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phenoscape / rphenoscape

R package to make phenotypic traits from the Phenoscape Knowledgebase available from within R.
https://rphenoscape.phenoscape.org/
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Add CSV example file for mutually_exclusive() opposites #271

Open johnbradley opened 2 years ago

johnbradley commented 2 years ago

Improve the mutually_exclusive function example to demonstrate how a user can use a CSV file of opposite IRIs. See https://github.com/phenoscape/rphenoscape/pull/270#pullrequestreview-1169691891

johnbradley commented 2 years ago

Commit https://github.com/phenoscape/rphenoscape/commit/2c1d347d94ab227fc5150d179a2a398d9c4f5e2c roughs out the changes. I think the example CSV file needs to be fleshed out more.

hlapp commented 2 years ago

@wdahdul would you mind helping out with this by providing a few pairs quality terms deemed opposites of each other?

Ideally, these pairs would be contextualized to determining mutually exclusive phenotypes with and without providing opposites. In the newly added example, we are starting with femur phenotypes, but this could be changed. The first example in the manual page starts with the Dillman study and then randomly samples 10 phenotypes.

This would probably benefit from making it more deterministic, but such that we end up with a full range of exclusivity types, and that some of them would change after providing the list of opposites.