GA4GH Phenopacket Schema
The Global Alliance for Genomics and Health (GA4GH) is an organization developing a suite of coordinated standards for genomics.
The GA4GH Phenopacket is designed to be a computable representation of a case report
The GA4GH Phenopacket Schema is a standard for sharing disease and phenotype information characterizing an individual person or biosample. The Phenopacket Schema is flexible and can represent clinical data for any kind of human disease including RD, complex disease, and cancer. It also allows consortia or databases to apply additional constraints to ensure uniform data collection for specific goals. The Phenopacket Schema was accepted by the International Standards Organization (ISO) as ISO 4454:2022.
Structure of the Phenopacket Schema
Figure 1: Phenopacket Schema Overview
Phenopacket Schema overview. The GA4GH Phenopacket Schema is a hierarchical structure that consists of two required fields, id and MetaData, as well as eight optional fields:
- Individual & Disease
- Interpretation & Biosample
- PhenotypicFeature & Measurement
- MedicalAction & Files
Example: PhenotypicFeature
The PhenotypicFeature is the central element of the Phenopacket Schema. In essence, it contextualizes an HPO term by providing additional information.
A PhenotypicFeature can be used to describe each phenotypic feature (often, but not necessarily, clinical abnormalities) including signs and symptoms, laboratory findings, imaging, and electrophysiological results, along with modifier and qualifier concepts. Each phenotypic feature is described using an ontology term. One can indicate whether a certain abnormality was excluded during the diagnostic process (e.g., whether a morphological cardiac defect was excluded by echocardiography), or optionally use other HPO terms to denote the severity of the phenotypic feature or add other modifiers that describe the frequency (e.g., number of occurrences of seizures per week), laterality (e.g., unilateral), or another pattern of a certain phenotypic feature in the patient being described. Finally, the onset (and if applicable the resolution) of specific features can be indicated .
Figure 2: PhenotypeFeature
PhenotypeFeature overview. The PhenotypeFeature of the Phenopacket Schema has fields for specifying:
- type: An HPO term
- excluded: If this is set to true, it means that the HPO term was explicitly excluded by clinical examination or some other diagnostic modality.
- Severity Optionally, a term from the HPO Severity subontology can be added
- Modifier: Optionally, one or more terms from the HPO Clinical modifier
HP:0012823subontology can be added - Onset: The age at which the clinical manifestation represented by the HPO term first occured in the individual.
- Resolution: Optionally, the age at which the clinical manifestation resolved
Phenopackets Ecosystem
Figure 3: Phenopacket Ecosystem
Phenopacket Ecosystem. The Phenopacket Schema was developed as a rosetta stone that connects many different clinical data sources and provides a common reference point for analysis software:
- Providers: Different data entry tools can capture data from sources including EHRs, Patient-facing apps, text-mining, and clinical data entry apps
- Ingest methods: Software tools to transform data from sources (ETL)
- Use cases: support genomic diagnostics, stratification, natural history studies, treanslational bioinformatics, data exchange.
- Users: A range of users in academic and commercial settings