GA4GH Phenopacket standard accepted by ISO
A stamp of approval from the International Organization for Standardization (ISO) means your standard has made the big time — and that’s what happened to the Phenopacket standard in July, when it was published by ISO as “ISO 4454 Genomics informatics — Phenopackets: A format for phenotypic data exchange.”
(If you just clicked that link and are shocked that ISO wants CHF 198 — about $205 USD — for the complete text of the standard, don’t panic; the Phenopacket schema is still available openly and free of cost on GitHub.)
The Phenopacket team is co-led by Peter Robinson, a professor of genomics and computational biology at the Jackson Laboratory, and Melissa Haendel, the Chief Research Informatics Officer at the UC Colorado Anschutz Medical Center. Julius O. B. Jacobsen, a senior software developer at Queen Mary University of London, is the chief architect.
Phenopacket’s journey to ISO approval started in 2019, when it was formally approved by The Global Alliance for Genomics and Health (GA4GH), which creates frameworks and standards to enable the responsible, voluntary, and secure sharing of genomic and health-related data. GA4GH supported the development of the Phenopacket standard as a much-needed approach to storing and sharing phenotypic data in standardized formats that can be parsed by humans and machines. Phenopackets are quickly becoming the preferred way to capture clinical data and integrate it with genomic data to help enable precision medicine.
In an August 2 press release, GA4GH reported that ISO experts in Japan, India, Canada, the U.S., and Korea reviewed the Phenopacket standard to ensure that it would work in diverse healthcare systems. “In Japan, a network of 14 major biobanks has implemented Phenopackets, with 920,000 samples and 250,000 genomic and omics data provided by 490,000 individuals,” said Soichi Ogishima, a professor of genomic informatics at Tohoku University and a member of the ISO team that reviewed Phenopackets.
“We finally have the very first standard for phenotype data available worldwide,” said Prof. Haendel in the GA4GH announcement. “Having this ISO standard will encourage software developers, infrastructure developers, healthcare systems to consider Phenopackets as a method for sharing patient-level information — securely and in a deidentified way — that can be useful for everything from rare to infectious diseases, and addressing many kinds of public health questions.”
ISO publication will accelerate the growing international acceptance of the Phenopacket standard. In addition to Japanese biobanks, databases such as BioSamples have already implemented Phenopackets. Electronic health record (EHR) vendors and national health systems are considering adopting it. “Many journals in human genetics are willing to consider cajoling or requiring authors to submit Phenopackets together with case reports,” said Dr. Robinson. Additionally, there is work in progress to extend Phenopackets to a standard for sharing complete EHRs, such as Fast Healthcare Interoperability Resources (FHIR) by the Health Level 7 (HL7) organization.
GenomeWeb reported that EHR vendors are enthusiastic about the development of Phenopackets. “I think it’s a huge step forward,” said a product manager for laboratory information systems and genomics at a prominent EHR vendor interviewed by GenomeWeb. “It really is one of the few ways that we’re ever going to be able to come up with standards necessary to do clinical decision [support] in rare diseases, which is minimal right now.”
- ISO 4454:2022: Genomics informatics — Phenopackets: A format for phenotypic data exchange: https://www.iso.org/standard/79991.html
- Press release: First GA4GH standard published by ISO will reshape how doctors and researchers share phenotypic information: https://www.ga4gh.org/news/first-ga4gh-standard-published-by-iso-will-reshape-how-doctors-and-researchers-share-phenotypic-information/
- GenomeWeb article: ISO Endorsement of Phenopackets Promises to Address Disease Interpretation From EHRs: https://www.genomeweb.com/advances-spatial-genomics/iso-endorsement-phenopackets-promises-address-disease-interpretation-ehrs
- Jacobsen, J.O.B., Baudis, M., Baynam, G.S. et al. The GA4GH Phenopacket schema defines a computable representation of clinical data. Nat. Biotechnol 40, 817–820 (2022). https://doi.org/10.1038/s41587-022-01357-4