# Sample ## Overview Sample data model hosts information about any biological material, normally extracted from an *Individual*, that is used for a particular analysis. This is the main data model, it stores the most basic and important information. ### Summary | Field | Create | Update | Unique | Required | | ---------------- | :-----------------------------------------------------------------------------------: | :-----------------------------------------------------------------------------------: | :-----------------------------------------------------------------------------------: | :-----------------------------------------------------------------------------------: | | id | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/yes.png?raw=true) | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/yes.png?raw=true) | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/yes.png?raw=true) | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/yes.png?raw=true) | | uuid | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/no.png?raw=true) | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/no.png?raw=true) | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/yes.png?raw=true) | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/no.png?raw=true) | | source | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/yes.png?raw=true) | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/yes.png?raw=true) | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/no.png?raw=true) | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/no.png?raw=true) | | processing | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/yes.png?raw=true) | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/yes.png?raw=true) | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/no.png?raw=true) | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/no.png?raw=true) | | collection | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/yes.png?raw=true) | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/yes.png?raw=true) | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/no.png?raw=true) | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/no.png?raw=true) | | qualityControl | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/yes.png?raw=true) | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/yes.png?raw=true) | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/no.png?raw=true) | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/no.png?raw=true) | | creationDate | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/yes.png?raw=true) | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/yes.png?raw=true) | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/no.png?raw=true) | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/no.png?raw=true) | | modificationDate | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/yes.png?raw=true) | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/yes.png?raw=true) | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/no.png?raw=true) | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/no.png?raw=true) | | description | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/yes.png?raw=true) | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/yes.png?raw=true) | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/no.png?raw=true) | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/no.png?raw=true) | | somatic | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/yes.png?raw=true) | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/yes.png?raw=true) | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/no.png?raw=true) | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/no.png?raw=true) | | phenotypes | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/yes.png?raw=true) | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/yes.png?raw=true) | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/no.png?raw=true) | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/no.png?raw=true) | | individualId | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/yes.png?raw=true) | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/yes.png?raw=true) | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/no.png?raw=true) | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/no.png?raw=true) | | fileIds | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/yes.png?raw=true) | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/yes.png?raw=true) | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/no.png?raw=true) | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/no.png?raw=true) | | cohortIds | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/yes.png?raw=true) | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/yes.png?raw=true) | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/no.png?raw=true) | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/no.png?raw=true) | | status | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/yes.png?raw=true) | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/yes.png?raw=true) | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/no.png?raw=true) | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/no.png?raw=true) | | attributes | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/yes.png?raw=true) | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/yes.png?raw=true) | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/no.png?raw=true) | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/no.png?raw=true) | | release | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/no.png?raw=true) | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/no.png?raw=true) | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/no.png?raw=true) | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/no.png?raw=true) | | version | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/no.png?raw=true) | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/no.png?raw=true) | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/no.png?raw=true) | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/no.png?raw=true) | | internal | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/no.png?raw=true) | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/no.png?raw=true) | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/no.png?raw=true) | ![](https://github.com/opencb/opencga/blob/develop/docs/data-models/no.png?raw=true) | ## Data Model ### Sample You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-1587/opencga-core/src/main/java/org/opencb/opencga/core/models/sample/Sample.java). | Field | Description | | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | |

id
String

| Sample data model hosts information about any biological material, normally extracted from an *Individual*, that is used for a particular analysis. This is the main data model, it stores the most basic and important information. | |

uuid
String

| Unique 32-character identifier assigned automatically by OpenCGA. | |

source
ExternalSource

since: 2.2

| The external source from where the example was imported. | |

processing
SampleProcessing

since: 2.0

| Describes how the sample was processed in the lab. | |

collection
SampleCollection

since: 2.0

| Describes how the sample was collected. | |

qualityControl
SampleQualityControl

since: 2.0

| Contains different metrics to evaluate the quality of the sample. | |

creationDate
String

since: 1.0

| Autogenerated date following the format YYYYMMDDhhmmss containing the date when the entry was first registered. | |

modificationDate
String

since: 1.0

| Autogenerated date following the format YYYYMMDDhhmmss containing the date when the entry was last modified. | |

