mirror of
https://github.com/msberends/AMR.git
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new species groups, updated clinical breakpoints
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data-raw/Species groups.xlsx
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data-raw/Species groups.xlsx
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@ -392,6 +392,32 @@ if (changed_md5(microorganisms)) {
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try(arrow::write_parquet(microorganisms, "data-raw/microorganisms.parquet"), silent = TRUE)
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}
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if (changed_md5(microorganisms.codes)) {
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usethis::ui_info(paste0("Saving {usethis::ui_value('microorganisms.codes')} to {usethis::ui_value('data-raw/')}"))
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write_md5(microorganisms.codes)
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try(saveRDS(microorganisms.codes, "data-raw/microorganisms.codes.rds", version = 2, compress = "xz"), silent = TRUE)
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try(write.table(microorganisms.codes, "data-raw/microorganisms.codes.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
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try(haven::write_xpt(microorganisms.codes, "data-raw/microorganisms.codes.xpt"), silent = TRUE)
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try(haven::write_sav(microorganisms.codes, "data-raw/microorganisms.codes.sav"), silent = TRUE)
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try(haven::write_dta(microorganisms.codes, "data-raw/microorganisms.codes.dta"), silent = TRUE)
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try(openxlsx::write.xlsx(microorganisms.codes, "data-raw/microorganisms.codes.xlsx"), silent = TRUE)
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try(arrow::write_feather(microorganisms.codes, "data-raw/microorganisms.codes.feather"), silent = TRUE)
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try(arrow::write_parquet(microorganisms.codes, "data-raw/microorganisms.codes.parquet"), silent = TRUE)
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}
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if (changed_md5(microorganisms.groups)) {
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usethis::ui_info(paste0("Saving {usethis::ui_value('microorganisms.groups')} to {usethis::ui_value('data-raw/')}"))
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write_md5(microorganisms.groups)
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try(saveRDS(microorganisms.groups, "data-raw/microorganisms.groups.rds", version = 2, compress = "xz"), silent = TRUE)
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try(write.table(microorganisms.groups, "data-raw/microorganisms.groups.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
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try(haven::write_xpt(microorganisms.groups, "data-raw/microorganisms.groups.xpt"), silent = TRUE)
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try(haven::write_sav(microorganisms.groups, "data-raw/microorganisms.groups.sav"), silent = TRUE)
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try(haven::write_dta(microorganisms.groups, "data-raw/microorganisms.groups.dta"), silent = TRUE)
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try(openxlsx::write.xlsx(microorganisms.groups, "data-raw/microorganisms.groups.xlsx"), silent = TRUE)
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try(arrow::write_feather(microorganisms.groups, "data-raw/microorganisms.groups.feather"), silent = TRUE)
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try(arrow::write_parquet(microorganisms.groups, "data-raw/microorganisms.groups.parquet"), silent = TRUE)
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}
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ab <- dplyr::mutate_if(antibiotics, ~ !is.numeric(.), as.character)
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if (changed_md5(ab)) {
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usethis::ui_info(paste0("Saving {usethis::ui_value('antibiotics')} to {usethis::ui_value('data-raw/')}"))
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@ -1 +1 @@
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10fb049c5071ca255d99c848dc498245
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87c6c20d117acd06c37bab6d93966a0b
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data-raw/microorganisms.codes.dta
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data-raw/microorganisms.codes.dta
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data-raw/microorganisms.codes.feather
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data-raw/microorganisms.codes.feather
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684dc6117966c478ecc7f5c87e0964d0
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data-raw/microorganisms.codes.parquet
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data-raw/microorganisms.codes.rds
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data-raw/microorganisms.codes.sav
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data-raw/microorganisms.codes.sav
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data-raw/microorganisms.codes.txt
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data-raw/microorganisms.codes.txt
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data-raw/microorganisms.codes.xlsx
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data-raw/microorganisms.groups.dta
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data-raw/microorganisms.groups.dta
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data-raw/microorganisms.groups.feather
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data-raw/microorganisms.groups.feather
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@ -0,0 +1 @@
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9f27f0779ed539f5eb2560bd24995df2
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data-raw/microorganisms.groups.parquet
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data-raw/microorganisms.groups.rds
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data-raw/microorganisms.groups.rds
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data-raw/microorganisms.groups.sav
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data-raw/microorganisms.groups.sav
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data-raw/microorganisms.groups.txt
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data-raw/microorganisms.groups.txt
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@ -0,0 +1,445 @@
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"mo_group" "mo" "mo_group_name" "mo_name"
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"B_ACNTB_BMNN-C" "B_ACNTB_BMNN" "Acinetobacter baumannii complex" "Acinetobacter baumannii"
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"B_ACNTB_BMNN-C" "B_ACNTB_CLCC" "Acinetobacter baumannii complex" "Acinetobacter calcoaceticus"
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"B_ACNTB_BMNN-C" "B_ACNTB_DJKS" "Acinetobacter baumannii complex" "Acinetobacter dijkshoorniae"
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"B_ACNTB_BMNN-C" "B_ACNTB_NSCM" "Acinetobacter baumannii complex" "Acinetobacter nosocomialis"
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"B_ACNTB_BMNN-C" "B_ACNTB_PITT" "Acinetobacter baumannii complex" "Acinetobacter pittii"
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"B_ACNTB_BMNN-C" "B_ACNTB_SFRT" "Acinetobacter baumannii complex" "Acinetobacter seifertii"
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"B_BCTRD_FRGL-C" "B_BCTRD_FRGL" "Bacteroides fragilis complex" "Bacteroides fragilis"
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"B_BCTRD_FRGL-C" "B_BCTRD_OVTS" "Bacteroides fragilis complex" "Bacteroides ovatus"
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"B_BCTRD_FRGL-C" "B_BCTRD_THTT" "Bacteroides fragilis complex" "Bacteroides thetaiotaomicron"
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"B_BCTRD_FRGL-C" "B_BCTRD_VLGT" "Bacteroides fragilis complex" "Bacteroides vulgatus"
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"B_BCTRD_FRGL-C" "B_PRBCT_DSTS" "Bacteroides fragilis complex" "Parabacteroides distasonis"
