# 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 | --- # Agent Instructions: Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter: ``` GET https://docs.opencga.opencb.org/develop-2/data-models/sample.md?ask= ``` The question should be specific, self-contained, and written in natural language. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.