phenopacket store

This repository offers cohorts of GA4GH Phenopackets that represent individuals with Mendelian diseases.

Please see the online documentation for information about available cohorts.

Availability

Phenopacket store releases are available for download from the Releases section.

The latest release ZIP archive is available for download from a stable URL:

ZIP

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

Python support

We provide special support for Python with Phenopacket Store Toolkit to simplify using the Phenopacket Store data in the downstream applications.

The toolkit is available for installation from PyPi:

python3 -m pip install phenopacket-store-toolkit

The toolkit makes loading phenopackets super easy. First, we create Phenopacket Store registry, an object for managing local data files of Phenopacket Store releases:

from ppktstore.registry import configure_phenopacket_registry
registry = configure_phenopacket_registry()

By default, the registry keeps the files in data directory at $HOME/.phenopacket-store (or similar on Windows), but this can be configured if desired.

Then, we can use registry to load phenopackets of a cohort, e.g. SUOX of release 0.1.18:

with registry.open_phenopacket_store(release="0.1.18") as ps:
  phenopackets = list(ps.iter_cohort_phenopackets("SUOX"))
assert len(phenopackets) == 35

The registry peeks into the data directory to check if the 0.1.18 release ZIP file has already been downloaded. If absent, the registry will download the ZIP file from Github. Then, we open Phenopacket Store as ps and we load 35 phenopackets of SUOX cohort.

Contributing

The cohorts were curated from data medical publications, mainly by parsing the tables or supplemental tables. The curation was done in Jupyter notebooks using pyphetools library. Pull requests with additional notebooks in the same style are welcome.