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Phenopacket Store

This repository contains a collection of Jupyter notebooks that generate GA4GH phenopackets. for analysis projects. The phenopackets represent case reports about individuals with Mendelian diseases.

A publication describing the case report curation methodology as well as the best practices for future curation is available at Danis et al., HGG Advances 2025

The notebooks are contained in the notebooks folder organized according to an affected gene.

Summary statistics

See Collections for a short documentation page for each case report collection included in this repository. The summary statistics for the entire phenopacket store as well as with Q/C checks can be seen in PhenopacketStoreStats notebook.

Availability

All case report collections are periodically released in a ZIP archive, which is available for download from the Releases section.

Versioned release

A specific Phenopacket store version can also be accessed programmatically. Just replace the VERSION placeholder with a release tag from the Releases section:

https://github.com/monarch-initiative/phenopacket-store/releases/download/VERSION/all_phenopackets.zip

For instance: 

https://github.com/monarch-initiative/phenopacket-store/releases/download/0.1.16/all_phenopackets.zip
for the 0.1.16 version.

Latest release

The latest release is also available for download programmatically:

ZIP

Download the latest ZIP archive with wget: 

wget https://github.com/monarch-initiative/phenopacket-store/releases/latest/download/all_phenopackets.zip

or with curl: 

curl -Lo all_phenopackets.zip https://github.com/monarch-initiative/phenopacket-store/releases/latest/download/all_phenopackets.zip

Citing Phenopacket Store

If you use Phenopacket Store in a scientific publication, we would appreciate citations to the following paper:

A corpus of GA4GH phenopackets: Case-level phenotyping for genomic diagnostics and discovery, Danis et al., Human Genetics and Genomics Advances, Volume 6, Issue 1, 100371

Feedback

The best place to leave feedback, ask questions, and report bugs is the GitHub Issue Tracker.