Individual
Overview
Created by jacobo on 11/09/14.
Summary
Field | create | update | unique | required |
id | ||||
name | ||||
father | ||||
mother | ||||
location | ||||
qualityControl | ||||
sex | ||||
karyotypicSex | ||||
ethnicity | ||||
population | ||||
dateOfBirth | ||||
lifeStatus | ||||
phenotypes | ||||
disorders | ||||
samples | ||||
parentalConsanguinity | ||||
status | ||||
internal | ||||
attributes | ||||
uuid | ||||
release | ||||
version | ||||
creationDate | ||||
modificationDate |
Data Model
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. |
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. |
IndividualQualityControl
You can find the Java code here.
Field | Description |
sampleId String | Sample ID, only germinal sample and indexed |
inferredSexReports List<InferredSexReport> | List of inferred sex reports, it depends on the method (currently by coverage ratio) |
mendelianErrorReport MendelianErrorReport | Mendelian errors |
fileIds List<String> | File IDs related to the quality control |
comments List<ClinicalComment> | Comments related to the quality control |
IndividualPopulation
You can find the Java code here.
Field | Description |
name String | |
subpopulation String | |
description String |
Location
You can find the Java code here.
Field | Description |
address String | |
postalCode String | |
city String | |
state String | |
country String |
SampleInternal
You can find the Java code here.
IndividualInternal
You can find the Java code here.
Field | Description |
status Status |
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> |
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 |
StudyInternal
You can find the Java code here.
Field | Description |
status Status | |
configuration StudyConfiguration |
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