pymetadata is a collection of python utilities for working with metadata in the context of COMBINE standards with source code available from https://github.com/matthiaskoenig/pymetadata.
Features include among others
- COMBINE archive version 1 support (OMEX)
- annotation classes and helpers
- SBO and KISAO ontology enums
If you have any questions or issues please open an issue.
Documentation is still work in progress. For an example usage of the COMBINE archive see omex_example.py.
Contributions are always welcome! Please read the contributing guidelines to get started.
- Source Code: MIT
- Documentation: CC BY-SA 4.0
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).
pymetadata is available from pypi and
can be installed via
pip install pymetadataThe latest develop version can be installed via
pip install git+https://github.com/matthiaskoenig/pymetadata.git@developOr via cloning the repository and installing via
git clone https://github.com/matthiaskoenig/pymetadata.git
cd pymetadata
pip install -e .pymetadata caches some information for faster retrieval. The cache path is set to
CACHE_PATH: Path = Path.home() / ".cache" / "pymetadata"To use a custom cache path use
import pymetadata
pymetadata.CACHE_PATH = <cache_path>© 2021-2025 Matthias König