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.

Data model

Definition of the Cohort element
Field Type Status Description
id string required arbitrary identifier
description string optional arbitrary text
members Phenopacket required Phenopackets that represent members of the cohort
hts_files HtsFile optional High-throughput sequencing files obtained from members of the cohort
meta_data MetaData required Metadata related to the ontologies and references used in this message

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.

hts_files

This element contains a list of pointers to the relevant HTS file(s) for the cohort. The HTS file MUST be a multi-sample file referring to the entire cohort, if appropriate. Individual HTS files MUST otherwise 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 genomic data derived from sequencing that biosample. Each element describes what type of file is meant (e.g., BAM file), which genome assembly was used for mapping, as well as a map of samples and individuals represented in that file. It also contains a URI element which refers to a file on a given file system or a resource on the web.

See HtsFile 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.