{"id":25359614,"url":"https://github.com/monarch-initiative/phenopacket-store","last_synced_at":"2025-10-04T11:29:11.298Z","repository":{"id":200702021,"uuid":"580002593","full_name":"monarch-initiative/phenopacket-store","owner":"monarch-initiative","description":"Collections of GA4GH phenopackets that represent individuals with Mendelian diseases.","archived":false,"fork":false,"pushed_at":"2025-10-03T06:31:20.000Z","size":35424,"stargazers_count":26,"open_issues_count":19,"forks_count":5,"subscribers_count":5,"default_branch":"main","last_synced_at":"2025-10-03T08:34:19.517Z","etag":null,"topics":["ga4gh","hpo","monarchinitiative","phenopackets"],"latest_commit_sha":null,"homepage":"https://monarch-initiative.github.io/phenopacket-store/","language":"Jupyter 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Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# phenopacket store\n\n[![DOI](https://zenodo.org/badge/580002593.svg)](https://zenodo.org/doi/10.5281/zenodo.13168726)\n\n\nThis repository offers cohorts of [GA4GH Phenopackets](https://phenopacket-schema.readthedocs.io/en/latest/) that\nrepresent individuals with Mendelian diseases,\nas described in [Danis *et al*, HGG Advances 2025](https://www.cell.com/hgg-advances/fulltext/S2666-2477(24)00111-8).\n\nPlease see the [online documentation](https://monarch-initiative.github.io/phenopacket-store) for information about available cohorts.\n\n## Availability\n\nPhenopacket store releases are available for download from the \n[Releases](https://github.com/monarch-initiative/phenopacket-store/releases) section.\n\nThe *latest* release ZIP archive is available for download from a stable URL:\n\n**ZIP**\n```\nhttps://github.com/monarch-initiative/phenopacket-store/releases/latest/download/all_phenopackets.zip\n```\n\n## Python support\n\nWe provide special support for Python with [Phenopacket Store Toolkit](https://github.com/monarch-initiative/phenopacket-store-toolkit)\nto simplify accessing the Phenopacket Store data in downstream applications.\n\nThe toolkit is available at [Python Package Index](https://pypi.org/project/phenopacket-store-toolkit/) (PyPi)\nand can be installed, e.g. with `pip`:\n\n```shell\npython3 -m pip install phenopacket-store-toolkit\n```\n\nAfter installation, loading phenopackets from Phenopacket Store is super easy.\nFirst, we create Phenopacket Store registry, an object for managing local data files\nof Phenopacket Store releases:\n\n```python\nfrom ppktstore.registry import configure_phenopacket_registry\nregistry = configure_phenopacket_registry()\n```\n\nBy default, the `registry` keeps the files in data directory at `$HOME/.phenopacket-store` (or similar on Windows), but this can be configured if desired.\n\nThen, we can use `registry` to load phenopackets of a cohort, e.g. *SUOX* of release `0.1.18`:\n\n```python\nwith registry.open_phenopacket_store(release=\"0.1.18\") as ps:\n  phenopackets = list(ps.iter_cohort_phenopackets(\"SUOX\"))\nassert len(phenopackets) == 35\n```\n\nThe registry peeks into the data directory to check if the `0.1.18` release ZIP file has already been downloaded.\nIf 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.\n\nMore info about Phenopacket Store Toolkit is available\nin its [documentation](https://monarch-initiative.github.io/phenopacket-store-toolkit/stable).\n\n\n## Contributing\n\nThe cohorts were curated from data medical publications, mainly by parsing the tables or supplemental tables. \nThe curation was done in Jupyter notebooks using [pyphetools](https://pypi.org/project/pyphetools/) library. \nPull requests with additional notebooks in the same style are welcome.\n\n\n## Citing Phenopacket Store\n\nIf you use Phenopacket Store in a scientific publication, we would appreciate citations to the following paper:\n\n[A corpus of GA4GH phenopackets: Case-level phenotyping for genomic diagnostics and discovery](https://www.cell.com/hgg-advances/fulltext/S2666-2477(24)00111-8), Danis et al., Human Genetics and Genomics Advances, Volume 6, Issue 1, 100371\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmonarch-initiative%2Fphenopacket-store","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmonarch-initiative%2Fphenopacket-store","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmonarch-initiative%2Fphenopacket-store/lists"}