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"B_STRPT_HAEM" "B_STRPT_GRPA" "Beta-haemolytic Streptococcus" "Streptococcus Group A"
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"B_STRPT_HAEM" "B_STRPT_ABCG" "Beta-haemolytic Streptococcus" "Streptococcus Group A, B, C, G"
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"B_STRPT_HAEM" "B_STRPT_GRPB" "Beta-haemolytic Streptococcus" "Streptococcus Group B"
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"B_STRPT_HAEM" "B_STRPT_GRPC" "Beta-haemolytic Streptococcus" "Streptococcus Group C"
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"B_STRPT_HAEM" "B_STRPT_GRPD" "Beta-haemolytic Streptococcus" "Streptococcus Group D"
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"B_STRPT_HAEM" "B_STRPT_GRPE" "Beta-haemolytic Streptococcus" "Streptococcus Group E"
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"B_STRPT_HAEM" "B_STRPT_GRPF" "Beta-haemolytic Streptococcus" "Streptococcus Group F"
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"B_STRPT_HAEM" "B_STRPT_GRPG" "Beta-haemolytic Streptococcus" "Streptococcus Group G"
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"B_STRPT_HAEM" "B_STRPT_GRPH" "Beta-haemolytic Streptococcus" "Streptococcus Group H"
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"B_STRPT_HAEM" "B_STRPT_GRPI" "Beta-haemolytic Streptococcus" "Streptococcus Group I"
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"B_STRPT_HAEM" "B_STRPT_GRPJ" "Beta-haemolytic Streptococcus" "Streptococcus Group J"
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"B_STRPT_HAEM" "B_STRPT_GRPK" "Beta-haemolytic Streptococcus" "Streptococcus Group K"
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"B_STRPT_HAEM" "B_STRPT_GRPL" "Beta-haemolytic Streptococcus" "Streptococcus Group L"
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"B_STRPT_HAEM" "B_STRPT_AGLC" "Beta-haemolytic Streptococcus" "Streptococcus agalactiae"
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"B_STRPT_HAEM" "B_STRPT_ANGN" "Beta-haemolytic Streptococcus" "Streptococcus anginosus"
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"B_STRPT_HAEM" "B_STRPT_ANGN_ANGN" "Beta-haemolytic Streptococcus" "Streptococcus anginosus anginosus"
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"B_STRPT_HAEM" "B_STRPT_ANGN_WHLY" "Beta-haemolytic Streptococcus" "Streptococcus anginosus whileyi"
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"B_STRPT_HAEM" "B_STRPT_CANS" "Beta-haemolytic Streptococcus" "Streptococcus canis"
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"B_STRPT_HAEM" "B_STRPT_DYSG" "Beta-haemolytic Streptococcus" "Streptococcus dysgalactiae"
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"B_STRPT_HAEM" "B_STRPT_DYSG_DYSG" "Beta-haemolytic Streptococcus" "Streptococcus dysgalactiae dysgalactiae"
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"B_STRPT_HAEM" "B_STRPT_DYSG_EQSM" "Beta-haemolytic Streptococcus" "Streptococcus dysgalactiae equisimilis"
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"B_STRPT_HAEM" "B_STRPT_EQUI" "Beta-haemolytic Streptococcus" "Streptococcus equi"
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"B_STRPT_HAEM" "B_STRPT_EQUI_EQUI" "Beta-haemolytic Streptococcus" "Streptococcus equi equi"
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"B_STRPT_HAEM" "B_STRPT_EQUI_RMNT" "Beta-haemolytic Streptococcus" "Streptococcus equi ruminatorum"
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"B_STRPT_HAEM" "B_STRPT_EQUI_ZPDM" "Beta-haemolytic Streptococcus" "Streptococcus equi zooepidemicus"
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"B_STRPT_HAEM" "B_STRPT_HYNT" "Beta-haemolytic Streptococcus" "Streptococcus hyointestinalis"
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"B_STRPT_HAEM" "B_STRPT_INFN" "Beta-haemolytic Streptococcus" "Streptococcus infantarius"
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"B_STRPT_HAEM" "B_STRPT_INFN_COLI" "Beta-haemolytic Streptococcus" "Streptococcus infantarius coli"
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"B_STRPT_HAEM" "B_STRPT_INFN_INFN" "Beta-haemolytic Streptococcus" "Streptococcus infantarius infantarius"
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"B_STRPT_HAEM" "B_STRPT_LTTN" "Beta-haemolytic Streptococcus" "Streptococcus lutetiensis"
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"B_STRPT_HAEM" "B_STRPT_PRCN" "Beta-haemolytic Streptococcus" "Streptococcus porcinus"
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"B_STRPT_HAEM" "B_STRPT_PYGN" "Beta-haemolytic Streptococcus" "Streptococcus pyogenes"
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"B_STRPT_HAEM" "B_STRPT_SLVR" "Beta-haemolytic Streptococcus" "Streptococcus salivarius"
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"B_STRPT_HAEM" "B_STRPT_SLVR_SLVR" "Beta-haemolytic Streptococcus" "Streptococcus salivarius salivarius"
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"B_STRPT_HAEM" "B_STRPT_SLVR_THRM" "Beta-haemolytic Streptococcus" "Streptococcus salivarius thermophilus"
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"B_STRPT_HAEM" "B_STRPT_SNGN" "Beta-haemolytic Streptococcus" "Streptococcus sanguinis"
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"B_BRKHL_CEPC-C" "B_BRKHL_AMBF" "Burkholderia cepacia complex" "Burkholderia ambifaria"
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"B_BRKHL_CEPC-C" "B_BRKHL_ANTH" "Burkholderia cepacia complex" "Burkholderia anthina"
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"B_BRKHL_CEPC-C" "B_BRKHL_CNCP" "Burkholderia cepacia complex" "Burkholderia cenocepacia"
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"B_BRKHL_CEPC-C" "B_BRKHL_CEPC" "Burkholderia cepacia complex" "Burkholderia cepacia"
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"B_BRKHL_CEPC-C" "B_BRKHL_DOLS" "Burkholderia cepacia complex" "Burkholderia dolosa"
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"B_BRKHL_CEPC-C" "B_BRKHL_MLTV" "Burkholderia cepacia complex" "Burkholderia multivorans"
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"B_BRKHL_CEPC-C" "B_BRKHL_PYRR" "Burkholderia cepacia complex" "Burkholderia pyrrocinia"
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"B_BRKHL_CEPC-C" "B_BRKHL_STBL" "Burkholderia cepacia complex" "Burkholderia stabilis"
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"B_BRKHL_CEPC-C" "B_BRKHL_UBNN" "Burkholderia cepacia complex" "Burkholderia ubonensis"
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"B_BRKHL_CEPC-C" "B_BRKHL_VTNM" "Burkholderia cepacia complex" "Burkholderia vietnamiensis"
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"F_CANDD_ALBC-C" "F_CANDD_AFRC" "Candida albicans complex" "Candida africana"
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"F_CANDD_ALBC-C" "F_CANDD_ALBC" "Candida albicans complex" "Candida albicans"
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"F_CANDD_ALBC-C" "F_CANDD_DBLN" "Candida albicans complex" "Candida dubliniensis"
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"F_CANDD_GLBR-C" "F_CANDD_BRCR" "Candida glabrata complex" "Candida bracarensis"
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"F_CANDD_GLBR-C" "F_CANDD_GLBR" "Candida glabrata complex" "Candida glabrata"
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"F_CANDD_GLBR-C" "F_CANDD_NVRN" "Candida glabrata complex" "Candida nivariensis"
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"F_CANDD_PRPS-C" "F_CANDD_MTPS" "Candida parapsilosis complex" "Candida metapsilosis"
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"F_CANDD_PRPS-C" "F_CANDD_ORTH" "Candida parapsilosis complex" "Candida orthopsilosis"
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"F_CANDD_PRPS-C" "F_CANDD_PRPS" "Candida parapsilosis complex" "Candida parapsilosis"
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"P_CHLMS" "F_CANDD_DBSH" "Chilomastix" "Candida duobushaemulonii"
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"P_CHLMS" "F_CANDD_HMLN" "Chilomastix" "Candida haemulonii"
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"P_CHLMS" "B_CANDD_HMLN-C" "Chilomastix" "Candida haemulonii complex"
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"B_CTRBC_AMLN-C" "B_CTRBC_AMLN" "Citrobacter amalonaticus complex" "Citrobacter amalonaticus"
