Clinical Analysis
Overview
Created by pfurio on 05/06/17.
Summary
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.
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.
disorder Disorder
panelLock boolean
locked boolean
analyst ClinicalAnalyst
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
comments List<ClinicalComment>
audit List<ClinicalAudit>
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.
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
Formats: file, folder, index.
Formats: txt, executable, image, ...
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
sampleIds List<String>
jobId String
tags List<String>
stats Map<Object,String>
An object describing the status of the File.
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.
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.
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.
DNA
RNA
Enum FileExperiment.Technology
Enumeration class. You can find the Java code here.
SEQUENCING
MICROARRAY
CustomStatus
You can find the Java code here.
name String
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Tags: required, immutable
description String
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Tags: required
date String
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Tags: internal, unique, immutable
Enum File.Format
Enumeration class. You can find the Java code here.
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.
comments List<ClinicalComment>
AlignmentFileQualityControl
You can find the Java code here.
fastQcMetrics FastQcMetrics
samtoolsStats SamtoolsStats
samtoolsFlagStats SamtoolsFlagstats
hsMetrics HsMetrics
CoverageFileQualityControl
You can find the Java code here.
geneCoverageStats List<GeneCoverageStats>
VariantFileQualityControl
You can find the Java code here.
variantSetMetrics VariantSetStats
ascatMetrics AscatMetrics
FileRelatedFile
You can find the Java code here.
Enum FileRelatedFile.Relation
Enumeration class. You can find the Java code here.
PRODUCED_FROM
PART_OF_PAIR
PEDIGREE
REFERENCE_GENOME
Enum File.Type
Enumeration class. You can find the Java code here.
FILE
DIRECTORY
Enum File.Bioformat
Enumeration class. You can find the Java code here.
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.
sampleMap Map<String>
FileIndex
You can find the Java code here.
userId String
creationDate String
jobId long
release long
attributes Map<Object,String>
FileIndex.TransformedFile
You can find the Java code here.
id long
metadataId long
FileIndex.LocalFileIndex
You can find the Java code here.
fileId long
indexer String
FileIndex.IndexStatus
You can find the Java code here.
NONE String
TRANSFORMING String
TRANSFORMED String
LOADING String
INDEXING String
STATUS_LIST List>
FileStatus
You can find the Java code here.
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.
existing List<String>
nonExisting List<String>
Family
You can find the Java code here.
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
phenotypes List<Phenotype>
disorders List<Disorder>
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
An object describing the status of the Family.
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.
relatedness List<RelatednessReport>
fileIds List<String>
comments List<ClinicalComment>
Individual
You can find the Java code here.
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
familyIds List<String>
sex Sex
karyotypicSex KaryotypicSex
ethnicity String
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.
A List with related samples.
parentalConsanguinity boolean
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.
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.
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
Describes how the sample was processed in the lab.
Describes how the sample was collected.
Note: The sample collection is a list of samples
Contains different metrics to evaluate the quality of the sample.
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>
Generic: Object to define the status of the entry.
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.
tissue String
organ String
quantity String
method String
date String
attributes Map<Object,String>
SampleQualityControl
You can find the Java code here.
fileIds List<String>
comments List<ClinicalComment>
SampleVariantQualityControlMetrics
You can find the Java code here.
variantStats List<SampleQcVariantStats>
signatures List<Signature>
genomePlots List<GenomePlot>
SampleProcessing
You can find the Java code here.
product String
preparationMethod String
extractionMethod String
labSampleId String
quantity String
date String
attributes Map<Object,String>
SampleInternal
You can find the Java code here.
RgaIndex
You can find the Java code here.
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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.
NOT_INDEXED
INDEXED
INVALID_PERMISSIONS
INVALID_METADATA
INVALID
Location
You can find the Java code here.
address String
postalCode String
city String
state String
country String
IndividualPopulation
You can find the Java code here.
name String
subpopulation String
description String
IndividualInternal
You can find the Java code here.
FamilyInternal
You can find the Java code here.
FamilyStatus
You can find the Java code here.
INCOMPLETE String
STATUS_LIST List<String>
ClinicalAnalysisQualityControl
You can find the Java code here.
comments List<ClinicalComment>
Enum ClinicalAnalysisQualityControl.QualityControlSummary
Enumeration class. You can find the Java code here.
HIGH
MEDIUM
LOW
DISCARD
NEEDS_REVIEW
UNKNOWN
Enum ClinicalAnalysis.Type
Enumeration class. You can find the Java code here.
SINGLE
FAMILY
CANCER
COHORT
AUTOCOMPARATIVE
ClinicalConsentAnnotation
You can find the Java code here.
date String
ClinicalConsentParam
You can find the Java code here.
id String
name String
description String
Enum ClinicalConsentParam.Value
Enumeration class. You can find the Java code here.
YES
NO
UNKNOWN
FlagAnnotation
You can find the Java code here.
id String
description String
date String
ClinicalPriorityAnnotation
You can find the Java code here.
id String
description String
rank int
date String
Interpretation
You can find the Java code here.
studyUid long
uid long
release int
InterpretationStats
You can find the Java code here.
InterpretationFindingStats
You can find the Java code here.
numVariants int
tierCount Map<Integer,String>
variantStatusCount Map<Integer,ClinicalVariant.Status>
geneCount Map<Integer,String>
Panel
You can find the Java code here.
uuid String
release int
version int
OpenCGA version of this panel, this is incremented when the panel is updated.
author String
studyUid long
uid long
Status
You can find the Java code here.
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.
InterpretationStatus
You can find the Java code here.
NOT_REVIEWED String
UNDER_REVIEW String
REVIEWED String
REJECTED String
STATUS_LIST List<String>
ClinicalAnalysisInternal
You can find the Java code here.
ClinicalAnalysisStatus
You can find the Java code here.
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>
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