description
String

| Users may provide a description for the entry. | |

somatic
boolean

| Describes if the sample is somatic or not . | |

phenotypes
List<Phenotype>

| List of phenotypes . | |

individualId
String

| Individual id of the sample. | |

fileIds
List\

| File ids of the sample. | |

cohortIds
List\

| Cohort ids of the sample. | |

status
Status

since: 2.0

| Cohort ids of the sample. | |

attributes
Map\

since: 1.0

| You can use this field to store any other information, keep in mind this is not indexed so you cannot search by attributes. | |

release
int

| An integer describing the current data release. | |

version
int

| Autoincremental version assigned to the registered entry. By default, updates does not create new versions. To enable versioning, users must set the `incVersion` flag from the /update web service when updating the document. | |

internal
SampleInternal

since: 2.0

| Sample internal information. | ### SampleCollection You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-1587/opencga-core/src/main/java/org/opencb/opencga/core/models/sample/SampleCollection.java). | Field | Description | | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------ | |

from
List<OntologyTermAnnotation>

| OntologyTermAnnotation list. | |

type
String

| Type of the sample collection. | |

quantity
String

| Quantity collected for the sample. | |

method
String

| Describes which method was used to collect the sample. | |

date
String

| Date when the sample was collected. | |

attributes
Map\

| Attributes of the sample collection. | ### Status You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/common/Status.java). ### SampleProcessing You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-1587/opencga-core/src/main/java/org/opencb/opencga/core/models/sample/SampleProcessing.java). | Field | Description | | -------------------------------------------------------------------------------------------------------------------------------------------------------------- | ----------------------------------------------------------------------------- | |

product
OntologyTermAnnotation

| Describes which product was used to process the sample in the lab. | |

preparationMethod
String

| Describes which preparation method was used to process the sample in the lab. | |

preparationMethod
String

| Describes which extraction method was used to process the samplein the lab. | |

labSampleId
String

| Original id has the sample in the lab. | |

quantity
String

| Number of process has done the sample. | |

date
String

| Date when the sample was processed in the lab. | |

attributes
Map\

| Attributes of the processing. | ### SampleInternal You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-1587/opencga-core/src/main/java/org/opencb/opencga/core/models/sample/SampleInternal.java). | Field | Description | | --------------------------------------------------------------------------------------------------------------------------------------------- | ----------------------------------------------------- | |

RgaIndex.rga
RgaIndex

| Rga index for Sample internal. | |

status
InternalStatus

| Status of the internal object. | |

registrationDate
String

| Registration date of the internal object. | |

lastModified
String

| Date of the last modification of the internal object. | ### SampleQualityControl You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-1587/opencga-core/src/main/java/org/opencb/opencga/core/models/sample/SampleQualityControl.java). | Field | Description | | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------- | |

files
List\

| Files used for the quality control of the sample. | |

comments
List<ClinicalComment>

| Comments for the quality control of the sample. | |

variant
SampleVariantQualityControlMetrics

| Describes variant quality control. | ### Phenotype You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/clinical/Phenotype.java). | Field | Description | | ---------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------- | |

id
String

| Id to identify the object | |

ageOfOnset
String

| Indicates the age of on set of the phenotype | |

status
Status

| Status of phenotype OBSERVED, NOT\_OBSERVED, UNKNOWN | |

name
String

| Object name | |

description
String

| Users may provide a description for the entry. | |

source
String

| Ontology source | |

url
String

| Ontology url | |

attributes
Map\

| Dictionary that can be customised by users to store any additional information users may require.. | ### ExternalSource You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-1587/opencga-core/src/main/java/org/opencb/opencga/core/models/common/ExternalSource.java). | Field | Description | | ---------------------------------------------------------- | --------------------- | |

id
String

| Source ID... | |

name
String

| Source name... | |

description
String

| Source description... | |

source
String

| Source ... | |

url
String

| Source ID | ### ClinicalComment You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/clinical/ClinicalComment.java). | Field | Description | | ---------------------------------------------------------- | ------------------------------------- | |

