Replaces taxa corpus with annotated-taxa/taxon-variation

phenoscape / rphenoscape

R package to make phenotypic traits from the Phenoscape Knowledgebase available from within R.

https://rphenoscape.phenoscape.org/

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Replaces taxa corpus with annotated-taxa/taxon-variation #254

Closed johnbradley closed 2 years ago

johnbradley commented 2 years ago

The KB API corpus parameter has replaced the "taxa" value with "annotated-taxa" and "taxon-variation". Users can now supply these two values where previously they passed the "taxa" corpus. Occurrences of "taxa" have been replaced by "annotated-taxa".

Fixes #253

johnbradley commented 2 years ago

The documentation on the various corpus values could probably be improved. I'm not 100% sure on the nuance between "taxon_annotations", "annotated-taxa", "taxon-variation.

hlapp commented 2 years ago

Given that we're already incompatibly retiring a corpus name ("taxa"), I decided that we might as well make the other carry-overs from earlier ("taxon_annotations" and "gene_annotations") consistently use the dash rather than underscore.