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https://github.com/astrazeneca/onto_merger
OntoMerger is an ontology alignment library for deduplicating knowledge graph nodes that represent the same domain.
https://github.com/astrazeneca/onto_merger
algorithm alignment biological-networks biology graph kg knowledge knowledge-graph mapping ontology ontology-alignment
Last synced: about 3 hours ago
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OntoMerger is an ontology alignment library for deduplicating knowledge graph nodes that represent the same domain.
- Host: GitHub
- URL: https://github.com/astrazeneca/onto_merger
- Owner: AstraZeneca
- License: apache-2.0
- Created: 2022-05-05T11:33:45.000Z (over 2 years ago)
- Default Branch: main
- Last Pushed: 2024-01-11T19:22:08.000Z (10 months ago)
- Last Synced: 2024-03-26T08:22:40.512Z (8 months ago)
- Topics: algorithm, alignment, biological-networks, biology, graph, kg, knowledge, knowledge-graph, mapping, ontology, ontology-alignment
- Language: HTML
- Homepage:
- Size: 32.8 MB
- Stars: 90
- Watchers: 7
- Forks: 5
- Open Issues: 5
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
[pypi-image]: https://badge.fury.io/py/onto_merger.svg
[pypi-url]: https://pypi.python.org/pypi/onto_merger
[size-image]: https://img.shields.io/github/repo-size/AstraZeneca/onto_merger.svg
[size-url]: https://github.com/AstraZeneca/onto_merger/archive/main.zip
[build-image]: https://github.com/AstraZeneca/onto_merger/workflows/CI/badge.svg
[build-url]: https://github.com/AstraZeneca/onto_merger/actions?query=workflow%3ACI
[docs-image]: https://readthedocs.org/projects/ontomerger/badge/?version=latest
[docs-url]: https://ontomerger.readthedocs.io/en/latest/?badge=latest
[coverage-image]: https://codecov.io/gh/AstraZeneca/onto_merger/branch/main/graph/badge.svg
[coverage-url]: https://codecov.io/github/AstraZeneca/onto_merger?branch=main
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[![PyPI Version][pypi-image]][pypi-url]
[![Docs Status][docs-image]][docs-url]
[![Code Coverage][coverage-image]][coverage-url]
[![Build Status][build-image]][build-url]
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**[Paper](https://arxiv.org/abs/2206.02238)** | **[Documentation](https://ontomerger.readthedocs.io)** | **[External Resources](https://ontomerger.readthedocs.io/en/latest/notes/resources.html)**
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*OntoMerger* is an ontology alignment library for **deduplicating** knowledge
graph nodes,(i.e. ontology concepts) that represent the *same domain*, e.g. diseases,
and **connecting** them to form a single directed acyclic hierarchical graph (DAG) (i.e. an ontology
class hierarchy). The library implements a pipeline that takes *nodes, mappings and
(disconnected) hierarchies* as input and produces *node merges* and a *connected hierarchy*.
It also provides analysis and data testing for fine tuning the inputs in order
to further reduce duplication, as well as to increase connectivity.
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**Citing**
If you find *OntoMerger* useful in your work or research, please consider adding the following citation:
```bibtex
@misc{ontomerger,
doi = {10.48550/ARXIV.2206.02238},
author = {Geleta, David and Nikolov, Andriy and ODonoghue, Mark and Rozemberczki, Benedek and Gogleva, Anna and Tamma, Valentina and Payne, Terry R.},
title = {OntoMerger: An Ontology Integration Library for Deduplicating and Connecting Knowledge Graph Nodes},
publisher = {arXiv},
year = {2022},
}
```
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**Getting Started**
```python
from onto_merger.pipeline import Pipeline
# initialise the pipeline
pipeline = Pipeline(project_folder_path="../path/to/project")
# run the process
pipeline.run_alignment_and_connection_process()
# view results in "../path/to/project/output/report/index.html"
```
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**Running tests**
```
$ tox -e py
```
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**License**
- [Apache 2.0 License](https://github.com/AstraZeneca/onto_merger/blob/main/LICENSE)
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**Credit**
The **Onto Merger** logo is based on:
- [Galguna Font](https://www.dafont.com/galguna.font)
- [Noun Project Icons](https://thenounproject.com/)