pkpdbib 0.1.0

pkpdbib: python utilities for metadata and COMBINE archives

pkpdbib is a collection of python utilities for working with pharmacokinetics/pharmacodynamics (PK/PD) literature with source code available from https://github.com/matthiaskoenig/pkpdbib.

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

How to cite

Contributing

Contributions are always welcome!

License

• Source Code: LGPLv3

• Documentation: CC BY-SA 4.0

The pkpdbib source is released under both the GPL and LGPL licenses version 2 or later. You may choose which license you choose to use the software under.

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License or the GNU Lesser General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

Funding

Matthias König (MK) 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). MK is supported by the Federal Ministry of Education and Research (BMBF, Germany) within ATLAS by grant number 031L0304B and by the German Research Foundation (DFG) within the Research Unit Program 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).

Installation

pkpdbib is available from pypi and can be installed via:

pip install pkpdbib

pip install git+https://github.com/matthiaskoenig/pkpdbib.git@develop

git clone https://github.com/matthiaskoenig/pkpdbib.git
cd pkpdbib
pip install -e .

pip install -e .[development]

Documentation

Retrieve PDFs via Sci-hub

• Open the zotero library, select items without PDF attachment, right click -> Export items -> CSV -> <substance>.csv

Run script from src/pkdb_literature/scihub.tools:

scihub_pdfs -z <substance>.csv

© 2021-2024 Matthias König