Public bundle repository
The public bundle repository provides access to complete, published GKM bundles and their schemas. Each bundle contains the dataset its producer releases for that version. For small, focused subsets of a producer's actual data, see the bundle examples.
Downloads
Public repository
Download the files below, or access them programmatically through the
Python API. This table lists datasets
available through BundleRepository and is generated during the documentation
build.
| Resource | Bundle Schema Description | Bundle | Schema |
|---|---|---|---|
civic |
CIViC organizes curated cancer variant knowledge around variants and molecular profiles with evidence from source publications, summary assertions, and clinical context such as diseases, therapies, phenotypes, variant origins, and curating organizations. This schema describes a GA4GH GKM representation of those CIViC concepts. Top-level keys use CIViC knowledge model terms where possible, with additional keys for supporting GKM representation details. For the CIViC data model, see https://civic.readthedocs.io/en/latest/model.html. | Download (745.47 KB) | Download (17.91 KB) |
Dataset contributions
Support for contributing additional datasets to the public repository is planned. Contribution guidance will be published when the hosting and review process is ready.
Implementer-hosted data
These datasets are hosted by their implementers and are not currently available
through BundleRepository or its Python API. Follow each site's instructions to
download and use the data. Support for accessing implementer-hosted datasets is
planned for future versions of the toolkit.
| Resource | Description | Download site |
|---|---|---|
| ClinVar-GKM | ClinVar variation and clinical interpretation data represented with GKM standards. In addition to bundles, the official download site provides monthly full releases, weekly deltas, and typed Parquet files, with instructions for downloading and querying the data. | Explore ClinVar-GKM downloads |