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"B_CTRBC_AMLN-C" "B_CTRBC_FRMR" "Citrobacter amalonaticus complex" "Citrobacter farmeri"
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"B_CTRBC_AMLN-C" "B_CTRBC_SDLK" "Citrobacter amalonaticus complex" "Citrobacter sedlakii"
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"B_STPHY_CONS" "B_STPHY_ARGN" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus argensis"
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"B_STPHY_CONS" "B_STPHY_ARLT" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus arlettae"
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"B_STPHY_CONS" "B_STPHY_ARCL" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus auricularis"
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"B_STPHY_CONS" "B_STPHY_BRLS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus borealis"
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"B_STPHY_CONS" "B_STPHY_CAEL" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus caeli"
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"B_STPHY_CONS" "B_STPHY_CLDN" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus caledonicus"
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"B_STPHY_CONS" "B_STPHY_CANS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus canis"
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"B_STPHY_CONS" "B_STPHY_CPTS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus capitis"
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"B_STPHY_CONS" "B_STPHY_CPTS_CPTS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus capitis capitis"
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"B_STPHY_CONS" "B_STPHY_CPTS_URLY" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus capitis urealyticus"
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"B_STPHY_CONS" "B_STPHY_CPTS_YTCS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus capitis ureolyticus"
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"B_STPHY_CONS" "B_STPHY_CAPR" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus caprae"
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"B_STPHY_CONS" "B_STPHY_CRNS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus carnosus"
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"B_STPHY_CONS" "B_STPHY_CRNS_CRNS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus carnosus carnosus"
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"B_STPHY_CONS" "B_STPHY_CRNS_UTLS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus carnosus utilis"
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"B_STPHY_CONS" "B_STPHY_CASE" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus casei"
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"B_STPHY_CONS" "B_STPHY_CSLY" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus caseolyticus"
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"B_STPHY_CONS" "B_STPHY_CHRM" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus chromogenes"
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"B_STPHY_CONS" "B_STPHY_COHN" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus cohnii"
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"B_STPHY_CONS" "B_STPHY_COHN_COHN" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus cohnii cohnii"
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"B_STPHY_CONS" "B_STPHY_COHN_URLY" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus cohnii urealyticum"
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"B_STPHY_CONS" "B_STPHY_COHN_YTCS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus cohnii urealyticus"
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"B_STPHY_CONS" "B_STPHY_CNDM" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus condimenti"
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"B_STPHY_CONS" "B_STPHY_CRCL" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus croceilyticus"
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"B_STPHY_CONS" "B_STPHY_DBCK" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus debuckii"
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"B_STPHY_CONS" "B_STPHY_DVRS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus devriesei"
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"B_STPHY_CONS" "B_STPHY_DRRL" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus durrellii"
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"B_STPHY_CONS" "B_STPHY_EDPH" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus edaphicus"
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"B_STPHY_CONS" "B_STPHY_EPDR" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus epidermidis"
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"B_STPHY_CONS" "B_STPHY_EQRM" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus equorum"
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"B_STPHY_CONS" "B_STPHY_EQRM_EQRM" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus equorum equorum"
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"B_STPHY_CONS" "B_STPHY_EQRM_LNNS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus equorum linens"
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"B_STPHY_CONS" "B_STPHY_FELS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus felis"
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"B_STPHY_CONS" "B_STPHY_FLRT" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus fleurettii"
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"B_STPHY_CONS" "B_STPHY_GLLN" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus gallinarum"
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"B_STPHY_CONS" "B_STPHY_HMLY" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus haemolyticus"
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"B_STPHY_CONS" "B_STPHY_HMNS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus hominis"
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"B_STPHY_CONS" "B_STPHY_HMNS_HMNS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus hominis hominis"
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"B_STPHY_CONS" "B_STPHY_HMNS_NVBS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus hominis novobiosepticus"
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"B_STPHY_CONS" "B_STPHY_JTTN" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus jettensis"
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"B_STPHY_CONS" "B_STPHY_KLOS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus kloosii"
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"B_STPHY_CONS" "B_STPHY_LNTS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus lentus"
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"B_STPHY_CONS" "B_STPHY_LLYD" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus lloydii"
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"B_STPHY_CONS" "B_STPHY_LGDN" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus lugdunensis"
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"B_STPHY_CONS" "B_STPHY_MSSL" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus massiliensis"
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"B_STPHY_CONS" "B_STPHY_MCRT" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus microti"
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"B_STPHY_CONS" "B_STPHY_MUSC" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus muscae"
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"B_STPHY_CONS" "B_STPHY_NPLN" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus nepalensis"
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"B_STPHY_CONS" "B_STPHY_PSTR" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus pasteuri"
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"B_STPHY_CONS" "B_STPHY_PTRS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus petrasii"
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"B_STPHY_CONS" "B_STPHY_PTRS_CRCL" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus petrasii croceilyticus"
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"B_STPHY_CONS" "B_STPHY_PTRS_JTTN" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus petrasii jettensis"
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"B_STPHY_CONS" "B_STPHY_PTRS_PTRS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus petrasii petrasii"
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||||
