Levi Waldron
Levi Waldron
Add ontology map to `inst/extdata` on GitHub
@schifferl I think you've made some changes here, can you provide rationale & keep the issue updated? 422dfd9535e809739949f88790c0eb5b81a1a78c The goal is to begin curating entirely based on ontology terms instead...
@QuanWan89 can you think of how to include ontology terms and the "informal" terms as synonyms in the metadata database? See the work on maps at https://github.com/waldronlab/curatedMetagenomicDataCuration/commit/422dfd9535e809739949f88790c0eb5b81a1a78c
@cmirzayi would you be willing to split medications and antibiotics_family into separate columns? I think the issue is unawareness of curators about what these medications are, so your help would...
No worries - my only concern is that it wasn't mentioned in this issue, and I don't want to lose track of the work done. It's not a bad place...
Direct link to files in GitHub repo for convenience: https://github.com/waldronlab/curatedMetagenomicDataCuration/tree/3e7fba1bcacbc65cb3ef3a5b36c7feb9bcae6acc/inst/extdata
Yes, in each metadata table individually. I hope it's not too much of a burden or can be done with scripts.
thanks @paolinomanghi. You should work with with @cmirzayi who is studying antibiotics specifically and can help to get it right.
Pinging @cmirzayi, would be great to resolve this for the Bioconductor 3.15 release.
@paolinomanghi would you respond?