# Clinical Analysis
## Overview
Created by pfurio on 05/06/17.
### Summary
| Field | Create | Update | Unique | Required |
| ------------------------ | :-----------------------------------------------------------------------------------: | :-----------------------------------------------------------------------------------: | :-----------------------------------------------------------------------------------: | :-----------------------------------------------------------------------------------: |
| id |  |  |  |  |
| description |  |  |  |  |
| type |  |  |  |  |
| disorder |  |  |  |  |
| files |  |  |  |  |
| proband |  |  |  |  |
| family |  |  |  |  |
| panels |  |  |  |  |
| panelLock |  |  |  |  |
| locked |  |  |  |  |
| interpretation |  |  |  |  |
| secondaryInterpretations |  |  |  |  |
| consent |  |  |  |  |
| analyst |  |  |  |  |
| priority |  |  |  |  |
| flags |  |  |  |  |
| dueDate |  |  |  |  |
| qualityControl |  |  |  |  |
| comments |  |  |  |  |
| audit |  |  |  |  |
| attributes |  |  |  |  |
| status |  |  |  |  |
| uuid |  |  |  |  |
| creationDate |  |  |  |  |
| modificationDate |  |  |  |  |
| release |  |  |  |  |
| internal |  |  |  |  |
## Data Model
### 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. |
### 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. |
### FileExperiment
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/FileExperiment.java).
| Field | Description |
| ---------------------------------------------------------------------------------------------------------------------------------------- | ----------- |
| technology
FileExperiment.Technology
| |
| method
FileExperiment.Method
| |
| nucleicAcidType
FileExperiment.NucleicAcidType
| |
| manufacturer
String
| |
| platform
String
| |
| library
String
| |
| date
String
| |
| center
String
| |
| lab
String
| |
| responsible
String
| |
| description
String
| |
| attributes
Map<Object,String>
| |
### Enum FileExperiment.Method
*Enumeration class.* 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/FileExperiment/Method.java).
| Field | Description |
| ----------------------------------------------------- | ----------- |
| WHOLE\_EXOME\_SEQUENCING
| |
| WHOLE\_GENOME\_SEQUENCING
| |
| TARGETED\_DNA\_SEQUENCING
| |
| AMPLICON\_SEQUENCING
| |
| GENOTYPING\_MICROARRAY
| |
### Enum FileExperiment.NucleicAcidType
*Enumeration class.* 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/FileExperiment/NucleicAcidType.java).
| Field | Description |
| ------------------------------- | ----------- |
| DNA
| |
| RNA
| |
### Enum FileExperiment.Technology
*Enumeration class.* 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/FileExperiment/Technology.java).
| Field | Description |
| -------------------------------------- | ----------- |
| SEQUENCING
| |
| MICROARRAY
| |
### CustomStatus
You can find the Java code [here](https://github.com/opencb/opencga/blob/master/opencga-core/src/main/java/org/opencb/opencga/core/models/common/CustomStatus.java).
| Field | Description |
| ---------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| name
String
| Lorem ipsum dolor sit amet, consectetur adipiscing elit. Sed vestibulum aliquet lobortis. Pellentesque venenatis lacus quis nibh
interdum finibus.
Tags: required, immutable
|
| description
String
| Proin aliquam ante in ligula tincidunt, cursus volutpat urna suscipit. Phasellus interdum, libero at posuere blandit, felis dui
dignissim leo, quis ullamcorper felis elit a augue.
Tags: required
|
| date
String
| Nullam commodo tortor nec lectus cursus finibus. Sed quis orci fringilla, cursus diam quis, vehicula sapien. Etiam bibendum dapibus
lectus, ut ultrices nunc vulputate ac.
