mOWL: Machine Learning Library with Ontologies
mOWL is a library that provides different machine learning methods in which ontologies are used as background knowledge. mOWL is developed mainly in Python, but we have integrated the functionalities of OWLAPI, which is written in Java, for which we use JPype to bind Python with the Java Virtual Machine (JVM).
Table of contents
Installation
System dependencies
- JDK version >= 22.x.x
- Python version: 3.9, 3.10, 3.11, 3.12
- Conda version >= 24.x.x
Python requirements
- torch
- gensim >= 4.3.0
- JPype1 == 1.5.1
- pykeen == 1.11.0
- scipy < 1.15.0
Install from PyPi
pip install mowl-borg
Install from source
pip install git+https://github.com/bio-ontology-research-group/mowl
Relevant papers:
- mOWL: Python library for machine learning with biomedical ontologies
- Ontology Embedding: A Survey of Methods, Applications and Resources
- Evaluating Different Methods for Semantic Reasoning Over Ontologies
- Prioritizing genomic variants through neuro-symbolic, knowledge-enhanced learning
Authors
mOWL is a project initiated and developed by the Bio-Ontology Research Group from KAUST. Furthermore, mOWL had other collaboration by being part of:
- Biohackathon Japan 2024
- Biohackathon MENA 2023 as project
#20. - Biohackathon Europe 2022 as project
#18. - Biohackathon Europe 2021 as project
#27.
License
This software library is distributed under the BSD-3-Clause license
Documentation
Full documentation and API reference can be found in our ReadTheDocs website.
ChangeLog
ChangeLog is available in our changelog file and also in the release section.
Citation
If you used mOWL in your work, please consider citing this article:
@article{10.1093/bioinformatics/btac811,
author = {Zhapa-Camacho, Fernando and Kulmanov, Maxat and Hoehndorf, Robert},
title = "{mOWL: Python library for machine learning with biomedical ontologies}",
journal = {Bioinformatics},
year = {2022},
month = {12},
issn = {1367-4803},
doi = {10.1093/bioinformatics/btac811},
url = {https://doi.org/10.1093/bioinformatics/btac811},
note = {btac811},
eprint = {https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btac811/48438324/btac811.pdf},
}
1 maintainer
Metadata
1 maintainer
Release files for mowl-borg 2.1.0
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Source distribution (sdist)
| File | Size | Uploaded | Provenance | |
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| mowl_borg-2.1.0.tar.gz | 70.1 MB | With provenance | Details |
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| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| mowl_borg-2.1.0-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 139.0 MB
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