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. |
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 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> | |
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 |
---|---|
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 | |
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> |
Last updated