# Individual
## Overview
Created by jacobo on 11/09/14.
### Summary
| Field | create | update | unique | required |
| --------------------- | :------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | :------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | :------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | :------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: |
| id |  |  |  |  |
| name |  |  |  |  |
| father |  |  |  |  |
| mother |  |  |  |  |
| location |  |  |  |  |
| qualityControl |  |  |  |  |
| sex |  |  |  |  |
| karyotypicSex |  |  |  |  |
| ethnicity |  |  |  |  |
| population |  |  |  |  |
| dateOfBirth |  |  |  |  |
| lifeStatus |  |  |  |  |
| phenotypes |  |  |  |  |
| disorders |  |  |  |  |
| samples |  |  |  |  |
| parentalConsanguinity |  |  |  |  |
| status |  |  |  |  |
| internal |  |  |  |  |
| attributes |  |  |  |  |
| uuid |  |  |  |  |
| release |  |  |  |  |
| version |  |  |  |  |
| creationDate |  |  |  |  |
| modificationDate |  |  |  |  |
## Data Model
### 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. |
### 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. |
### IndividualQualityControl
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/IndividualQualityControl.java).
| Field | Description |
| ------------------------------------------------------------------------------------ | ------------------------------------------------------------------------------------ |
| sampleId
String
| Sample ID, only germinal sample and indexed |
| inferredSexReports
List<InferredSexReport>
| List of inferred sex reports, it depends on the method (currently by coverage ratio) |
| mendelianErrorReport
MendelianErrorReport
| Mendelian errors |
| fileIds
List<String>
| File IDs related to the quality control |
| comments
List<ClinicalComment>
| Comments related to the quality control |
### IndividualPopulation
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/IndividualPopulation.java).
| Field | Description |
| -------------------------------------------------------------- | ----------- |
| name
String
| |
| subpopulation
String
| |
| description
String
| |
### Location
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/Location.java).
| Field | Description |
| ----------------------------------------------------------- | ----------- |
| address
String
| |
| postalCode
String
| |
| city
String
| |
| state
String
| |
| country
String
| |
### 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
| |
### 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>
| |
### 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
| |
### 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
| |