"B_STPHY_CONS" "B_STPHY_PTRS_PRGN" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus petrasii pragensis"
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"B_STPHY_CONS" "B_STPHY_PTTN" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus pettenkoferi"
|
||||
"B_STPHY_CONS" "B_STPHY_PSCF" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus piscifermentans"
|
||||
"B_STPHY_CONS" "B_STPHY_PRGN" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus pragensis"
|
||||
"B_STPHY_CONS" "B_STPHY_PSDX" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus pseudoxylosus"
|
||||
"B_STPHY_CONS" "B_STPHY_PLVR" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus pulvereri"
|
||||
"B_STPHY_CONS" "B_STPHY_RATT" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus ratti"
|
||||
"B_STPHY_CONS" "B_STPHY_RSTR" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus rostri"
|
||||
"B_STPHY_CONS" "B_STPHY_SCCH" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus saccharolyticus"
|
||||
"B_STPHY_CONS" "B_STPHY_SPRP" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus saprophyticus"
|
||||
"B_STPHY_CONS" "B_STPHY_SPRP_BOVS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus saprophyticus bovis"
|
||||
"B_STPHY_CONS" "B_STPHY_SPRP_SPRP" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus saprophyticus saprophyticus"
|
||||
"B_STPHY_CONS" "B_STPHY_SCHL" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus schleiferi"
|
||||
"B_STPHY_CONS" "B_STPHY_SCHL_SCHL" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus schleiferi schleiferi"
|
||||
"B_STPHY_CONS" "B_STPHY_SCIR" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus sciuri"
|
||||
"B_STPHY_CONS" "B_STPHY_SCIR_CRNT" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus sciuri carnaticus"
|
||||
"B_STPHY_CONS" "B_STPHY_SCIR_LNTS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus sciuri lentus"
|
||||
"B_STPHY_CONS" "B_STPHY_SCIR_RDNT" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus sciuri rodentium"
|
||||
"B_STPHY_CONS" "B_STPHY_SCIR_SCIR" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus sciuri sciuri"
|
||||
"B_STPHY_CONS" "B_STPHY_SMLN" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus simulans"
|
||||
"B_STPHY_CONS" "B_STPHY_STPN" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus stepanovicii"
|
||||
"B_STPHY_CONS" "B_STPHY_SCCN" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus succinus"
|
||||
"B_STPHY_CONS" "B_STPHY_SCCN_CASE" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus succinus casei"
|
||||
"B_STPHY_CONS" "B_STPHY_SCCN_SCCN" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus succinus succinus"
|
||||
"B_STPHY_CONS" "B_STPHY_TWNN" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus taiwanensis"
|
||||
"B_STPHY_CONS" "B_STPHY_URLYT" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus urealyticus"
|
||||
"B_STPHY_CONS" "B_STPHY_URLY" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus ureilyticus"
|
||||
"B_STPHY_CONS" "B_STPHY_VRTR" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus veratri"
|
||||
"B_STPHY_CONS" "B_STPHY_VTLN" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus vitulinus"
|
||||
"B_STPHY_CONS" "B_STPHY_VTLS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus vitulus"
|
||||
"B_STPHY_CONS" "B_STPHY_WRNR" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus warneri"
|
||||
"B_STPHY_CONS" "B_STPHY_XYLS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus xylosus"
|
||||
"B_STPHY_COPS" "B_STPHY_AGNT" "Coagulase-positive Staphylococcus (CoPS)" "Staphylococcus agnetis"
|
||||
"B_STPHY_COPS" "B_STPHY_GNTS" "Coagulase-positive Staphylococcus (CoPS)" "Staphylococcus argenteus"
|
||||
"B_STPHY_COPS" "B_STPHY_CGLN" "Coagulase-positive Staphylococcus (CoPS)" "Staphylococcus coagulans"
|
||||
"B_STPHY_COPS" "B_STPHY_CRNB" "Coagulase-positive Staphylococcus (CoPS)" "Staphylococcus cornubiensis"
|
||||
"B_STPHY_COPS" "B_STPHY_DLPH" "Coagulase-positive Staphylococcus (CoPS)" "Staphylococcus delphini"
|
||||
"B_STPHY_COPS" "B_STPHY_HYCS" "Coagulase-positive Staphylococcus (CoPS)" "Staphylococcus hyicus"
|
||||
"B_STPHY_COPS" "B_STPHY_HYCS_CHRM" "Coagulase-positive Staphylococcus (CoPS)" "Staphylococcus hyicus chromogenes"
|
||||
"B_STPHY_COPS" "B_STPHY_HYCS_HYCS" "Coagulase-positive Staphylococcus (CoPS)" "Staphylococcus hyicus hyicus"
|
||||
"B_STPHY_COPS" "B_STPHY_INTR" "Coagulase-positive Staphylococcus (CoPS)" "Staphylococcus intermedius"
|
||||
"B_STPHY_COPS" "B_STPHY_LUTR" "Coagulase-positive Staphylococcus (CoPS)" "Staphylococcus lutrae"
|
||||
"B_STPHY_COPS" "B_STPHY_PSDN" "Coagulase-positive Staphylococcus (CoPS)" "Staphylococcus pseudintermedius"
|
||||
"B_STPHY_COPS" "B_STPHY_RTRD" "Coagulase-positive Staphylococcus (CoPS)" "Staphylococcus roterodami"
|
||||
"B_STPHY_COPS" "B_STPHY_SCHL_CGLN" "Coagulase-positive Staphylococcus (CoPS)" "Staphylococcus schleiferi coagulans"
|
||||
"B_STPHY_COPS" "B_STPHY_SCHW" "Coagulase-positive Staphylococcus (CoPS)" "Staphylococcus schweitzeri"
|
||||
"B_STPHY_COPS" "B_STPHY_SIMI" "Coagulase-positive Staphylococcus (CoPS)" "Staphylococcus simiae"
|
||||
"B_STPHY_COPS" "B_STPHY_SNGP" "Coagulase-positive Staphylococcus (CoPS)" "Staphylococcus singaporensis"
|
||||
"B_CORYNF" "B_ARCNB" "Coryneform bacterium" "Arcanobacterium"
|
||||
"B_CORYNF" "B_ARCNB_HMLY" "Coryneform bacterium" "Arcanobacterium haemolyticum"
|
||||
"B_CORYNF" "B_BCTRM" "Coryneform bacterium" "Brevibacterium"
|
||||
"B_CORYNF" "B_BCTRM_CASE" "Coryneform bacterium" "Brevibacterium casei"
|
||||
"B_CORYNF" "B_BCTRM_EPDR" "Coryneform bacterium" "Brevibacterium epidermidis"
|
||||
"B_CORYNF" "B_BCTRM_MCBR" "Coryneform bacterium" "Brevibacterium mcbrellneri"
|
||||
"B_CORYNF" "B_CLLLM" "Coryneform bacterium" "Cellulomonas"
|
||||
"B_CORYNF" "B_CLLLSM" "Coryneform bacterium" "Cellulosimicrobium"
|
||||
"B_CORYNF" "B_CLLLSM_CLLL" "Coryneform bacterium" "Cellulosimicrobium cellulans"
|
||||
"B_CORYNF" "B_CRYNB" "Coryneform bacterium" "Corynebacterium"
|
||||
"B_CORYNF" "B_CRYNB_ACCL" "Coryneform bacterium" "Corynebacterium accolens"
|
||||
"B_CORYNF" "B_CRYNB_AFRM" "Coryneform bacterium" "Corynebacterium afermentans"
|
||||
"B_CORYNF" "B_CRYNB_AMYC" "Coryneform bacterium" "Corynebacterium amycolatum"
|
||||
"B_CORYNF" "B_CRYNB_ARGN" "Coryneform bacterium" "Corynebacterium argentoratense"
|
||||
"B_CORYNF" "B_CRYNB_ARMC" "Coryneform bacterium" "Corynebacterium aurimucosum"
|
||||
"B_CORYNF" "B_CRYNB_AURS" "Coryneform bacterium" "Corynebacterium auris"
|
||||
"B_CORYNF" "B_CRYNB_BOVS" "Coryneform bacterium" "Corynebacterium bovis"
|
||||
"B_CORYNF" "B_CRYNB_COYL" "Coryneform bacterium" "Corynebacterium coyleae"
|
||||
"B_CORYNF" "B_CRYNB_CYST" "Coryneform bacterium" "Corynebacterium cystitidis"
|
||||
"B_CORYNF" "B_CRYNB_DPHT" "Coryneform bacterium" "Corynebacterium diphtheriae"
|
||||
"B_CORYNF" "B_CRYNB_GLCR" "Coryneform bacterium" "Corynebacterium glucuronolyticum"
|
||||
"B_CORYNF" "B_CRYNB_GLTM" "Coryneform bacterium" "Corynebacterium glutamicum"
|
||||
"B_CORYNF" "B_CRYNB_JEKM" "Coryneform bacterium" "Corynebacterium jeikeium"
|
||||
"B_CORYNF" "B_CRYNB_KTSC" "Coryneform bacterium" "Corynebacterium kutscheri"
|
||||
"B_CORYNF" "B_CRYNB_MCGN" "Coryneform bacterium" "Corynebacterium macginleyi"
|
||||
"B_CORYNF" "B_CRYNB_MTRC" "Coryneform bacterium" "Corynebacterium matruchotii"
|
||||
"B_CORYNF" "B_CRYNB_MNTS" "Coryneform bacterium" "Corynebacterium minutissimum"
|
||||
"B_CORYNF" "B_CRYNB_MCFC" "Coryneform bacterium" "Corynebacterium mucifaciens"
|
||||
"B_CORYNF" "B_CRYNB_MYCT" "Coryneform bacterium" "Corynebacterium mycetoides"
|
||||
"B_CORYNF" "B_CRYNB_PLSM" "Coryneform bacterium" "Corynebacterium pilosum"
|
||||
"B_CORYNF" "B_CRYNB_PRPN" "Coryneform bacterium" "Corynebacterium propinquum"
|
||||
"B_CORYNF" "B_CRYNB_PSDD" "Coryneform bacterium" "Corynebacterium pseudodiphtheriticum"
|
||||
"B_CORYNF" "B_CRYNB_PSDT" "Coryneform bacterium" "Corynebacterium pseudotuberculosis"
|
||||
"B_CORYNF" "B_CRYNB_RENL" "Coryneform bacterium" "Corynebacterium renale"
|
||||
"B_CORYNF" "B_CRYNB_STRT" "Coryneform bacterium" "Corynebacterium striatum"
|
||||
"B_CORYNF" "B_CRYNB_ULCR" "Coryneform bacterium" "Corynebacterium ulcerans"
|
||||
"B_CORYNF" "B_CRYNB_URLY" "Coryneform bacterium" "Corynebacterium urealyticum"
|
||||
"B_CORYNF" "B_CRYNB_XRSS" "Coryneform bacterium" "Corynebacterium xerosis"
|
||||
"B_CORYNF" "B_DRMBC" "Coryneform bacterium" "Dermabacter"
|
||||
