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pkpdbib

pkpdbib logo

pkpdbib is a collection of python utilities for working with pharmacokinetics/pharmacodynamics (PK/PD) literature and bibliographies. It supports the curation of the literature of PK-DB and of the PK/PD models built on it.

Features include

  • PDF retrieval - the PDFs of the DOIs of a Zotero export (Better BibTeX JSON), via the scihub_pdfs command
  • Zotero libraries - programmatic access to a Zotero library and a table of the tags of its items

The source code is available from github.com/matthiaskoenig/pkpdbib. If you have any questions or issues please open an issue.

Quickstart

pip install pkpdbib
scidownl domain.update
scihub_pdfs -j aliskiren.json

See Installation and PDF retrieval for the details.

How to cite

DOI

If you use pkpdbib please cite the archived software on Zenodo. The DOI always resolves to the latest version, the current release is archived as:

König, M. (2026). pkpdbib: python utilities for PK/PD literature and bibliography management (Version 0.2.1) [Computer software]. Zenodo. https://doi.org/10.5281/zenodo.23154802

@software{konig_pkpdbib,
  author    = {König, Matthias},
  title     = {pkpdbib: python utilities for PK/PD literature and bibliography management},
  year      = {2026},
  month     = oct,
  version   = {0.2.1},
  publisher = {Zenodo},
  doi       = {10.5281/zenodo.23154802},
  url       = {https://doi.org/10.5281/zenodo.23154802},
}

The citation metadata is in CITATION.cff.

License

Funding

Matthias König is supported by the German Research Foundation (DFG) within the Research Unit Programme FOR 5151 "QuaLiPerF (Quantifying Liver Perfusion-Function Relationship in Complex Resection - A Systems Medicine Approach)" by grant number 436883643 and by grant number 465194077 (Priority Programme SPP 2311, Subproject SimLivA).

Matthias König was supported by the Federal Ministry of Education and Research (BMBF, Germany) within the research network Systems Medicine of the Liver (LiSyM, grant number 031L0054) and within ATLAS by grant number 031L0304B.