Tags: internal, unique, immutable
|
### Enum File.Format
*Enumeration class.* 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/Format.java).
| Field | Description |
| ---------------------------------------------------- | ----------- |
| VCF
| |
| BCF
| |
| GVCF
| |
| TBI
| |
| BIGWIG
| |
| SAM
| |
| BAM
| |
| BAI
| |
| CRAM
| |
| CRAI
| |
| FASTQ
| |
| FASTA
| |
| PED
| |
| TAB\_SEPARATED\_VALUES
| |
| COMMA\_SEPARATED\_VALUES
| |
| XML
| |
| PROTOCOL\_BUFFER
| |
| JSON
| |
| AVRO
| |
| PARQUET
| |
| IMAGE
| |
| PLAIN
| |
| BINARY
| |
| NONE
| |
| UNKNOWN
| |
### FileQualityControl
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/FileQualityControl.java).
| Field | Description |
| ------------------------------------------------------------------------------------------------------------------------ | ----------- |
| variant
VariantFileQualityControl
| |
| alignment
AlignmentFileQualityControl
| |
| coverage
CoverageFileQualityControl
| |
| comments
List<ClinicalComment>
| |
### AlignmentFileQualityControl
You can find the Java code [here](https://github.com/opencb/opencga/blob/master/opencga-core/src/main/java/org/opencb/opencga/core/models/alignment/AlignmentFileQualityControl.java).
| Field | Description |
| --------------------------------------------------------------------------- | ----------- |
| fastQcMetrics
FastQcMetrics
| |
| samtoolsStats
SamtoolsStats
| |
| samtoolsFlagStats
SamtoolsFlagstats
| |
| hsMetrics
HsMetrics
| |
### CoverageFileQualityControl
You can find the Java code [here](https://github.com/opencb/opencga/blob/master/opencga-core/src/main/java/org/opencb/opencga/core/models/alignment/CoverageFileQualityControl.java).
| Field | Description |
| --------------------------------------------------------------------------------- | ----------- |
| geneCoverageStats
List<GeneCoverageStats>
| |
### VariantFileQualityControl
You can find the Java code [here](https://github.com/opencb/opencga/blob/master/opencga-core/src/main/java/org/opencb/opencga/core/models/variant/VariantFileQualityControl.java).
| Field | Description |
| ------------------------------------------------------------------------- | ----------- |
| variantSetMetrics
VariantSetStats
| |
| ascatMetrics
AscatMetrics
| |
### FileRelatedFile
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/FileRelatedFile.java).
| Field | Description |
| --------------------------------------------------------------------------------------------------------------------- | ----------- |
| file
File
| |
| relation
FileRelatedFile.Relation
| |
### Enum FileRelatedFile.Relation
*Enumeration class.* 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/FileRelatedFile/Relation.java).
| Field | Description |
| --------------------------------------------- | ----------- |
| PRODUCED\_FROM
| |
| PART\_OF\_PAIR
| |
| PEDIGREE
| |
| REFERENCE\_GENOME
| |
### Enum File.Type
*Enumeration class.* 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/Type.java).
| Field | Description |
| ------------------------------------- | ----------- |
| FILE
| |
| DIRECTORY
| |
### Enum File.Bioformat
*Enumeration class.* 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/Bioformat.java).
| Field | Description |
| -------------------------------------------------------------------------- | ----------- |
| MICROARRAY\_EXPRESSION\_ONECHANNEL\_AGILENT
| |
| MICROARRAY\_EXPRESSION\_ONECHANNEL\_AFFYMETRIX
| |
| MICROARRAY\_EXPRESSION\_ONECHANNEL\_GENEPIX
| |
| MICROARRAY\_EXPRESSION\_TWOCHANNELS\_AGILENT
| |
| MICROARRAY\_EXPRESSION\_TWOCHANNELS\_GENEPIX
| |
| DATAMATRIX\_EXPRESSION
| |
| IDLIST
| |
| IDLIST\_RANKED
| |
| ANNOTATION\_GENEVSANNOTATION
| |
| OTHER\_NEWICK
| |
| OTHER\_BLAST
| |
| OTHER\_INTERACTION
| |
| OTHER\_GENOTYPE
| |
| OTHER\_PLINK
| |
| OTHER\_VCF
| |
| OTHER\_PED
| |
| VCF4
| |
| VARIANT
| |
| ALIGNMENT
| |
| COVERAGE
| |
| SEQUENCE
| |
| PEDIGREE
| |
| REFERENCE\_GENOME
| |
| NONE
| |
| UNKNOWN
| |
### 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
| |
### FileIndex
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/FileIndex.java).
