# 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](https://github.com/opencb/opencga/blob/master/opencga-core/src/main/java/org/opencb/opencga/core/models/study/Study.java).
| 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](https://github.com/opencb/opencga/blob/master/opencga-core/src/main/java/org/opencb/opencga/core/models/file/File.java).
| 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](https://github.com/opencb/opencga/blob/master/opencga-core/src/main/java/org/opencb/opencga/core/models/sample/Sample.java).
| 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*\*More info at*: [ZetaGenomics](https://www.zettagenomics.com) |
| 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](https://github.com/opencb/opencga/blob/master/opencga-core/src/main/java/org/opencb/opencga/core/models/study/VariableSet.java).
| 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](https://github.com/opencb/opencga/blob/master/opencga-core/src/main/java/org/opencb/opencga/core/models/individual/Individual.java).
| 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](https://github.com/opencb/opencga/blob/master/opencga-core/src/main/java/org/opencb/opencga/core/models/study/Group.java).
| 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](https://github.com/opencb/opencga/blob/master/opencga-core/src/main/java/org/opencb/opencga/core/models/job/Job.java).
| 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](https://github.com/opencb/opencga/blob/master/opencga-core/src/main/java/org/opencb/opencga/core/models/cohort/Cohort.java).
| 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](https://github.com/opencb/opencga/blob/master/opencga-core/src/main/java/org/opencb/opencga/core/models/clinical/ClinicalAnalysis.java).
| 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](https://github.com/opencb/opencga/blob/master/opencga-core/src/main/java/org/opencb/opencga/core/models/family/Family.java).
| 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](https://github.com/opencb/opencga/blob/master/opencga-core/src/main/java/org/opencb/opencga/core/models/sample/SampleInternal.java).
| Field | Description |
| --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ----------- |
| status
Status
| |
| rga
RgaIndex
| |
### IndividualInternal
You can find the Java code [here](https://github.com/opencb/opencga/blob/master/opencga-core/src/main/java/org/opencb/opencga/core/models/individual/IndividualInternal.java).
| Field | Description |
| -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ----------- |
| status
Status
| |
### FamilyInternal
You can find the Java code [here](https://github.com/opencb/opencga/blob/master/opencga-core/src/main/java/org/opencb/opencga/core/models/family/FamilyInternal.java).
| Field | Description |
| -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ----------- |
| status
FamilyStatus
| |
### FileInternal
You can find the Java code [here](https://github.com/opencb/opencga/blob/master/opencga-core/src/main/java/org/opencb/opencga/core/models/file/FileInternal.java).
| Field | Description |
| -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ----------- |
| status
FileStatus
| |
| index
FileIndex
| |
| sampleMap
Map<String>
| |
| missingSamples
MissingSamples
| |
### JobInternal
You can find the Java code [here](https://github.com/opencb/opencga/blob/master/opencga-core/src/main/java/org/opencb/opencga/core/models/job/JobInternal.java).
| Field | Description |
| --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ----------- |
| status
ExecutionStatus
| |
| webhook
JobInternalWebhook
| |
| events
List<Event>
| |
### InterpretationInternal
You can find the Java code [here](https://github.com/opencb/opencga/blob/master/opencga-core/src/main/java/org/opencb/opencga/core/models/clinical/InterpretationInternal.java).
| Field | Description |
| ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | ----------- |
| status
InterpretationStatus
| |
### ProjectInternal
You can find the Java code [here](https://github.com/opencb/opencga/blob/master/opencga-core/src/main/java/org/opencb/opencga/core/models/project/ProjectInternal.java).
| Field | Description |
| ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ----------- |
| datastores
Datastores
| |
| cellbase
CellBaseConfiguration
| |
| status
Status
| |
### CohortInternal
You can find the Java code [here](https://github.com/opencb/opencga/blob/master/opencga-core/src/main/java/org/opencb/opencga/core/models/cohort/CohortInternal.java).
| Field | Description |
| -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ----------- |
| status
CohortStatus
| |
### ClinicalAnalysisInternal
You can find the Java code [here](https://github.com/opencb/opencga/blob/master/opencga-core/src/main/java/org/opencb/opencga/core/models/clinical/ClinicalAnalysisInternal.java).
| Field | Description |
| ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ----------- |
| status
ClinicalAnalysisStatus
| |
### UserInternal
You can find the Java code [here](https://github.com/opencb/opencga/blob/master/opencga-core/src/main/java/org/opencb/opencga/core/models/user/UserInternal.java).
| Field | Description |
| ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ----------- |
| status
UserStatus
| |
### StudyInternal
You can find the Java code [here](https://github.com/opencb/opencga/blob/master/opencga-core/src/main/java/org/opencb/opencga/core/models/study/StudyInternal.java).
| Field | Description |
| --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ----------- |
| status
Status
| |
| configuration
StudyConfiguration
| |
---
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