Support annotated-taxa and taxon-variation corpus

phenoscape / rphenoscape

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

https://rphenoscape.phenoscape.org/

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Support annotated-taxa and taxon-variation corpus #253

Closed johnbradley closed 2 years ago

johnbradley commented 2 years ago

With the latest version of the kb phenoscape API the "taxa" corpus was replaced by "annotated-taxa" and "taxon-variation". Update functions with corpus parameters to support these new values.

johnbradley commented 2 years ago

The following API endpoints have been changed to support "annotated-taxa" and "taxon-variation" for the corpus parameter:

/similarity/matrix
/similarity/corpus_size
/similarity/frequency

See https://github.com/phenoscape/rphenoscape/issues/243#issuecomment-1167656358 for earlier KB API implementation details.

johnbradley commented 2 years ago

We currently don't pass corpus when using /similarity/matrix in rphenoscape: https://github.com/phenoscape/rphenoscape/blob/a9659db5f81c3be74be68cab553e302e7b963e26/R/semsim.R#L78-L81

We do pass corpus for /similarity/frequency and /similarity/corpus_size:

https://github.com/phenoscape/rphenoscape/blob/a9659db5f81c3be74be68cab553e302e7b963e26/R/term-weights.R#L95-L99

https://github.com/phenoscape/rphenoscape/blob/a9659db5f81c3be74be68cab553e302e7b963e26/R/term-weights.R#L139-L140

johnbradley commented 2 years ago

With the new API the "taxa" equivalent is "taxon-variation".