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msberends / AMR

Functions to simplify and standardise antimicrobial resistance (AMR) data analysis and to work with microbial and antimicrobial properties by using evidence-based methods, as described in https://doi.org/10.18637/jss.v104.i03.
https://msberends.github.io/AMR/
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Add Bartlett et al. (2022) for human pathogenicity? #90

Closed msberends closed 1 year ago

msberends commented 1 year ago

Last week, Bartlett et al. published a comprehensive list with human pathogens:

Bartlett et al., 2022, A comprehensive list of bacterial pathogens infecting humans, https://doi.org/10.1099/mic.0.001269

This might be a good source to replace the prevalence column in the microorganisms data set, which is used to calculate the MO matching score.

Their full list is on GitHub, which we forked to keep it available: https://github.com/msberends/bartlett_et_al_2022_human_pathogens (sheet "Tab 6 Full List").

msberends commented 1 year ago

Incorporated already :smile: