OpenCGA
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On this page
  • Overview
  • Summary
  • Data Model
  • Family
  • Status
  • FamilyInternal
  • Phenotype
  • FamilyQualityControl
  • Disorder
  • RelatednessReport
  • InternalStatus
  • ClinicalComment

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  1. Data Models

Family

Overview

Family data model hosts information about any family.

Summary

Field
Create
Update
Unique
Required

id

uuid

name

members

phenotypes

disorders

qualityControl

creationDate

modificationDate

expectedSize

description

status

internal

roles

attributes

release

version

Data Model

Family

Field
Description

id String

Family is a mandatory parameter when creating a new sample, this ID cannot be changed at the moment.

uuid String

Unique 32-character identifier assigned automatically by OpenCGA.

name String

Family name.

List of individuals who are family members.

List of phenotypes .

Family disorders.

Contains different metrics to evaluate the quality of the individual.

creationDate String since: 1.0

Autogenerated date following the format YYYYMMDDhhmmss containing the date when the entry was first registered.

modificationDate String since: 1.0

Autogenerated date following the format YYYYMMDDhhmmss containing the date when the entry was last modified.

expectedSize int

Family expected size.

description String

Users may provide a description for the entry.

Object to set a custom status.

Internal field for manage the object.

roles Map<String,Map<String,FamiliarRelationship>

Map of members ids and enum of roles (FATHER, MOTHER, IDENTICAL_TWIN, SON, UNCLE, PATERNAL_GRANDFATHER.) .

attributes Map<String,Object> since: 1.0

You can use this field to store any other information, keep in mind this is not indexed so you cannot search by attributes.

release int

An integer describing the current data release.

version int

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.

Status

FamilyInternal

Field
Description

Status of the internal object.

registrationDate String

Registration date of the internal object.

lastModified String

Date of the last modification of the internal object.

Phenotype

Field
Description

id String

Id to identify the object

ageOfOnset String

Indicates the age of on set of the phenotype

status Status

Status of phenotype OBSERVED, NOT_OBSERVED, UNKNOWN

name String

Object name

description String

Users may provide a description for the entry.

source String

Ontology source

url String

Ontology url

attributes Map<String,String>

Dictionary that can be customised by users to store any additional information users may require..

FamilyQualityControl

Field
Description

Reports of family relationship.

files List<String>

File IDs related to the quality control.

Comments related to the quality control.

Disorder

Field
Description

id String

Id to identify the object

name String

Object name

description String

Users may provide a description for the entry.

source String

Ontology source

url String

Ontology url

attributes Map<String,String>

Dictionary that can be customised by users to store any additional information users may require..

RelatednessReport

Field
Description

method String

Method of the relatedness report

maf String

Minor allele frequency to filter variants, e.g.: 1kg_phase3:CEU>0.35, cohort:ALL>0.05

scores List<RelatednessScore>

Relatedness scores for pair of samples

files List<String>

List of files of Relatedness Report

InternalStatus

ClinicalComment

Field
Description

author String

Clinical comment author

message String

Clinical comment message

tags List<String>

List of tags for the clinical comment

date String

Date of the clinical comment

PreviousIndividualNextCohort

Last updated 2 years ago

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You can find the Java code .

members List<>

phenotypes List<>

disorders List<>

qualityControl

status since: 2.0

internal since: 2.0

You can find the Java code .

You can find the Java code .

status

You can find the Java code .

You can find the Java code .

relatedness List<>

comments List<>

You can find the Java code .

You can find the Java code .

You can find the Java code .

You can find the Java code .

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Individual
Phenotype
Disorder
FamilyQualityControl
Status
FamilyInternal
InternalStatus
RelatednessReport
ClinicalComment