pymetadata 0.5.3

pymetadata are python utilities for working with metadata.

pymetadata: python utilities for metadata and COMBINE archives

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

• coreCOMBINE 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

Documentation is still work in progress. For an example usage of the COMBINE archive see omex_example.py.

How to cite

Contributing

Contributions are always welcome! Please read the contributing guidelines to get started.

License

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

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

pymetadata is available from pypi and can be installed via

pip install pymetadata

Develop version

The latest develop version can be installed via

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

Or via cloning the repository and installing via

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

Cache path

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