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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 PATO shorthand for term_classification() #264

Open wdahdul opened 2 years ago

wdahdul commented 2 years ago

"quality" can be used for PATO (similar to how "anatomy" and "taxon" can be used for UBERON and VTO).

hlapp commented 2 years ago

Note that you can already give "pato" as the value for the as parameter in get_term_iri() and the definedBy parameter in find_term(). (This is documented; that is, you can supply ontology ID instead of the full ontology IRI.)

The reason one can use "anatomy" and "taxon" as shorthands is that there are (or in case of taxon reasonably could be) multiple corresponding ontologies, and it seems unnecessary to burden the user with having to know which ones are in the database.

For the case of quality, perhaps a case could be made too that there could reasonably be multiple quality ontologies in the database, and one shouldn't have to know in advance against which one a label would match. Are we sure that's a reasonably likely use case?