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PK-DB data utilities.

Project description

GitHub Actions CI/CD Status Current PyPI Version Supported Python Versions GNU Lesser General Public License 3 Black

pkdb_data: python utilities for PK-DB data

This repository stores the curated study data for and provides helpers for uploading studies to the database. The available choices are defined as part of this repository.

See the ./ for detailed instructions on how to curate studies.


Installation instructions are available here.

Functionality in a nutshell

The following provides a short overview over the main functionality. Detailed information is provided in the ./

Upload study

To upload a study use

(pkdb_data) upload_study -s <study_dir>

Upload studies

A set of studies can be uploaded via

(pkdb_data) upload_studies

Use the -s flag to only upload subsets, e.g., to upload all caffeine and acetaminophen studies use

(pkdb_data) upload_studies -s caffeine acetaminophen

Delete study

(pkdb_data) delete_study -s <study_sid>

Update InfoNodes

Modifying and uploading InfoNodes which can be used as choices in the curation is restricted to the admins. To update the notes modify the information in ./pkdb_data/info_nodes/ and create the json information via

(pkdb_data) create_nodes

In a second step the nodes are uploaded via

(pkdb_data) upload_nodes


The pkdb_data 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.


Matthias König is 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 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).

© 2017-2024 Jan Grzegorzewski & Matthias König

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