Cleanup/rename antibiotics_family column in combined metadata table

[cmirzayi]

Is your feature request related to a problem? Please describe. The antibiotics_family column in the combined metadata table contains information on medications and treatments that are not antibiotics (antivirals, beta blockers, blood pressure meds, diabetes meds, etc.). While it's not an issue to filter these non-antibiotic treatments out myself, this could potentially cause confusion for users who would not know to look at this column for general medication information.

Describe the solution you'd like Rename this column to better reflect what it actually is: medications.

You could also split medications and antibiotics into separate columns, since antibiotics probably have a stronger impact on the microbiome compared to most other medications. This would ensure backward compatibility with the antibiotics_family column while properly labeling medications.

[schifferl]

This would have to be a handled in the curation repo, I am going to move it there. The variables are simply created from the files in inst/curated, so the medications variable would have to exist there first.

[lwaldron]

@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 be valuable. @paolinomanghi FYI.

[paolinomanghi]

Should I correct all the metadata tables singularly? Is not big deal, for me.

On Thu, Apr 22, 2021 at 8:51 AM Levi Waldron @.***> wrote:

@cmirzayi https://github.com/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 be valuable. @paolinomanghi https://github.com/paolinomanghi FYI.

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[lwaldron]

Yes, in each metadata table individually. I hope it's not too much of a burden or can be done with scripts.

[paolinomanghi]

No it can be done easily.

On Fri, Apr 23, 2021 at 1:43 PM Levi Waldron @.***> wrote:

Yes, in each metadata table individually. I hope it's not too much of a burden or can be done with scripts.

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[lwaldron]

thanks @paolinomanghi. You should work with with @cmirzayi who is studying antibiotics specifically and can help to get it right.

[lwaldron]

Pinging @cmirzayi, would be great to resolve this for the Bioconductor 3.15 release.