>
An object describing the status of the File.
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
Describes how the sample was processed in the lab.
Describes how the sample was collected.Note: The sample collection is a list of samples
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
fileIds List<String> Deprecated
List of File ID containing this sample, eg BAM, VCF, QC images, ...
An object describing the status of the Sample.
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
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
sex Sex
karyotypicSex KaryotypicSex
ethnicity String
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.
A List with related samples.
parentalConsanguinity boolean
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.
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.
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
An object describing the internal information of the Sample. This is managed by OpenCGA.Tags: internal
tags List<String>
visited boolean
OPENCGA_PARENTS String
release int
An integer describing the current data release.Tags: internal
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
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.
numSamples int
release int
An integer describing the current data release.Tags: internal
An object describing the status of the Sample.
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.
disorder Disorder
panelLock boolean
locked boolean
analyst ClinicalAnalyst
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
comments List<ClinicalComment>
audit List<ClinicalAudit>
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
phenotypes List<Phenotype>
disorders List<Disorder>
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
An object describing the status of the Family.
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
IndividualInternal
You can find the Java code here.
Field
Description
FamilyInternal
You can find the Java code here.
Field
Description
FileInternal
You can find the Java code here.
Field
Description
sampleMap Map<String>
JobInternal
You can find the Java code here.
Field
Description
events List<Event>
InterpretationInternal
You can find the Java code here.
Field
Description
ProjectInternal
You can find the Java code here.
Field
Description
CohortInternal
You can find the Java code here.
Field
Description
ClinicalAnalysisInternal
You can find the Java code here.
Field
Description
UserInternal
You can find the Java code here.
Field
Description
StudyInternal
You can find the Java code here.
Field
Description
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