Databases were pre-generated for ease-of-use, sharing, and backwards compatibility when using older versions of pb-StarPhase. Though we will do our best to avoid breaking changes, database files are not guaranteed to work on versions that do not match. Additionally, these databases represent a snapshot in time of upstream data sources (e.g., CPIC, IMGTHLA, and PharmVar). Running the same command at a later date may produce a different database with updated annotations.
As of v0.12.0, each file is labeled as {version}/pbstarphase_{YYYYMMDD}.json.gz and represents a run of the following command using the specified {version} of pb-StarPhase on the corresponding date ({YYYYMMDD}):
pbstarphase build \
--output-db {version}/pbstarphase_{YYYYMMDD}.json.gzAll CPIC variants are sourced via the CPIC API.
As of this writing, versioning is not available via the API, so we instead tag the creation date in the database_metadata/cpic_version for all database files.
CPIC data is released under CC0 1.0 Universal (CC0 1.0) Public Domain Dedication license.
If you use the CPIC data within our database files, the authors and maintainers of CPIC ask that you follow their instructions for citing the relevant publications and resources: https://cpicpgx.org/license/.
All HLA sequences are sourced and unmodified from https://github.com/ANHIG/IMGTHLA.
The exact git tag version is stored in the database_metadata/hla_version for all database versions after v0.8.0.
If you use the HLA sequences within our database files, the authors and maintainers of IMGTHLA ask that you cite the following:
- Robinson J, Barker DJ, Georgiou X, Cooper MA, Flicek P, Marsh SGE: IPD-IMGT/HLA Database. Nucleic Acids Research (2020), 48:D948-55
- Robinson J, Malik A, Parham P, Bodmer JG, Marsh SGE: IMGT/HLA - a sequence database for the human major histocompatibility complex Tissue Antigens (2000), 55:280-287
For more details, see the IMGTHLA license file.
All CYP2D6 sequences are sourced and unmodified from PharmVar's "Download Gene Data" ZIP file on https://www.pharmvar.org/gene/CYP2D6.
The version is stored in the database_metadata/pharmvar_version for all database versions after v0.9.0.
PharmVar data is released under a Creative Commons Attribution-ShareAlike 4.0 International license license, see https://www.pharmvar.org/terms-and-conditions for more details.
If you use the CYP2D6 sequences within our database files, the authors and maintainers of PharmVar ask that you cite the relevant publications from their website: https://www.pharmvar.org/publications.