Phenopacket Schema

The goal of the phenopacket-schema is to define a machine-readable phenotypic description of a patient/sample in the context of rare disease, common/complex disease, or cancer. It aims to provide sufficient and shareable information of the data outside of the EHR (Electronic Health Record) with the aim of enabling capturing of sufficient structured data at the point of care by a clinician or clinical geneticist for sharing with other labs or computational analysis of the data in clinical or research environments.

This work has been produced as part of the GA4GH Clinical Phenotype Data Capture Workstream and is designed to be compatible with GA4GH metadata-schemas.

The phenopacket schema defines a common, limited set of data types which may be composed into more specialised types for data sharing between resources using an agreed upon common schema.

This common schema has been used to define the ‘Phenopacket’ which is a catch-all collection of data types, specifically focused on representing disease data both initial data capture and analysis. The phenopacket schema is designed to be both human and machine-readable, and to inter-operate with standards being developed in organizations such as in the ISO TC215 committee and the HL7 Fast Healthcare Interoperability Resources Specification (aka FHIR®).


The diagram below shows an overview of the schema elements.


The schema is defined in protobuf. You can find out more in the section ‘A short introduction to protobuf’.