"B_CORYNF" "B_DRMBC_HMNS" "Coryneform bacterium" "Dermabacter hominis"
|
||||
"B_CORYNF" "B_LEFSN" "Coryneform bacterium" "Leifsonia"
|
||||
"B_CORYNF" "B_LEFSN_AQTC" "Coryneform bacterium" "Leifsonia aquatica"
|
||||
"B_CORYNF" "B_MCRBC" "Coryneform bacterium" "Microbacterium"
|
||||
"B_CORYNF" "B_MCRBC_ARBR" "Coryneform bacterium" "Microbacterium arborescens"
|
||||
"B_CORYNF" "B_MCRBC_IMPR" "Coryneform bacterium" "Microbacterium imperiale"
|
||||
"B_CORYNF" "B_MCRBC_LQFC" "Coryneform bacterium" "Microbacterium liquefaciens"
|
||||
"B_CORYNF" "B_MCRBC_OXYD" "Coryneform bacterium" "Microbacterium oxydans"
|
||||
"B_CORYNF" "B_ORSKV" "Coryneform bacterium" "Oerskovia"
|
||||
"B_CORYNF" "B_ORSKV_TRBT" "Coryneform bacterium" "Oerskovia turbata"
|
||||
"B_CORYNF" "B_ROTHI" "Coryneform bacterium" "Rothia"
|
||||
"B_CORYNF" "B_ROTHI_DNTC" "Coryneform bacterium" "Rothia dentocariosa"
|
||||
"B_CORYNF" "B_ROTHI_MCLG" "Coryneform bacterium" "Rothia mucilaginosa"
|
||||
"B_CORYNF" "B_TRPRL" "Coryneform bacterium" "Trueperella"
|
||||
"B_CORYNF" "B_TRPRL_BRNR" "Coryneform bacterium" "Trueperella bernardiae"
|
||||
"B_CORYNF" "B_TRPRL_PYGN" "Coryneform bacterium" "Trueperella pyogenes"
|
||||
"B_CORYNF" "B_TRCLL" "Coryneform bacterium" "Turicella"
|
||||
"B_CORYNF" "B_TRCLL_OTTD" "Coryneform bacterium" "Turicella otitidis"
|
||||
"B_ENTRBC_CLOC-C" "B_ENTRBC_ASBR" "Enterobacter cloacae complex" "Enterobacter asburiae"
|
||||
"B_ENTRBC_CLOC-C" "B_ENTRBC_CLOC" "Enterobacter cloacae complex" "Enterobacter cloacae"
|
||||
"B_ENTRBC_CLOC-C" "B_ENTRBC_CLOC_DSSL" "Enterobacter cloacae complex" "Enterobacter cloacae dissolvens"
|
||||
"B_ENTRBC_CLOC-C" "B_ENTRBC_HRMC" "Enterobacter cloacae complex" "Enterobacter hormaechei"
|
||||
"B_ENTRBC_CLOC-C" "B_ENTRBC_KOBE" "Enterobacter cloacae complex" "Enterobacter kobei"
|
||||
"B_ENTRBC_CLOC-C" "B_ENTRBC_LDWG" "Enterobacter cloacae complex" "Enterobacter ludwigii"
|
||||
"B_ENTRBC_CLOC-C" "B_ENTRBC_NMPR" "Enterobacter cloacae complex" "Enterobacter nimipressuralis"
|
||||
"B_HACEK" "B_ACTNB_ACTN" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Actinobacillus actinomycetemcomitans"
|
||||
"B_HACEK" "B_AGGRG" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Aggregatibacter"
|
||||
"B_HACEK" "B_AGGRG_ACTN" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Aggregatibacter actinomycetemcomitans"
|
||||
"B_HACEK" "B_AGGRG_APHR" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Aggregatibacter aphrophilus"
|
||||
"B_HACEK" "B_AGGRG_KILN" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Aggregatibacter kilianii"
|
||||
"B_HACEK" "B_AGGRG_PRPH" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Aggregatibacter paraphrophilus"
|
||||
"B_HACEK" "B_AGGRG_SGNS" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Aggregatibacter segnis"
|
||||
"B_HACEK" "B_CRDBC_HMNS" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Cardiobacterium hominis"
|
||||
"B_HACEK" "B_EKNLL_CRRD" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Eikenella corrodens"
|
||||
"B_HACEK" "B_HMPHL" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus"
|
||||
"B_HACEK" "B_HMPHL_ACTN" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus actinomycetemcomitans"
|
||||
"B_HACEK" "B_HMPHL_AEGY" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus aegyptius"
|
||||
"B_HACEK" "B_HMPHL_APHR" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus aphrophilus"
|
||||
"B_HACEK" "B_HMPHL_AVIM" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus avium"
|
||||
"B_HACEK" "B_HMPHL_DCRY" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus ducreyi"
|
||||
"B_HACEK" "B_HMPHL_EQGN" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus equigenitalis"
|
||||
"B_HACEK" "B_HMPHL_FELS" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus felis"
|
||||
"B_HACEK" "B_HMPHL_HMGL" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus haemoglobinophilus"
|
||||
"B_HACEK" "B_HMPHL_HMLY" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus haemolyticus"
|
||||
"B_HACEK" "B_HMPHL_INFL" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus influenzae"
|
||||
"B_HACEK" "B_HMPHL_MSSL" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus massiliensis"
|
||||
"B_HACEK" "B_HMPHL_PRCN" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus paracuniculus"
|
||||
"B_HACEK" "B_HMPHL_PRGL" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus paragallinarum"
|
||||
"B_HACEK" "B_HMPHL_PRHM" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus parahaemolyticus"
|
||||
"B_HACEK" "B_HMPHL_PRNF" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus parainfluenzae"
|
||||
"B_HACEK" "B_HMPHL_PRPH" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus paraphrohaemolyticus"
|
||||
"B_HACEK" "B_HMPHL_PHLS" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus paraphrophilus"
|
||||
"B_HACEK" "B_HMPHL_PRSS" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus parasuis"
|
||||
"B_HACEK" "B_HMPHL_PSCM" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus piscium"
|
||||
"B_HACEK" "B_HMPHL_PTTM" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus pittmaniae"
|
||||
"B_HACEK" "B_HMPHL_PLRP" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus pleuropneumoniae"
|
||||
"B_HACEK" "B_HMPHL_QNTN" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus quentini"
|
||||
"B_HACEK" "B_HMPHL_SGNS" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus segnis"
|
||||
"B_HACEK" "B_HMPHL_SMNL" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus seminalis"
|
||||
"B_HACEK" "B_HMPHL_SPTR" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus sputorum"
|
||||
"B_HACEK" "B_HMPHL_VGNL" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Haemophilus vaginalis"
|
||||
"B_HACEK" "B_KGLLA" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Kingella"
|
||||
"B_HACEK" "B_KGLLA_DNTR" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Kingella denitrificans"
|
||||
"B_HACEK" "B_KGLLA_INDL" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Kingella indologenes"
|
||||
"B_HACEK" "B_KGLLA_KING" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Kingella kingae"
|
||||
"B_HACEK" "B_KGLLA_NGVN" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Kingella negevensis"
|
||||
"B_HACEK" "B_KGLLA_ORAL" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Kingella orale"
|
||||
"B_HACEK" "B_KGLLA_ORLS" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Kingella oralis"
|
||||
"B_HACEK" "B_KGLLA_POTS" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Kingella potus"
|
||||
"F_MYRZY_GLLR-C" "F_CANDD_FRMN" "Meyerozyma guilliermondii complex" "Candida fermentati"
|
||||
"F_MYRZY_GLLR-C" "F_MYRZY_CRBB" "Meyerozyma guilliermondii complex" "Meyerozyma caribbica"
|
||||
"F_MYRZY_GLLR-C" "F_MYRZY_CRPP" "Meyerozyma guilliermondii complex" "Meyerozyma carpophila"
|
||||
"F_MYRZY_GLLR-C" "F_MYRZY_GLLR" "Meyerozyma guilliermondii complex" "Meyerozyma guilliermondii"
|
||||
"B_MYCBC_AVIM-C" "B_MYCBC_AVIM" "Mycobacterium avium-intracellulare complex" "Mycobacterium avium"
|
||||
"B_MYCBC_AVIM-C" "B_MYCBC_AVIM_PRTB" "Mycobacterium avium-intracellulare complex" "Mycobacterium avium paratuberculosis"
|
||||
"B_MYCBC_AVIM-C" "B_MYCBC_LLRE" "Mycobacterium avium-intracellulare complex" "Mycobacterium intracellulare"
|
||||
"B_MYCBC_AVIM-C" "B_MYCBC_LLRE_CHMR" "Mycobacterium avium-intracellulare complex" "Mycobacterium intracellulare chimaera"
|
||||
"B_MYCBC_TBRC-C" "B_MYCBC_AFRC" "Mycobacterium tuberculosis complex" "Mycobacterium africanum"
|
||||
"B_MYCBC_TBRC-C" "B_MYCBC_BOVS" "Mycobacterium tuberculosis complex" "Mycobacterium bovis"
|
||||
"B_MYCBC_TBRC-C" "B_MYCBC_CAPR" "Mycobacterium tuberculosis complex" "Mycobacterium caprae"
|
||||
"B_MYCBC_TBRC-C" "B_MYCBC_MCRT" "Mycobacterium tuberculosis complex" "Mycobacterium microti"
|
||||
"B_MYCBC_TBRC-C" "B_MYCBC_MUNG" "Mycobacterium tuberculosis complex" "Mycobacterium mungi"
|
||||
"B_MYCBC_TBRC-C" "B_MYCBC_ORYG" "Mycobacterium tuberculosis complex" "Mycobacterium orygis"
|
||||
"B_MYCBC_TBRC-C" "B_MYCBC_PNNP" "Mycobacterium tuberculosis complex" "Mycobacterium pinnipedii"
|
||||
"B_MYCBC_TBRC-C" "B_MYCBC_TBRC" "Mycobacterium tuberculosis complex" "Mycobacterium tuberculosis"
|
||||
"B_PSDMN_FLRS-C" "B_PSDMN_FLRS" "Pseudomonas fluorescens complex" "Pseudomonas fluorescens"
|
||||
"B_MYCBC_RGM" "B_MYCBC_ABSC_ABSC" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium abscessus abscessus"
|
||||