| Field | Description |
| ------------------------------------------------------------------------------------------------------------------------- | ----------- |
| userId
String
| |
| creationDate
String
| |
| status
FileIndex.IndexStatus
| |
| jobId
long
| |
| release
long
| |
| transformedFile
FileIndex.TransformedFile
| |
| localFileIndex
FileIndex.LocalFileIndex
| |
| attributes
Map<Object,String>
| |
### FileIndex.TransformedFile
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/FileIndex/TransformedFile.java).
| Field | Description |
| ------------------------------------------------------- | ----------- |
| id
long
| |
| metadataId
long
| |
### FileIndex.LocalFileIndex
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/FileIndex/LocalFileIndex.java).
| Field | Description |
| ------------------------------------------------------ | ----------- |
| fileId
long
| |
| indexer
String
| |
### FileIndex.IndexStatus
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/FileIndex/IndexStatus.java).
| Field | Description |
| ----------------------------------------------------------- | ----------- |
| NONE
String
| |
| TRANSFORMING
String
| |
| TRANSFORMED
String
| |
| LOADING
String
| |
| INDEXING
String
| |
| STATUS\_LIST
List>
| |
### FileStatus
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/FileStatus.java).
| Field | Description |
| ----------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------- |
| TRASHED
String
| TRASHED name means that the object is marked as deleted although is still available in the database. |
| STAGE
String
| |
| MISSING
String
| |
| PENDING\_DELETE
String
| |
| DELETING
String
| |
| REMOVED
String
| |
| MISSING\_SAMPLES
String
| |
| STATUS\_LIST
List<String>
| |
### MissingSamples
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/MissingSamples.java).
| Field | Description |
| ---------------------------------------------------------------- | ----------- |
| existing
List<String>
| |
| nonExisting
List<String>
| |
### 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. |
### FamilyQualityControl
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/FamilyQualityControl.java).
| Field | Description |
| --------------------------------------------------------------------------- | ----------- |
| relatedness
List<RelatednessReport>
| |
| fileIds
List<String>
| |
| comments
List<ClinicalComment>
| |
### 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
| |
| familyIds
List<String>
| |
| 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. |
### 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 |
| ---------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------ |
| inferredSexReports
List<InferredSexReport>
| List of inferred sex reports, it depends on the method (currently by coverage ratio) |
| sampleRelatednessReport
SampleRelatednessReport
| |
| mendelianErrorReports
List<MendelianErrorReport>
| Mendelian errors |
| fileIds
List<String>
| File IDs related to the quality control |
| comments
List<ClinicalComment>
| Comments related to the quality control |
### 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
| Generic: Unique 32-character identifier assigned automatically by OpenCGA.
Tags: immutable, unique
|
| 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
|
| release
int
| An integer describing the current data release.
Tags: immutable
|
| version
int
| Generic: 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.
Tags: immutable
|
| creationDate
String
| Generic: Autogenerated date following the format YYYYMMDDhhmmss containing the date when the entry was first registered.
Tags: immutable
|
| modificationDate
String
| Generic: Autogenerated date following the format YYYYMMDDhhmmss containing the date when the entry was last modified.
Tags: immutable
|
| description
String
| Generic: Users may provide a description for the entry. |
| somatic
boolean
| Indicates if the sample is somatic or germline (default) |
| phenotypes
List<Phenotype>
| |
| individualId
String
| |
| fileIds
List<String>
| |
| cohortIds
List<String>
| |
| status
CustomStatus
| Generic: Object to define the status of the entry. |
| internal
SampleInternal
| Generic: Field automatically managed by OpenCGA containing relevant information of the entry. This field is used for internal
purposes and is visible for users.
Tags: immutable
|
| attributes
Map<Object,String>
| Dictionary that can be customised by users to store any additional information users may require.
