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
| 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-thoughput 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.