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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