Note: This field is not meant to be queried. It should only contain extra information. To store additional information meant to
be queried, please use annotationSets.
|
### SampleCollection
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/SampleCollection.java).
| Field | Description |
| ------------------------------------------------------------------------------ | ----------- |
| tissue
String
| |
| organ
String
| |
| quantity
String
| |
| method
String
| |
| date
String
| |
| attributes
Map<Object,String>
| |
### SampleQualityControl
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/SampleQualityControl.java).
| Field | Description |
| ------------------------------------------------------------------------------------------------------------------------------------ | ----------- |
| fileIds
List<String>
| |
| comments
List<ClinicalComment>
| |
| variant
SampleVariantQualityControlMetrics
| |
### SampleVariantQualityControlMetrics
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/SampleVariantQualityControlMetrics.java).
| Field | Description |
| ------------------------------------------------------------------------------- | ----------- |
| variantStats
List<SampleQcVariantStats>
| |
| signatures
List<Signature>
| |
| genomePlots
List<GenomePlot>
| |
### SampleProcessing
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/SampleProcessing.java).
| Field | Description |
| ------------------------------------------------------------------------------ | ----------- |
| product
String
| |
| preparationMethod
String
| |
| extractionMethod
String
| |
| labSampleId
String
| |
| quantity
String
| |
| date
String
| |
| attributes
Map<Object,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 |
| ---------------------------------------------------------------------------- | ----------- |
| rga
RgaIndex
| |
### RgaIndex
You can find the Java code [here](https://github.com/opencb/opencga/blob/master/opencga-core/src/main/java/org/opencb/opencga/core/models/common/RgaIndex.java).
| Field | Description |
| ------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| status
RgaIndex.Status
| Nullam commodo tortor nec lectus cursus finibus. Sed quis orci fringilla, cursus diam quis, vehicula sapien. Etiam bibendum dapibus
lectus, ut ultrices nunc vulputate ac.
Tags: internal, unique, immutable
|
| date
String
| Nullam commodo tortor nec lectus cursus finibus. Sed quis orci fringilla, cursus diam quis, vehicula sapien. Etiam bibendum dapibus
lectus, ut ultrices nunc vulputate ac.
Tags: internal, unique, immutable
|
### Enum RgaIndex.Status
*Enumeration class.* You can find the Java code [here](https://github.com/opencb/opencga/blob/master/opencga-core/src/main/java/org/opencb/opencga/core/models/common/RgaIndex/Status.java).
| Field | Description |
| ------------------------------------------------ | ----------- |
| NOT\_INDEXED
| |
| INDEXED
| |
| INVALID\_PERMISSIONS
| |
| INVALID\_METADATA
| |
| INVALID
| |
### 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
| |
### 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
| |
### 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).
### 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
| |
### FamilyStatus
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/FamilyStatus.java).
| Field | Description |
| ----------------------------------------------------------------- | ----------- |
| INCOMPLETE
String
| |
| STATUS\_LIST
List<String>
| |
### ClinicalAnalysisQualityControl
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/ClinicalAnalysisQualityControl.java).
| Field | Description |
| ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ----------- |
| summary
ClinicalAnalysisQualityControl.QualityControlSummary
| |
| comments
List<ClinicalComment>
| |
### Enum ClinicalAnalysisQualityControl.QualityControlSummary
*Enumeration class.* 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/ClinicalAnalysisQualityControl/QualityControlSummary.java).
| Field | Description |
| ----------------------------------------- | ----------- |
| HIGH
| |
| MEDIUM
| |
| LOW
| |
| DISCARD
| |
| NEEDS\_REVIEW
| |
| UNKNOWN
| |
### Enum ClinicalAnalysis.Type
*Enumeration class.* 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/Type.java).
| Field | Description |
| ------------------------------------------- | ----------- |
| SINGLE
| |
| FAMILY
| |
| CANCER
| |
| COHORT
| |
| AUTOCOMPARATIVE
| |
### ClinicalConsentAnnotation
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/configuration/ClinicalConsentAnnotation.java).
| Field | Description |
| --------------------------------------------------------------------------------------------------------------- | ----------- |
| consents
List<ClinicalConsentParam>
| |
| date
String
| |
### ClinicalConsentParam
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/configuration/ClinicalConsentParam.java).
