Cohort

This element describes a group of individuals related in some phenotypic or genotypic aspect. For instance, a cohort can consist of individuals all of whom have been diagnosed with a certain disease or have been found to have a certain phenotypic feature.

We recommend using the Family element to describe families being investigated for the presence of a Mendelian disease.

The GA4GH is in the process of creating a Computable Cohort Working Group to define how a cohort is generated. It is the intention that the results of this definition should be collected into a Cohort message.

Data model

Definition of the Cohort element

Field	Type	Multiplicity	Description
id	string	1..1	An arbitrary identifier for the cohort. REQUIRED
description	string	0..1	text description of the cohort
members	Phenopacket	1..*	Phenopackets that represent members of the cohort. REQUIRED
files	File	0..*	list of files related to the whole cohort, e.g. multi-sample high-throughput sequencing files
meta_data	MetaData	1..1	Metadata related to the ontologies and references used in this message. REQUIRED

Explanations

id

The id is an identifier specific for this cohort. The syntax of the identifier is application specific.

description

Any information relevant to the study can be added here as free text.

members

One Phenopacket is included for each member of the cohort.

files

This element contains a list of pointers to relevant file(s) for the cohort. The file(s) MUST refer to the entire cohort. Otherwise individual files MUST be contained within their appropriate scope. e.g. within a Phenopacket for germline samples of an individual or within the scope of the Phenopacket.Biosample in the case of data derived from that biosample.

See File for further information.

meta_data

This element contains structured definitions of the resources and ontologies used within the phenopacket. It is expected that every valid Phenopacket contains a metaData element. See MetaData for further information.