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.

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.

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.

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.

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.

Field	Description
DNA
RNA

Enum FileExperiment.Technology

Enumeration class. You can find the Java code here.

Field	Description
SEQUENCING
MICROARRAY

CustomStatus

You can find the Java code here.

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.

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.

Field	Description
variant VariantFileQualityControl
alignment AlignmentFileQualityControl
coverage CoverageFileQualityControl
comments List<ClinicalComment>

AlignmentFileQualityControl

You can find the Java code here.

Field	Description
fastQcMetrics FastQcMetrics
samtoolsStats SamtoolsStats
samtoolsFlagStats SamtoolsFlagstats
hsMetrics HsMetrics

CoverageFileQualityControl

You can find the Java code here.

Field	Description
geneCoverageStats List<GeneCoverageStats>

VariantFileQualityControl

You can find the Java code here.

Field	Description
variantSetMetrics VariantSetStats
ascatMetrics AscatMetrics

FileRelatedFile

You can find the Java code here.

Field	Description
file File
relation FileRelatedFile.Relation

Enum FileRelatedFile.Relation

Enumeration class. You can find the Java code here.

Field	Description
PRODUCED_FROM
PART_OF_PAIR
PEDIGREE
REFERENCE_GENOME

Enum File.Type

Enumeration class. You can find the Java code here.

Field	Description
FILE
DIRECTORY

Enum File.Bioformat

Enumeration class. You can find the Java code here.

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.

Field	Description
status FileStatus
index FileIndex
sampleMap Map<String>
missingSamples MissingSamples

FileIndex

You can find the Java code here.

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.

Field	Description
id long
metadataId long

FileIndex.LocalFileIndex

You can find the Java code here.

Field	Description
fileId long
indexer String

FileIndex.IndexStatus

You can find the Java code here.

Field	Description
NONE String
TRANSFORMING String
TRANSFORMED String
LOADING String
INDEXING String
STATUS_LIST List>

FileStatus

You can find the Java code here.

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.

Field	Description
existing List<String>
nonExisting List<String>

Family

You can find the Java code here.

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.

Field	Description
relatedness List<RelatednessReport>
fileIds List<String>
comments List<ClinicalComment>

Individual

You can find the Java code here.

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.

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.

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.

Field	Description
tissue String
organ String
quantity String
method String
date String
attributes Map<Object,String>

SampleQualityControl

You can find the Java code here.

Field	Description
fileIds List<String>
comments List<ClinicalComment>
variant SampleVariantQualityControlMetrics

SampleVariantQualityControlMetrics

You can find the Java code here.

Field	Description
variantStats List<SampleQcVariantStats>
signatures List<Signature>
genomePlots List<GenomePlot>

SampleProcessing

You can find the Java code here.

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.

Field	Description
rga RgaIndex

RgaIndex

You can find the Java code here.

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.

Field	Description
NOT_INDEXED
INDEXED
INVALID_PERMISSIONS
INVALID_METADATA
INVALID

Location

You can find the Java code here.

Field	Description
address String
postalCode String
city String
state String
country String

IndividualPopulation

You can find the Java code here.

Field	Description
name String
subpopulation String
description String

IndividualInternal

You can find the Java code here.

FamilyInternal

You can find the Java code here.

Field	Description
status FamilyStatus

FamilyStatus

You can find the Java code here.

Field	Description
INCOMPLETE String
STATUS_LIST List<String>

ClinicalAnalysisQualityControl

You can find the Java code here.

Field	Description
summary ClinicalAnalysisQualityControl.QualityControlSummary
comments List<ClinicalComment>

Enum ClinicalAnalysisQualityControl.QualityControlSummary

Enumeration class. You can find the Java code here.

Field	Description
HIGH
MEDIUM
LOW
DISCARD
NEEDS_REVIEW
UNKNOWN

Enum ClinicalAnalysis.Type

Enumeration class. You can find the Java code here.

Field	Description
SINGLE
FAMILY
CANCER
COHORT
AUTOCOMPARATIVE

ClinicalConsentAnnotation

You can find the Java code here.

Field	Description
consents List<ClinicalConsentParam>
date String

ClinicalConsentParam

You can find the Java code here.

Field	Description
id String
name String
description String
value ClinicalConsentParam.Value

Enum ClinicalConsentParam.Value

Enumeration class. You can find the Java code here.

Field	Description
YES
NO
UNKNOWN

FlagAnnotation

You can find the Java code here.

Field	Description
id String
description String
date String

ClinicalPriorityAnnotation

You can find the Java code here.

Field	Description
id String
description String
rank int
date String

Interpretation

You can find the Java code here.

Field	Description
studyUid long
uid long
panels List<Panel>
stats InterpretationStats
internal InterpretationInternal
release int

InterpretationStats

You can find the Java code here.

Field	Description
primaryFindings InterpretationFindingStats
secondaryFindings InterpretationFindingStats

InterpretationFindingStats

You can find the Java code here.

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.

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.

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.

Field	Description
status InterpretationStatus

InterpretationStatus

You can find the Java code here.

Field	Description
NOT_REVIEWED String
UNDER_REVIEW String
REVIEWED String
REJECTED String
STATUS_LIST List<String>

ClinicalAnalysisInternal

You can find the Java code here.

Field	Description
status ClinicalAnalysisStatus

ClinicalAnalysisStatus

You can find the Java code here.

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>