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 documentation available from https://matthiaskoenig.github.io/pymetadata.

Features include

• COMBINE archive support (OMEX)
• annotation classes and helpers
• SBO, KISAO and PBPKO ontology terms with label, definition and synonyms

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

How to cite

If you use pymetadata please cite the archived software on Zenodo:

König, M. (2026). pymetadata are python utilities for working with metadata (Version 0.8.2) [Computer software]. Zenodo. https://doi.org/10.5281/zenodo.23555354

@software{konig_pymetadata,
  author    = {König, Matthias},
  title     = {pymetadata are python utilities for working with metadata},
  year      = {2026},
  month     = oct,
  version   = {0.8.2},
  publisher = {Zenodo},
  doi       = {10.5281/zenodo.23555354},
  url       = {https://doi.org/10.5281/zenodo.23555354},
}

License

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

Funding

Matthias König is supported 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).

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).

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