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 >= 11
- Python version: 3.8, 3.9, 3.10, 3.11
- Conda version >= 4.x.x
Python requirements
- Gensim >= 4.x.x
- PyTorch >= 1.12.x
- PyKEEN >= 1.10.1
Install from PyPi
pip install mowl-borg
Build from source
Installation can be done with the following commands:
git clone https://github.com/bio-ontology-research-group/mowl.git
cd mowl
conda env create -f envs/environment_3_8.yml
conda activate mowl
./build_jars.sh
python setup.py install
The line ./build_jars.sh
will generate the necessary jar
files to bind Python with the code that runs in the JVM. After building, a .tar.gz
file will be generated under dist
and can be used to install mOWL.
List of contributors
- Fernando Zhapa
- Maxat Kulmanov
- Sarah Alghamdi
- Robert Hoehndorf
- Carsten Jahn
- Sonja Katz
- Marco Anteghini
- Francesco Gualdi
- luis-sribeiro
- Leduin Cuenca (logo)
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},
}