Phenopackets Version 2.0

Monarch Initiative
2 min readFeb 18, 2022

New release of the Phenopackets standard captures a more complete medical picture

Illustration by GA4GH

The Global Alliance for Genomics and Health (GA4GH) Phenopacket standard provides a human- and machine-readable way to structure phenotypic data about a patient and share it across clinical and research environments to support translational research, diagnostics, and personalized healthcare. The Phenopacket standard is a product of the NIH-funded Phenomics First Center of Excellence, led by Melissa Haendel (CU Anschutz), Chris Mungall (LBNL) and Peter Robinson (Jackson Laboratory).

The Phenopacket standard has been in development for several years; v1 was approved by GA4GH in 2019. Phenopackets v1 focused on the rare disease use case; the newly approved Phenopacket schema v2.0 builds and expands on this, now enabling representation of cancer and common disease phenotypes as well. Three new elements in v2.0 help to capture a more complete medical picture:

  • The Measurements property captures quantitative or categorical measurements such as platelet count in a blood sample or body temperature.
  • The MedicalAction property captures medications, procedures, and other actions taken for clinical management, including cancer treatment.
  • The TimeElement property consolidates ways of expressing time or age, which can enable modeling of disease progression or response to therapeutic regimens.

These new elements were added in collaboration with community members. For example, the Measurements element was initially proposed by Núria Queralt Rosinach, a member of the European Joint Programme on Rare Diseases Driver Project and GA4GH and a researcher at Leiden University Medical Center, during a COVID-19 BioHackathon. To better capture cancer-relevant information, the Phenopackets team collaborated with ICGC-ARGO, which leverages genomics to accelerate cancer research, and mCODE, an initiative aiming to create a common cancer data model.

Phenopackets Version 2.0 is better aligned with other relevant standards such as the Fast Healthcare Interoperability Resource (FHIR) HL7 — a widely-adopted standard for exchanging electronic health records — as well as the GA4GH-developed Variation Representation Specification (VRS) and VRSATILE, which aim to standardize the exchange of genetic variation data.

More information:

Preprint: The GA4GH Phenopacket schema: A computable representation of clinical data for precision medicine

GA4GH press release: Phenopackets v2 expands utility to provide a more complete medical picture



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