"B_MYCBC_RGM" "B_MYCBC_ABSC_BLLT" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium abscessus bolletii"
|
||||
"B_MYCBC_RGM" "B_MYCBC_ABSC_MSSL" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium abscessus massiliense"
|
||||
"B_MYCBC_RGM" "B_MYCBC_AGRI" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium agri"
|
||||
"B_MYCBC_RGM" "B_MYCBC_ACHN" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium aichiense"
|
||||
"B_MYCBC_RGM" "B_MYCBC_ALGR" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium algericum"
|
||||
"B_MYCBC_RGM" "B_MYCBC_ALVE" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium alvei"
|
||||
"B_MYCBC_RGM" "B_MYCBC_ANYN" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium anyangense"
|
||||
"B_MYCBC_RGM" "B_MYCBC_ARBN" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium arabiense"
|
||||
"B_MYCBC_RGM" "B_MYCBC_ARMT" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium aromaticivorans"
|
||||
"B_MYCBC_RGM" "B_MYCBC_ABGN" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium aubagnense"
|
||||
"B_MYCBC_RGM" "B_MYCBC_AURM" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium aurum"
|
||||
"B_MYCBC_RGM" "B_MYCBC_ASTR" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium austroafricanum"
|
||||
"B_MYCBC_RGM" "B_MYCBC_BCTR" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium bacteremicum"
|
||||
"B_MYCBC_RGM" "B_MYCBC_BNCK" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium boenickei"
|
||||
"B_MYCBC_RGM" "B_MYCBC_BRGL" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium bourgelatii"
|
||||
"B_MYCBC_RGM" "B_MYCBC_BRSB" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium brisbanense"
|
||||
"B_MYCBC_RGM" "B_MYCBC_BRUM" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium brumae"
|
||||
"B_MYCBC_RGM" "B_MYCBC_CNRS" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium canariasense"
|
||||
"B_MYCBC_RGM" "B_MYCBC_CLRF" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium celeriflavum"
|
||||
"B_MYCBC_RGM" "B_MYCBC_CHLN" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium chelonae"
|
||||
"B_MYCBC_RGM" "B_MYCBC_CHIT" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium chitae"
|
||||
"B_MYCBC_RGM" "B_MYCBC_CHLR" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium chlorophenolicum"
|
||||
"B_MYCBC_RGM" "B_MYCBC_CHBN" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium chubuense"
|
||||
"B_MYCBC_RGM" "B_MYCBC_CNFL" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium confluentis"
|
||||
"B_MYCBC_RGM" "B_MYCBC_CSMT" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium cosmeticum"
|
||||
"B_MYCBC_RGM" "B_MYCBC_CRCN" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium crocinum"
|
||||
"B_MYCBC_RGM" "B_MYCBC_DRNH" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium diernhoferi"
|
||||
"B_MYCBC_RGM" "B_MYCBC_DUVL" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium duvalii"
|
||||
"B_MYCBC_RGM" "B_MYCBC_ELPH" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium elephantis"
|
||||
"B_MYCBC_RGM" "B_MYCBC_FLLX" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium fallax"
|
||||
"B_MYCBC_RGM" "B_MYCBC_FLVS" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium flavescens"
|
||||
"B_MYCBC_RGM" "B_MYCBC_VRNS" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium fluoranthenivorans"
|
||||
"B_MYCBC_RGM" "B_MYCBC_FRTT" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium fortuitum"
|
||||
"B_MYCBC_RGM" "B_MYCBC_FRNK" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium franklinii"
|
||||
"B_MYCBC_RGM" "B_MYCBC_FRDR" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium frederiksbergense"
|
||||
"B_MYCBC_RGM" "B_MYCBC_GADM" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium gadium"
|
||||
"B_MYCBC_RGM" "B_MYCBC_GLVM" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium gilvum"
|
||||
"B_MYCBC_RGM" "B_MYCBC_GOOD" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium goodii"
|
||||
"B_MYCBC_RGM" "B_MYCBC_HSSC" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium hassiacum"
|
||||
"B_MYCBC_RGM" "B_MYCBC_HPPC" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium hippocampi"
|
||||
"B_MYCBC_RGM" "B_MYCBC_HDLR" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium hodleri"
|
||||
"B_MYCBC_RGM" "B_MYCBC_HLST" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium holsaticum"
|
||||
"B_MYCBC_RGM" "B_MYCBC_HSTN" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium houstonense"
|
||||
"B_MYCBC_RGM" "B_MYCBC_IMMN" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium immunogenum"
|
||||
"B_MYCBC_RGM" "B_MYCBC_INSB" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium insubricum"
|
||||
"B_MYCBC_RGM" "B_MYCBC_IRNC" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium iranicum"
|
||||
"B_MYCBC_RGM" "B_MYCBC_KMSS" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium komossense"
|
||||
"B_MYCBC_RGM" "B_MYCBC_LTRL" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium litorale"
|
||||
"B_MYCBC_RGM" "B_MYCBC_LLTZ" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium llatzerense"
|
||||
"B_MYCBC_RGM" "B_MYCBC_MDGS" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium madagascariense"
|
||||
"B_MYCBC_RGM" "B_MYCBC_MGRT" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium mageritense"
|
||||
"B_MYCBC_RGM" "B_MYCBC_MNCN" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium monacense"
|
||||
"B_MYCBC_RGM" "B_MYCBC_MRKN" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium moriokaense"
|
||||
"B_MYCBC_RGM" "B_MYCBC_MCGN" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium mucogenicum"
|
||||
"B_MYCBC_RGM" "B_MYCBC_MURL" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium murale"
|
||||
"B_MYCBC_RGM" "B_MYCBC_NERM" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium neoaurum"
|
||||
"B_MYCBC_RGM" "B_MYCBC_NWRL" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium neworleansense"
|
||||
"B_MYCBC_RGM" "B_MYCBC_NVCS" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium novocastrense"
|
||||
"B_MYCBC_RGM" "B_MYCBC_OBNS" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium obuense"
|
||||
"B_MYCBC_RGM" "B_MYCBC_PLLN" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium pallens"
|
||||
"B_MYCBC_RGM" "B_MYCBC_PRFR" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium parafortuitum"
|
||||
"B_MYCBC_RGM" "B_MYCBC_GRNM" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium peregrinum"
|
||||
"B_MYCBC_RGM" "B_MYCBC_PHLE" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium phlei"
|
||||
"B_MYCBC_RGM" "B_MYCBC_PHCC" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium phocaicum"
|
||||
"B_MYCBC_RGM" "B_MYCBC_PRCN" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium porcinum"
|
||||
"B_MYCBC_RGM" "B_MYCBC_RFRE" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium poriferae"
|
||||
"B_MYCBC_RGM" "B_MYCBC_PSYC" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium psychrotolerans"
|
||||
"B_MYCBC_RGM" "B_MYCBC_PYRN" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium pyrenivorans"
|
||||
"B_MYCBC_RGM" "B_MYCBC_RHDS" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium rhodesiae"
|
||||
"B_MYCBC_RGM" "B_MYCBC_RUFM" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium rufum"
|
||||
"B_MYCBC_RGM" "B_MYCBC_RTLM" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium rutilum"
|
||||
"B_MYCBC_RGM" "B_MYCBC_SLMN" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium salmoniphilum"
|
||||
"B_MYCBC_RGM" "B_MYCBC_SDMN" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium sediminis"
|
||||
"B_MYCBC_RGM" "B_MYCBC_SNGL" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium senegalense"
|
||||
"B_MYCBC_RGM" "B_MYCBC_SPTC" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium septicum"
|
||||
"B_MYCBC_RGM" "B_MYCBC_STNS" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium setense"
|
||||
"B_MYCBC_RGM" "B_MYCBC_SMGM" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium smegmatis"
|
||||
"B_MYCBC_RGM" "B_MYCBC_SPHG" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium sphagni"
|
||||
"B_MYCBC_RGM" "B_MYCBC_THRM" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium thermoresistibile"
|
||||
"B_MYCBC_RGM" "B_MYCBC_TKNS" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium tokaiense"
|
||||
"B_MYCBC_RGM" "B_MYCBC_VACC" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium vaccae"
|
||||
