pkpdbib: python utilities for PK/PD literature

pkpdbib is a collection of python utilities for working with pharmacokinetics/pharmacodynamics (PK/PD) literature and bibliographies.

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 (optional zotero extra)

The documentation is available at https://matthiaskoenig.github.io/pkpdbib.

If you have any questions or issues please open an issue.

Installation

pkpdbib is available from pypi and can be installed via

pip install pkpdbib

The Zotero utilities need the optional zotero extra:

pip install "pkpdbib[zotero]"

See the installation guide for the develop version and the development guide for setting up a development environment.

Quickstart

Open the Zotero library, select the items without a PDF attachment and export them via right click -> Export items... -> Better BibTeX JSON to <substance>.json. Then run

scidownl domain.update
scihub_pdfs -j <substance>.json

The PDFs are written to the directory <substance>/ next to the JSON file, named by the citation keys.

How to cite

If you use pkpdbib please cite the archived software on Zenodo, see also CITATION.cff:

König, M. (2024). pkpdbib: python utilities for PK/PD literature and bibliography management (Version 0.1.0) [Computer software]. Zenodo. https://doi.org/10.5281/zenodo.11076700

@software{konig_pkpdbib,
  author    = {König, Matthias},
  title     = {pkpdbib: python utilities for PK/PD literature and bibliography management},
  year      = {2024},
  version   = {0.1.0},
  publisher = {Zenodo},
  doi       = {10.5281/zenodo.11076700},
  url       = {https://doi.org/10.5281/zenodo.11076700},
}

License

• Source Code: LGPLv3
• Documentation: CC BY-SA 4.0

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.

© 2021-2026 Matthias König, https://livermetabolism.com