ontodiff-curator

Curates differences in ontology resources during pull requests in KGCL format using oaklib.

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.

pip install poetry
git clone https://github.com/hrshdhgd/ontodiff-curator
cd ontodiff-curator
poetry install

Scrape the repository

⚠️ You'll need a GitHub token stored as any environment variable name (GITHUB_ACCESS_TOKEN in this case).

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.

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)

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Acknowledgements

This cookiecutter project was developed from the monarch-project-template template and will be kept up-to-date using cruft.