"B_MYCBC_RGM" "B_MYCBC_VNBL" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium vanbaalenii"
|
||||
"B_MYCBC_RGM" "B_MYCBC_WLNS" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium wolinskyi"
|
||||
"B_MYCBC_SGM" "B_MYCBC_FRCN" "Slowly growing Mycobacterium (SGM)" "Mycobacterium farcinogenes"
|
||||
"B_MYCBC_SGM" "B_MYCBC_GSTR" "Slowly growing Mycobacterium (SGM)" "Mycobacterium gastri"
|
||||
"B_MYCBC_SGM" "B_MYCBC_GNVN" "Slowly growing Mycobacterium (SGM)" "Mycobacterium genavense"
|
||||
"B_MYCBC_SGM" "B_MYCBC_HMPH" "Slowly growing Mycobacterium (SGM)" "Mycobacterium haemophilum"
|
||||
"B_MYCBC_SGM" "B_MYCBC_KNSS" "Slowly growing Mycobacterium (SGM)" "Mycobacterium kansasii"
|
||||
"B_MYCBC_SGM" "B_MYCBC_LEPR" "Slowly growing Mycobacterium (SGM)" "Mycobacterium leprae"
|
||||
"B_MYCBC_SGM" "B_MYCBC_LPRM" "Slowly growing Mycobacterium (SGM)" "Mycobacterium lepraemurium"
|
||||
"B_MYCBC_SGM" "B_MYCBC_MLMN" "Slowly growing Mycobacterium (SGM)" "Mycobacterium malmoense"
|
||||
"B_MYCBC_SGM" "B_MYCBC_MRNM" "Slowly growing Mycobacterium (SGM)" "Mycobacterium marinum"
|
||||
"B_STRPT_GRPA" "B_STRPT_PYGN" "Streptococcus Group A" "Streptococcus pyogenes"
|
||||
"B_STRPT_ABCG" "B_STRPT_AGLC" "Streptococcus Group A, B, C, G" "Streptococcus agalactiae"
|
||||
"B_STRPT_ABCG" "B_STRPT_CANS" "Streptococcus Group A, B, C, G" "Streptococcus canis"
|
||||
"B_STRPT_ABCG" "B_STRPT_DYSG" "Streptococcus Group A, B, C, G" "Streptococcus dysgalactiae"
|
||||
"B_STRPT_ABCG" "B_STRPT_DYSG_DYSG" "Streptococcus Group A, B, C, G" "Streptococcus dysgalactiae dysgalactiae"
|
||||
"B_STRPT_ABCG" "B_STRPT_DYSG_EQSM" "Streptococcus Group A, B, C, G" "Streptococcus dysgalactiae equisimilis"
|
||||
"B_STRPT_ABCG" "B_STRPT_EQUI" "Streptococcus Group A, B, C, G" "Streptococcus equi"
|
||||
"B_STRPT_ABCG" "B_STRPT_EQUI_EQUI" "Streptococcus Group A, B, C, G" "Streptococcus equi equi"
|
||||
"B_STRPT_ABCG" "B_STRPT_EQUI_RMNT" "Streptococcus Group A, B, C, G" "Streptococcus equi ruminatorum"
|
||||
"B_STRPT_ABCG" "B_STRPT_EQUI_ZPDM" "Streptococcus Group A, B, C, G" "Streptococcus equi zooepidemicus"
|
||||
"B_STRPT_ABCG" "B_STRPT_PYGN" "Streptococcus Group A, B, C, G" "Streptococcus pyogenes"
|
||||
"B_STRPT_GRPB" "B_STRPT_AGLC" "Streptococcus Group B" "Streptococcus agalactiae"
|
||||
"B_STRPT_GRPC" "B_STRPT_DYSG" "Streptococcus Group C" "Streptococcus dysgalactiae"
|
||||
"B_STRPT_GRPC" "B_STRPT_DYSG_DYSG" "Streptococcus Group C" "Streptococcus dysgalactiae dysgalactiae"
|
||||
"B_STRPT_GRPC" "B_STRPT_DYSG_EQSM" "Streptococcus Group C" "Streptococcus dysgalactiae equisimilis"
|
||||
"B_STRPT_GRPC" "B_STRPT_EQUI" "Streptococcus Group C" "Streptococcus equi"
|
||||
"B_STRPT_GRPC" "B_STRPT_EQUI_EQUI" "Streptococcus Group C" "Streptococcus equi equi"
|
||||
"B_STRPT_GRPC" "B_STRPT_EQUI_RMNT" "Streptococcus Group C" "Streptococcus equi ruminatorum"
|
||||
"B_STRPT_GRPC" "B_STRPT_EQUI_ZPDM" "Streptococcus Group C" "Streptococcus equi zooepidemicus"
|
||||
"B_STRPT_GRPF" "B_STRPT_ANGN" "Streptococcus Group F" "Streptococcus anginosus"
|
||||
"B_STRPT_GRPF" "B_STRPT_ANGN_ANGN" "Streptococcus Group F" "Streptococcus anginosus anginosus"
|
||||
"B_STRPT_GRPF" "B_STRPT_ANGN_WHLY" "Streptococcus Group F" "Streptococcus anginosus whileyi"
|
||||
"B_STRPT_GRPG" "B_STRPT_CANS" "Streptococcus Group G" "Streptococcus canis"
|
||||
"B_STRPT_GRPG" "B_STRPT_DYSG" "Streptococcus Group G" "Streptococcus dysgalactiae"
|
||||
"B_STRPT_GRPG" "B_STRPT_DYSG_DYSG" "Streptococcus Group G" "Streptococcus dysgalactiae dysgalactiae"
|
||||
"B_STRPT_GRPG" "B_STRPT_DYSG_EQSM" "Streptococcus Group G" "Streptococcus dysgalactiae equisimilis"
|
||||
"B_STRPT_GRPH" "B_STRPT_SNGN" "Streptococcus Group H" "Streptococcus sanguinis"
|
||||
"B_STRPT_GRPK" "B_STRPT_SLVR" "Streptococcus Group K" "Streptococcus salivarius"
|
||||
"B_STRPT_GRPK" "B_STRPT_SLVR_SLVR" "Streptococcus Group K" "Streptococcus salivarius salivarius"
|
||||
"B_STRPT_GRPK" "B_STRPT_SLVR_THRM" "Streptococcus Group K" "Streptococcus salivarius thermophilus"
|
||||
"B_STRPT_VIRI" "B_STRPT_MILL" "Viridans Group Streptococcus (VGS)" "Milleri Group Streptococcus (MGS)"
|
||||
"B_STRPT_VIRI" "B_STRPT_ACDM" "Viridans Group Streptococcus (VGS)" "Streptococcus acidominimus"
|
||||
"B_STRPT_VIRI" "B_STRPT_ANGN" "Viridans Group Streptococcus (VGS)" "Streptococcus anginosus"
|
||||
"B_STRPT_VIRI" "B_STRPT_CNST" "Viridans Group Streptococcus (VGS)" "Streptococcus constellatus"
|
||||
"B_STRPT_VIRI" "B_STRPT_CRCT" "Viridans Group Streptococcus (VGS)" "Streptococcus criceti"
|
||||
"B_STRPT_VIRI" "B_STRPT_CRST" "Viridans Group Streptococcus (VGS)" "Streptococcus cristatus"
|
||||
"B_STRPT_VIRI" "B_STRPT_DOWN" "Viridans Group Streptococcus (VGS)" "Streptococcus downei"
|
||||
"B_STRPT_VIRI" "B_STRPT_EQNS" "Viridans Group Streptococcus (VGS)" "Streptococcus equinus"
|
||||
"B_STRPT_VIRI" "B_STRPT_FERS" "Viridans Group Streptococcus (VGS)" "Streptococcus ferus"
|
||||
"B_STRPT_VIRI" "B_STRPT_GRDN" "Viridans Group Streptococcus (VGS)" "Streptococcus gordonii"
|
||||
"B_STRPT_VIRI" "B_STRPT_INTR" "Viridans Group Streptococcus (VGS)" "Streptococcus intermedius"
|
||||
"B_STRPT_VIRI" "B_STRPT_MACC" "Viridans Group Streptococcus (VGS)" "Streptococcus macacae"
|
||||
"B_STRPT_VIRI" "B_STRPT_MITS" "Viridans Group Streptococcus (VGS)" "Streptococcus mitis"
|
||||
"B_STRPT_VIRI" "B_STRPT_MTNS" "Viridans Group Streptococcus (VGS)" "Streptococcus mutans"
|
||||
"B_STRPT_VIRI" "B_STRPT_ORLS" "Viridans Group Streptococcus (VGS)" "Streptococcus oralis"
|
||||
"B_STRPT_VIRI" "B_STRPT_PRSN" "Viridans Group Streptococcus (VGS)" "Streptococcus parasanguinis"
|
||||
"B_STRPT_VIRI" "B_STRPT_RATT" "Viridans Group Streptococcus (VGS)" "Streptococcus ratti"
|
||||
"B_STRPT_VIRI" "B_STRPT_SLVR" "Viridans Group Streptococcus (VGS)" "Streptococcus salivarius"
|
||||
"B_STRPT_VIRI" "B_STRPT_SNGN" "Viridans Group Streptococcus (VGS)" "Streptococcus sanguinis"
|
||||
"B_STRPT_VIRI" "B_STRPT_SBRN" "Viridans Group Streptococcus (VGS)" "Streptococcus sobrinus"
|
||||
"B_STRPT_VIRI" "B_STRPT_SUIS" "Viridans Group Streptococcus (VGS)" "Streptococcus suis"
|
||||
"B_STRPT_VIRI" "B_STRPT_UBRS" "Viridans Group Streptococcus (VGS)" "Streptococcus uberis"
|
||||
"B_STRPT_VIRI" "B_STRPT_VSTB" "Viridans Group Streptococcus (VGS)" "Streptococcus vestibularis"
|
||||
BIN
data-raw/microorganisms.groups.xlsx
Normal file
BIN
data-raw/microorganisms.groups.xlsx
Normal file
Binary file not shown.
0
data-raw/microorganisms.groups.xpt
Normal file
0
data-raw/microorganisms.groups.xpt
Normal file
@ -1 +1 @@
|
||||
2d19b559a6c4b6f26449271ed1e37ea8
|
||||
fb5a6892877b6ac86040e1f0508486c5
|
||||
|
||||
Binary file not shown.
Binary file not shown.
Binary file not shown.
File diff suppressed because it is too large
Load Diff
Binary file not shown.
Binary file not shown.
Binary file not shown.
BIN
data-raw/organisms.rds
Normal file
BIN
data-raw/organisms.rds
Normal file
Binary file not shown.
@ -35,10 +35,12 @@ library(readr)
|
||||
library(tidyr)
|
||||
devtools::load_all()
|
||||
|
||||
# Install the WHONET 2022 software on Windows (http://www.whonet.org/software.html),
|
||||
# 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
|
||||
# (for ASIARS-Net update, also copy C:\WHONET\Codes to the data-raw/WHONET/ folder)
|
||||
|
||||
# BE SURE TO RUN data-raw/reproduction_of_microorganisms.groups.R FIRST TO GET THE GROUPS!
|
||||
|
||||
# READ DATA ----
|
||||
|
||||
whonet_organisms <- read_tsv("data-raw/WHONET/Resources/Organisms.txt", na = c("", "NA", "-"), show_col_types = FALSE) %>%
|
||||
@ -71,13 +73,6 @@ whonet_organisms <- whonet_organisms %>%
|
||||
bind_rows(data.frame(ORGANISM_CODE = "ebc", ORGANISM = "Enterobacterales", mo = as.mo("Enterobacterales"))) %>%
|
||||
arrange(ORGANISM)
|
||||
|
||||
# check non-existing species groups in the microorganisms table
|
||||
complexes <- whonet_organisms %>%
|
||||
filter(ORGANISM %like% " (group|complex)$" & toupper(SPECIES_GROUP) == toupper(ORGANISM_CODE)) %>%
|
||||
mutate(mo = as.mo(ORGANISM, minimum_matching_score = 0.6, keep_synonyms = TRUE)) %>%
|
||||
mutate(mo_new = paste0(mo, "-C"))
|
||||
complexes[which(!complexes$mo_new %in% AMR::microorganisms$mo), ]
|
||||
|
||||
|
||||
## Add new WHO codes to microorganisms.codes ----
|
||||
|
||||
@ -87,8 +82,8 @@ unmatched <- whonet_organisms %>% filter(is.na(mo))
|
||||
# generate the mo codes and add their names
|
||||
message("Getting MO codes for WHONET input...")