author
String

| Clinical comment author | |

message
String

| Clinical comment message | |

tags
List\

| List of tags for the clinical comment | |

date
String

| Date of the clinical comment | ### RgaIndex You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-1587/opencga-core/src/main/java/org/opencb/opencga/core/models/common/RgaIndex.java). | Field | Description | | ----------------------------------------------------- | ------------------------------------------------------------------------------------------------ | |

status
Status

| Status of the Rga index NOT\_INDEXED, INDEXED, INVALID\_PERMISSIONS, INVALID\_METADATA, INVALID. | |

date
String

| Date of Rga index. | ### InternalStatus You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-1587/opencga-core/src/main/java/org/opencb/opencga/core/models/common/InternalStatus.java). ### OntologyTermAnnotation You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/core/OntologyTermAnnotation.java). | Field | Description | | ---------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------- | |

id
String

| Id to identify the object | |

name
String

| Object name | |

description
String

| Users may provide a description for the entry. | |

source
String

| Ontology source | |

url
String

| Ontology url | |

attributes
Map\

| Dictionary that can be customised by users to store any additional information users may require.. | ### SampleVariantQualityControlMetrics You can find the Java code [here](https://github.com/opencb/opencga/tree/TASK-1587/opencga-core/src/main/java/org/opencb/opencga/core/models/sample/SampleVariantQualityControlMetrics.java). | Field | Description | | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------- | |

variantStats
List<SampleQcVariantStats>

| Variant stats for the quality control of the sample. | |

signatures
List<Signature>

| Signature for the quality control of the sample. | |

genomePlot
GenomePlot

| Genome plot for the quality control of the sample. | |

files
List\

| File for the quality control metrics of the sample. | ### GenomePlot You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/clinical/qc/GenomePlot.java). | Field | Description | | ------------------------------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------- | |

id
String

| Id to identify the object | |

description
String

| Users may provide a description for the entry. | |

config
GenomePlotConfig

| Config of the genomePlot | |

file
String

| File of the genomePlot | ### SampleQcVariantStats You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/clinical/qc/SampleQcVariantStats.java). | Field | Description | | ----------------------------------------------------------------- | ---------------------------------------------- | |

id
String

| Id to identify the object | |

description
String

| Users may provide a description for the entry. | |

query
Map\

| Map for query | |

stats
SampleVariantStats

| Stats result set | |

sampleId
String

| Stats result set | ### Signature You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/clinical/qc/Signature.java). | Field | Description | | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------- | |

id
String

| Id to identify the object | |

description
String

| Users may provide a description for the entry. | |

query
ObjectMap

| Map for query | |

type
String

| Signature type SNV, INDEL... | |

counts
List<GenomeContextCount>

| List of GenomeContextCount | |

files
List\

| List of files of signature | |

fitting
SignatureFitting

| Signature fitting | ### GenomePlotConfig You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/clinical/qc/GenomePlotConfig.java). | Field | Description | | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------- | |

title
String

| Title of the genome plot configuration | |

density
String

| Density of the genome plot configuration | |

generalQuery
Map\

| Map for the general query of the genome plot configuration | |

tracks
List<GenomePlotTrack>

| List of GenomePlotTrack | ### SignatureFitting You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/clinical/qc/SignatureFitting.java). | Field | Description | | --------------------------------------------------------------- | ------------------------------------------ | |

method
String

| Method used to fit the signature | |

signatureSource
String

| Source of the fitting signature | |

signatureVersion
String

| Signature version of the fitting signature | |

scores
List\

| Scores of the fitting signature | |

coeff
double

| Coefficient of the fitting signature | |

file
String

| Files of the fitting signature | ### GenomeContextCount You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/clinical/qc/Signature/GenomeContextCount.java). | Field | Description | | ------------------------------------------------------ | ----------------------- | |

context
String

| Genome context to count | |

total
int

| Counted integer | ### GenomePlotTrack You can find the Java code [here](https://github.com/opencb/biodata/tree/develop/biodata-models/src/main/java/org/opencb/biodata/models/clinical/qc/GenomePlotTrack.java). | Field | Description | | ----------------------------------------------------------------- | ------------------------------- | |

type
String

| Genome Plot Track Type | |

description
String

| Genome Plot Track description | |

query
Map\

| Genome Plot Track map for query |