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https://github.com/hrshdhgd/ontodiff-curator
https://github.com/hrshdhgd/ontodiff-curator
Last synced: 14 days ago
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- Host: GitHub
- URL: https://github.com/hrshdhgd/ontodiff-curator
- Owner: hrshdhgd
- License: mit
- Created: 2024-08-14T00:51:14.000Z (5 months ago)
- Default Branch: main
- Last Pushed: 2024-09-05T15:38:45.000Z (4 months ago)
- Last Synced: 2024-11-05T20:05:38.771Z (2 months ago)
- Language: Python
- Size: 48.7 MB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
Awesome Lists containing this project
README
# ontodiff-curator
[](https://zenodo.org/doi/10.5281/zenodo.13694123)
Curates differences in ontology resources during pull requests in KGCL format using [oaklib](https://github.com/INCATools/ontology-access-kit).
Currently curates diff for the following:
- monarch-initiative/mondo
- geneontology/go-ontology
- EnvironmentOntology/envo
- obophenotype/cell-ontology
- obophenotype/uberon
- pato-ontology/pato
## Setup
Currently just clone the git repo and proceed.
```shell
pip install poetry
git clone https://github.com/hrshdhgd/ontodiff-curator
cd ontodiff-curator
poetry install
```
## Scrape the repository
> **:warning:** You'll need a GitHub token stored as any environment variable name (`GITHUB_ACCESS_TOKEN` in this case).
```shell
ontodiff scrape --repository monarch-initiative/mondo --token $(GITHUB_ACCESS_TOKEN)
```
This grabs the information of all pull requests in the MONDO repository that change the `mondo-edit.obo` file & have an associated issue(s) that they close. The output is stored as `raw_data.yaml`.
An upper and lower limit for the pull request number can also be provided here using parameters `--max-pr` and `--min-pr`.
```shell
ontodiff analyze --repository monarch-initiative/mondo
```
This grabs the resource (mondo-edit.obo) in the branch associated with the pull request and the `main` branch at the time and compares the two using `oaklib` and generates the difference between them in KGCL format. The output si another YAML file (`data_with_changes.yaml`)
---
### Acknowledgements
This [cookiecutter](https://cookiecutter.readthedocs.io/en/stable/README.html) project was developed from the [monarch-project-template](https://github.com/monarch-initiative/monarch-project-template) template and will be kept up-to-date using [cruft](https://cruft.github.io/cruft/).