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Added C. freundii complex and Y. pseudotuberculosis complex

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dr. M.S. (Matthijs) Berends
2023-07-14 10:49:06 +02:00
parent fd480d1a9a
commit 7a4628b73f
26 changed files with 52 additions and 18 deletions
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17
data-raw/reproduction_of_microorganisms.groups.R
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@ -38,6 +38,13 @@ devtools::load_all()
# Install the WHONET software on Windows (http://www.whonet.org/software.html),
# and copy the folder C:\WHONET\Resources to the data-raw/WHONET/ folder
# BACTERIAL COMPLEXES
# find all bacterial complex in the NCBI Taxonomy Browser here:
# https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=2&lvl=6&lin=f&keep=1&srchmode=1&unlock
# and search the page for 'complex', then follow the link and add the missing ones in this R file
# READ DATA ----
whonet_organisms <- read_tsv("data-raw/WHONET/Resources/Organisms.txt", na = c("", "NA", "-"), show_col_types = FALSE) %>%
@ -131,6 +138,16 @@ microorganisms.groups <- whonet_organisms %>%
bind_rows(tibble(mo_group = as.mo("HACEK"), mo = as.mo("Eikenella corrodens", keep_synonyms = TRUE))) %>%
bind_rows(tibble(mo_group = as.mo("HACEK"), mo = microorganisms %>% filter(genus == "Kingella") %>% pull(mo))) %>%
bind_rows(tibble(mo_group = as.mo("HACEK"), mo = as.mo("Actinobacillus actinomycetemcomitans", keep_synonyms = TRUE))) %>%
# Citrobacter freundii complex in the NCBI Taxonomy Browser:
# https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1344959
filter(mo_group != "B_CTRBC_FRND-C") %>%
bind_rows(tibble(mo_group = as.mo("B_CTRBC_FRND-C"),
mo = paste("Citrobacter", c("freundii", "braakii", "gillenii", "murliniae", "portucalensis", "sedlakii", "werkmanii", "youngae")) %>% as.mo(keep_synonyms = TRUE))) %>%
# Yersinia pseudotuberculosis complex in the NCBI Taxonomy Browser:
# https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1649845
filter(mo_group != "B_YERSN_PSDT-C") %>%
bind_rows(tibble(mo_group = as.mo("B_YERSN_PSDT-C"),
mo = paste("Yersinia", c("pseudotuberculosis", "pestis", "similis", "wautersii")) %>% as.mo(keep_synonyms = TRUE))) %>%
# RGM are Rapidly-grwoing Mycobacteria, see https://pubmed.ncbi.nlm.nih.gov/28084211/
filter(mo_group != "B_MYCBC_RGM") %>%
bind_rows(tibble(mo_group = as.mo("B_MYCBC_RGM"),