pymetadata
Python utilities for working with metadata and COMBINE archives
Science Score: 49.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 6 DOI reference(s) in README -
✓Academic publication links
Links to: zenodo.org -
○Committers with academic emails
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (15.4%) to scientific vocabulary
Repository
Python utilities for working with metadata and COMBINE archives
Basic Info
Statistics
- Stars: 6
- Watchers: 3
- Forks: 3
- Open Issues: 7
- Releases: 48
Metadata Files
README.md
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
bash
pip install pymetadata
Develop version
The latest develop version can be installed via
bash
pip install git+https://github.com/matthiaskoenig/pymetadata.git@develop
Or via cloning the repository and installing via
bash
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
python
CACHE_PATH: Path = Path.home() / ".cache" / "pymetadata"
To use a custom cache path use
python
import pymetadata
pymetadata.CACHE_PATH = <cache_path>
© 2021-2025 Matthias König
Owner
- Name: Matthias König
- Login: matthiaskoenig
- Kind: user
- Location: Berlin
- Company: Humboldt University
- Website: https://livermetabolism.com
- Repositories: 146
- Profile: https://github.com/matthiaskoenig
Matthias König (PhD. in Biophysics) leads a junior research group for Systems Biology and Systems Medicine of the liver.
GitHub Events
Total
- Create event: 7
- Release event: 4
- Issues event: 7
- Delete event: 3
- Issue comment event: 3
- Push event: 28
- Pull request event: 3
Last Year
- Create event: 7
- Release event: 4
- Issues event: 7
- Delete event: 3
- Issue comment event: 3
- Push event: 28
- Pull request event: 3
Committers
Last synced: about 3 years ago
All Time
- Total Commits: 172
- Total Committers: 1
- Avg Commits per committer: 172.0
- Development Distribution Score (DDS): 0.0
Top Committers
| Name | Commits | |
|---|---|---|
| Matthias Koenig | k****t@g****m | 172 |
Issues and Pull Requests
Last synced: 7 months ago
All Time
- Total issues: 48
- Total pull requests: 12
- Average time to close issues: about 1 month
- Average time to close pull requests: 1 day
- Total issue authors: 4
- Total pull request authors: 3
- Average comments per issue: 0.27
- Average comments per pull request: 0.08
- Merged pull requests: 10
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 4
- Pull requests: 4
- Average time to close issues: about 1 month
- Average time to close pull requests: 1 minute
- Issue authors: 1
- Pull request authors: 1
- Average comments per issue: 0.25
- Average comments per pull request: 0.0
- Merged pull requests: 4
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- matthiaskoenig (45)
- fbergmann (1)
- Conni2461 (1)
Pull Request Authors
- matthiaskoenig (7)
- cheriimoya (4)
- UtkarshChaurasia (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- pypi 2,936 last-month
- Total dependent packages: 4
- Total dependent repositories: 1
- Total versions: 48
- Total maintainers: 1
pypi.org: pymetadata
pymetadata are python utilities for working with metadata.
- Documentation: https://pymetadata.readthedocs.io/
- License: MIT License
-
Latest release: 0.5.3
published 11 months ago
Rankings
Maintainers (1)
Dependencies
- actions/checkout v3 composite
- actions/create-release v1 composite
- actions/setup-python v4 composite