| Field | Description |
| ---------------------------------------------------------------------------------------------------------------------- | ----------- |
| id
String
| |
| name
String
| |
| description
String
| |
| value
ClinicalConsentParam.Value
| |
### Enum ClinicalConsentParam.Value
*Enumeration class.* 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/configuration/ClinicalConsentParam/Value.java).
| Field | Description |
| ----------------------------------- | ----------- |
| YES
| |
| NO
| |
| UNKNOWN
| |
### FlagAnnotation
You can find the Java code [here](https://github.com/opencb/opencga/blob/master/opencga-core/src/main/java/org/opencb/opencga/core/models/common/FlagAnnotation.java).
| Field | Description |
| ---------------------------------------------------------- | ----------- |
| id
String
| |
| description
String
| |
| date
String
| |
### ClinicalPriorityAnnotation
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/configuration/ClinicalPriorityAnnotation.java).
| Field | Description |
| ---------------------------------------------------------- | ----------- |
| id
String
| |
| description
String
| |
| rank
int
| |
| date
String
| |
### Interpretation
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/Interpretation.java).
| Field | Description |
| ------------------------------------------------------------------------------------------------------------- | ----------- |
| studyUid
long
| |
| uid
long
| |
| panels
List<Panel>
| |
| stats
InterpretationStats
| |
| internal
InterpretationInternal
| |
| release
int
| |
### InterpretationStats
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/InterpretationStats.java).
| Field | Description |
| ------------------------------------------------------------------------------------------------------------------------------ | ----------- |
| primaryFindings
InterpretationFindingStats
| |
| secondaryFindings
InterpretationFindingStats
| |
### InterpretationFindingStats
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/InterpretationFindingStats.java).
| Field | Description |
| ------------------------------------------------------------------------------------------------------- | ----------- |
| numVariants
int
| |
| tierCount
Map<Integer,String>
| |
| variantStatusCount
Map<Integer,ClinicalVariant.Status>
| |
| geneCount
Map<Integer,String>
| |
### Panel
You can find the Java code [here](https://github.com/opencb/opencga/blob/master/opencga-core/src/main/java/org/opencb/opencga/core/models/panel/Panel.java).
| Field | Description |
| --------------------------------------------------------------------------- | ----------------------------------------------------------------------------- |
| uuid
String
| |
| release
int
| |
| version
int
| OpenCGA version of this panel, this is incremented when the panel is updated. |
| author
String
| |
| status
Status
| |
| studyUid
long
| |
| uid
long
| |
### Status
You can find the Java code [here](https://github.com/opencb/opencga/blob/master/opencga-core/src/main/java/org/opencb/opencga/core/models/common/Status.java).
| Field | Description |
| ----------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------- |
| name
String
| |
| date
String
| |
| description
String
| |
| message
String
| |
| READY
String
| READY name means that the object is being used. |
| DELETED
String
| DELETED name means that the object is marked as removed, so it can be completely removed from the database with a clean action. |
| STATUS\_LIST
List<String>
| |
### 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
| |
### InterpretationStatus
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/InterpretationStatus.java).
| Field | Description |
| ----------------------------------------------------------------- | ----------- |
| NOT\_REVIEWED
String
| |
| UNDER\_REVIEW
String
| |
| REVIEWED
String
| |
| REJECTED
String
| |
| STATUS\_LIST
List<String>
| |
### 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
| |
### ClinicalAnalysisStatus
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/ClinicalAnalysisStatus.java).
| Field | Description |
| ----------------------------------------------------------------------------------- | ----------- |
| INCOMPLETE
String
| |
| READY\_FOR\_VALIDATION
String
| |
| READY\_FOR\_INTERPRETATION
String
| |
| INTERPRETATION\_IN\_PROGRESS
String
| |
| READY\_FOR\_INTEPRETATION\_REVIEW
String
| |
| INTERPRETATION\_REVIEW\_IN\_PROGRESS
String
| |
| READY\_FOR\_REPORT
String
| |
| REPORT\_IN\_PROGRESS
String
| |
| DONE
String
| |
| REVIEW\_IN\_PROGRESS
String
| |
| CLOSED
String
| |
| REJECTED
String
| |
| STATUS\_LIST
List<String>
| |