Study
Overview
Created by jacobo on 11/09/14.
Summary
Field | create | update | unique | required |
id | ||||
name | ||||
alias | ||||
description | ||||
size | ||||
fqn | ||||
notification | ||||
groups | ||||
files | ||||
jobs | ||||
individuals | ||||
families | ||||
samples | ||||
cohorts | ||||
panels | ||||
clinicalAnalyses | ||||
variableSets | ||||
permissionRules | ||||
uri | ||||
release | ||||
status | ||||
attributes | ||||
uuid | ||||
creationDate | ||||
modificationDate | ||||
internal |
Data Model
Study
You can find the Java code here.
Field | Description |
id String | Study ID 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 study creation and cannot be changed.Tags: internal, unique, immutable |
name String | |
alias String | |
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 |
description String | An string to describe the properties of the sample. |
size long | |
fqn String | |
notification StudyNotification | |
groups List<Group> | A List with related groups. |
files List<File> | A List with related files. |
jobs List<Job> | A List with related jobs. |
individuals List<Individual> | A List with related individuals. |
families List<Family> | A List with related families. |
samples List<Sample> | A List with related samples. |
cohorts List<Cohort> | A List with related cohorts. |
panels List<org.opencb.opencga.core.models.panel.Panel> | A List with related panels. |
clinicalAnalyses List<ClinicalAnalysis> | A List with related clinicalAnalyses. |
variableSets List<VariableSet> | A List with related variableSets. |
permissionRules Map<ListPermissionRule,Enums.Entity> | |
uri URI | |
release int | |
status CustomStatus | An object describing the status of the Sample. |
internal StudyInternal | An object describing the internal information of the Sample. 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. |
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. |
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 | Global unique ID at the whole OpenCGA installation. This is automatically created during the sample creation and cannot be changed.Tags: internal, unique, immutable |
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</br>More info at: ZetaGenomics |
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 |
description String | An string to describe the properties of the sample. |
somatic boolean | Indicates if the sample is somatic or germline (default) |
phenotypes List<Phenotype> | A List with related phenotypes. |
individualId String | A reference to the Individual containing this sample. Notice that samples can exist without and Individual ID, this field is not mandatory..More info at: ZetaGenomics |
fileIds List<String> Deprecated | List of File ID containing this sample, eg BAM, VCF, QC images, ... |
status CustomStatus | An object describing the status of the Sample. |
internal SampleInternal | An object describing the internal information of the Sample. 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. |
VariableSet
You can find the Java code here.
Field | Description |
id String | |
name String | |
unique boolean | |
confidential boolean | |
internal boolean | |
description String | |
variables Set<Variable> | |
entities List<AnnotableDataModels> | |
release int | |
attributes Map<Object,String> |
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 | |
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. |
Group
You can find the Java code here.
Field | Description |
id String | Group id, unique in the belonging study. |
userIds List<String> | Set of users belonging to this group. |
syncedFrom Group.Sync | Group has been synchronised from an external authorization. |
Job
You can find the Java code here.
Field | Description |
id String | Job ID 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 sample creation and cannot be changed.Tags: internal, unique, immutable |
description String | An string to describe the properties of the Job. |
tool ToolInfo | |
userId String | |
commandLine String | |
params Map<Object,String> | |
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 |
priority Priority | |
internal JobInternal | An object describing the internal information of the Sample. This is managed by OpenCGA.Tags: internal |
outDir File | |
input List<File> | |
output List<File> | |
tags List<String> | |
dependsOn List<Job> | |
execution ExecutionResult | |
stdout File | |
stderr File | |
visited boolean | |
OPENCGA_PARENTS String | |
release int | An integer describing the current data release.Tags: internal |
study JobStudyParam | |
attributes Map<Object,String> |
Cohort
You can find the Java code here.
Field | Description |
id String | Cohort ID is a mandatory parameter when creating a new Cohort, 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 Cohort creation and cannot be changed.Tags: internal, unique, immutable |
type CohortType | |
creationDate String | String representing when the Cohort was created, this is automatically set by OpenCGA.Tags: internal |
modificationDate String | String representing when was the last time the Cohort was modified, this is automatically set by OpenCGA.Tags: internal |
description String | An string to describe the properties of the Cohort. |
samples List<Sample> | |
numSamples int | |
release int | An integer describing the current data release.Tags: internal |
status CustomStatus | An object describing the status of the Sample. |
internal CohortInternal | An object describing the internal information of the Sample. 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. |
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. |
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. |
SampleInternal
You can find the Java code here.
IndividualInternal
You can find the Java code here.
Field | Description |
status Status |
FamilyInternal
You can find the Java code here.
Field | Description |
status FamilyStatus |
FileInternal
You can find the Java code here.
Field | Description |
status FileStatus | |
index FileIndex | |
sampleMap Map<String> | |
missingSamples MissingSamples |
JobInternal
You can find the Java code here.
Field | Description |
status ExecutionStatus | |
webhook JobInternalWebhook | |
events List<Event> |
InterpretationInternal
You can find the Java code here.
Field | Description |
status InterpretationStatus |
ProjectInternal
You can find the Java code here.
Field | Description |
datastores Datastores | |
cellbase CellBaseConfiguration | |
status Status |
CohortInternal
You can find the Java code here.
Field | Description |
status CohortStatus |
ClinicalAnalysisInternal
You can find the Java code here.
Field | Description |
status ClinicalAnalysisStatus |
UserInternal
You can find the Java code here.
Field | Description |
status UserStatus |
StudyInternal
You can find the Java code here.
Field | Description |
status Status | |
configuration StudyConfiguration |
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