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darwin-eu / CodelistGenerator

Identifying relevant concepts from the OMOP CDM vocabularies
https://darwin-eu.github.io/CodelistGenerator/
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have addRoute as a new argument #92

Closed tiozab closed 1 month ago

tiozab commented 1 year ago

Is your feature request related to a problem? Please describe. It would be convenient to have concept ids of drugs pre-selected according to route. We have suggested a new route hierarchy that links to dose form which could be exploited here.

Describe the solution you'd like The route linked to dose form could be used instead of dose form as an argument because it is clinically more meaningful. For extreme cases, it may be nice to also separately have the addDoseForm argument, so why not have both? Of course, they could not be mutually exclusively used (that would not make sense), e.g. selecting "topical" as route and "auto-injector" as dose form

Describe alternatives you've considered Do the process manually after receiving the whole list of drugs.

Additional context Here is the excel file that contains the final version of how dose form (name and ids) links to a new route hierarchy (names only, no ids yet, the issue in v5.0 cdm vocabulary was made here: https://github.com/OHDSI/Vocabulary-v5.0/issues/860

dose form_TB_AG_CR_final.xlsx

catalamarti commented 1 year ago

@edward-burn can you assign this issue to Kim? she is working on that and I dont have the power

edward-burn commented 1 month ago

I believe this was done (e.g. is supported in https://darwin-eu.github.io/CodelistGenerator/reference/getDrugIngredientCodes.html)

tiozab commented 2 weeks ago

Route will change again as we update the route vocabulary in OMOP CDM with the update february 2025. Just to keep this open until then. I can make a new excel file for CodelistGenerator once it is decided.