Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

add PATO shorthand for term_classification() #264

Open
wdahdul opened this issue Oct 27, 2022 · 1 comment
Open

add PATO shorthand for term_classification() #264

wdahdul opened this issue Oct 27, 2022 · 1 comment

Comments

@wdahdul
Copy link
Contributor

wdahdul commented Oct 27, 2022

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

@hlapp
Copy link
Member

hlapp commented Nov 4, 2022

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?

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants