The health of an individual organism results from a complex interplay between its genes and environment. Although great strides have been made in standardizing the representation of genetic information for exchange, there are no comparable standards to represent phenotypes (e.g. patient symptoms and disease features) and environmental factors. Phenotypic abnormalities of individual organisms are currently described in diverse places and in diverse formats: publications, databases, health records, registries, clinical trials, and even social media. However, the lack of standardization, accessibility, and computability among these contexts makes it extremely difficult to effectively extract and utilize these data, hindering the understanding of genetic and environmental contributions to disease.
See the Phenopackets.org site for the public-facing project documentation.
Or, see the detailed Markdown-based documentation via GitHub.
The Wiki has additional documentation, although it may be out-of-date.
- phenopacket-reference-implementation: Java Reference Implementation.
- phenopacket-python: Python Implementation.
- pxftools: Command-line Utility for manipulating PhenoPackets.
The PhenoPackets standard is still evolving, and there are many opportunities to help, including improving the expressivity of the format and providing implementations that enable.
The Issue Tracker is a good start.