|
||||
unmatched <- unmatched %>%
|
||||
mutate(mo = as.mo(gsub("(sero[a-z]*| complex| group| nontypable| non[-][a-zA-Z]+|var[.]| not .*|sp[.],.*|, .*variant.*|, .*toxin.*|, microaer.*| beta-haem[.])", "", ORGANISM),
|
||||
minimum_matching_score = 0.6,
|
||||
mutate(mo = as.mo(gsub("(sero[a-z]*| nontypable| non[-][a-zA-Z]+|var[.]| not .*|sp[.],.*|, .*variant.*|, .*toxin.*|, microaer.*| beta-haem[.])", "", ORGANISM),
|
||||
minimum_matching_score = 0.55,
|
||||
keep_synonyms = TRUE,
|
||||
language = "en"),
|
||||
mo = case_when(ORGANISM %like% "Anaerobic" & ORGANISM %like% "negative" ~ as.mo("B_ANAER-NEG"),
|
||||
@ -103,13 +98,15 @@ unmatched <- unmatched %>%
|
||||
mutate(
|
||||
first_part = sapply(ORGANISM, function(x) strsplit(gsub("[^a-zA-Z _-]+", "", x), " ")[[1]][1], USE.NAMES = FALSE),
|
||||
keep = mo_name %like_case% first_part | ORGANISM %like% "Gram " | ORGANISM == "Other" | ORGANISM %like% "anaerobic") %>%
|
||||
arrange(keep)
|
||||
unmatched %>%
|
||||
View()
|
||||
unmatched <- unmatched %>%
|
||||
filter(keep == TRUE)
|
||||
|
||||
organisms <- matched %>% transmute(code = toupper(ORGANISM_CODE), group = SPECIES_GROUP, mo) %>%
|
||||
bind_rows(unmatched %>% transmute(code = toupper(ORGANISM_CODE), group = SPECIES_GROUP, mo)) %>%
|
||||
mutate(name = mo_name(mo, keep_synonyms = TRUE)) %>%
|
||||
# remove the species groups themselves, we'll look the species within these groups later
|
||||
filter(is.na(group) | code != group) %>%
|
||||
arrange(code)
|
||||
|
||||
# some subspecies exist, while their upper species do not, add them as the species level:
|
||||
@ -126,10 +123,20 @@ organisms <- organisms %>%
|
||||
bind_rows(subspp) %>%
|
||||
arrange(code)
|
||||
|
||||
organism_groups <- organisms %>%
|
||||
filter(!is.na(group)) %>%
|
||||
arrange(group, name)
|
||||
saveRDS(organism_groups, "data-raw/organism_groups.rds", version = 2)
|
||||
# add the groups
|
||||
organisms <- organisms %>%
|
||||
bind_rows(tibble(code = organisms %>% filter(!is.na(group)) %>% pull(group) %>% unique(),
|
||||
group = NA,
|
||||
mo = organisms %>% filter(!is.na(group)) %>% pull(group) %>% unique() %>% as.mo(keep_synonyms = TRUE),
|
||||
name = mo_name(mo, keep_synonyms = TRUE))) %>%
|
||||
arrange(code, group) %>%
|
||||
select(-group) %>%
|
||||
distinct()
|
||||
|
||||
# 2023-07-08 SGM must be Slowly-growing Mycobacterium, not Strep Gamma, not sure why this went wrong
|
||||
|
||||
|
||||
saveRDS(organisms, "data-raw/organisms.rds", version = 2)
|
||||
|
||||
#---
|
||||
# AT THIS POINT, `organisms` is clean and all entries have an mo code
|
||||
@ -138,10 +145,11 @@ saveRDS(organism_groups, "data-raw/organism_groups.rds", version = 2)
|
||||
# update microorganisms.codes with the latest WHONET codes
|
||||
microorganisms.codes2 <- microorganisms.codes %>%
|
||||
# remove all old WHONET codes, whether we (in the end) keep them or not
|
||||
filter(!toupper(code) %in% toupper(organisms$code) | toupper(code) %in% complexes$SPECIES_GROUP) %>%
|
||||
filter(!toupper(code) %in% toupper(organisms$code)) %>%
|
||||
# and add the new ones
|
||||
bind_rows(organisms %>% filter(code != group) %>% select(code, mo)) %>%
|
||||
arrange(code)
|
||||
bind_rows(organisms %>% select(code, mo)) %>%
|
||||
arrange(code) %>%
|
||||
distinct(code, .keep_all = TRUE)
|
||||
# new codes:
|
||||
microorganisms.codes2$code[which(!microorganisms.codes2$code %in% microorganisms.codes$code)]
|
||||
mo_name(microorganisms.codes2$mo[which(!microorganisms.codes2$code %in% microorganisms.codes$code)], keep_synonyms = TRUE)
|
||||
@ -173,6 +181,7 @@ microorganisms.codes <- microorganisms.codes2
|
||||
# # end
|
||||
|
||||
## Save to package ----
|
||||
class(microorganisms.codes$mo) <- c("mo", "character")
|
||||
usethis::use_data(microorganisms.codes, overwrite = TRUE, compress = "xz", version = 2)
|
||||
rm(microorganisms.codes)
|
||||
devtools::load_all()
|
||||
@ -195,14 +204,15 @@ breakpoints <- whonet_breakpoints %>%
|
||||
mo = rep(as.mo("UNKNOWN"), 2))))
|
||||
# these ones lack an MO name, they cannot be used:
|
||||
unknown <- breakpoints %>%
|
||||
filter(is.na(mo) & !ORGANISM_CODE %in% organism_groups$group) %>%
|
||||
filter(is.na(mo)) %>%
|
||||
pull(code) %>%
|
||||
unique()
|
||||
breakpoints %>%
|
||||
filter(code %in% unknown) %>%
|
||||
count(GUIDELINES, YEAR, ORGANISM_CODE, BREAKPOINT_TYPE, sort = TRUE)
|
||||
# these codes are currently (2023-07-08): clu, kma. No clue, so remove them:
|
||||
breakpoints <- breakpoints %>%
|
||||
filter(!is.na(mo) | ORGANISM_CODE %in% organism_groups$group)
|
||||
filter(!is.na(mo))
|
||||
|
||||
# and these ones have unknown antibiotics according to WHONET itself:
|
||||
breakpoints %>%
|
||||
@ -216,38 +226,6 @@ breakpoints %>%
|
||||
# they are at the moment all old codes that have right replacements in `antibiotics`, so we can use as.ab()
|
||||
|
||||
|
||||
## Extend species groups ----
|
||||
message("Extending breakpoints table on species groups...")
|
||||
# get the species groups, they must be converted to rules per-species and added
|
||||
breakpoints.bak <- breakpoints
|
||||
spp_groups <- breakpoints %>% filter(ORGANISM_CODE_TYPE == "SPECIES_GROUP")
|
||||
p <- progress_ticker(nrow(spp_groups))
|
||||
for (i in seq_len(nrow(spp_groups))) {
|
||||
p$tick()
|
||||
mos <- organism_groups %>% filter(group == spp_groups[i, "ORGANISM_CODE", drop = TRUE]) %>% pull(mo)
|
||||
for (m in mos) {
|
||||
breakpoints <- breakpoints %>%
|
||||
bind_rows(spp_groups %>%
|
||||
slice(i) %>%
|
||||
mutate(mo = m))
|
||||
}
|
||||
}
|
||||
close(p)
|
||||
|
||||
# extend all group A and B streptococci
|
||||
breakpoints_new <- breakpoints_new %>%
|
||||
bind_rows(breakpoints_new %>%
|
||||
filter(mo == as.mo("Streptococcus Group A")) %>%
|
||||
mutate(mo = as.mo("Streptococcus pyogenes"))) %>%
|
||||
bind_rows(breakpoints_new %>%
|
||||
filter(mo == as.mo("Streptococcus Group B")) %>%
|
||||
mutate(mo = as.mo("Streptococcus agalactiae")))
|
||||
# remove duplicates again for CoNS/CoPS/GBS and arrange
|
||||
breakpoints_new <- breakpoints_new %>%
|
||||
mutate(mo = as.mo(mo, keep_synonyms = TRUE)) %>%
|
||||
distinct(guideline, ab, mo, method, site, .keep_all = TRUE) %>%
|
||||
arrange(desc(guideline), ab, mo, method)
|
||||
|
||||
## Build new breakpoints table ----
|
||||
|
||||
breakpoints_new <- breakpoints %>%
|
||||
@ -262,6 +240,7 @@ breakpoints_new <- breakpoints %>%
|
||||
is.na(mo_rank(mo, keep_synonyms = TRUE)) ~ 6, # for UNKNOWN, B_GRAMN, B_ANAER, B_ANAER-NEG, etc.
|
||||
mo_rank(mo, keep_synonyms = TRUE) %like% "(infra|sub)" ~ 1,
|
||||
mo_rank(mo, keep_synonyms = TRUE) == "species" ~ 2,
|
||||
mo_rank(mo, keep_synonyms = TRUE) == "species group" ~ 2.5,
|
||||
mo_rank(mo, keep_synonyms = TRUE) == "genus" ~ 3,
|
||||
mo_rank(mo, keep_synonyms = TRUE) == "family" ~ 4,
|
||||
mo_rank(mo, keep_synonyms = TRUE) == "order" ~ 5,
|
||||
@ -279,7 +258,7 @@ breakpoints_new <- breakpoints %>%
|
||||
gsub("μ", "u", ., fixed = TRUE) %>% # this is 'mu', \u03bc
|
||||
gsub("µ", "u", ., fixed = TRUE) %>% # this is 'micro', u00b5 (yes, they look the same)
|
||||
gsub("–", "-", ., fixed = TRUE)) %>%
|
||||
arrange(desc(guideline), ab, mo, method) %>%
|
||||
arrange(desc(guideline), mo, ab, type, method) %>%
|
||||
filter(!(is.na(breakpoint_S) & is.na(breakpoint_R)) & !is.na(mo) & !is.na(ab)) %>%
|
||||
distinct(guideline, ab, mo, method, site, breakpoint_S, .keep_all = TRUE)
|
||||
|
||||
@ -292,7 +271,7 @@ breakpoints_new <- breakpoints_new %>%
|
||||
distinct(guideline, ab, mo, method, site, .keep_all = TRUE)
|
||||
|
||||
# fix reference table names
|
||||
breakpoints_new %>% filter(guideline %like% "EUCAST", is.na(ref_tbl))
|
||||
breakpoints_new %>% filter(guideline %like% "EUCAST", is.na(ref_tbl)) %>% View()
|
||||
breakpoints_new <- breakpoints_new %>%
|
||||
mutate(ref_tbl = case_when(is.na(ref_tbl) & guideline %like% "EUCAST 202" ~ lead(ref_tbl),
|
||||
is.na(ref_tbl) ~ "Unknown",
|
||||
|
||||
@ -869,7 +869,7 @@ taxonomy <- taxonomy %>%
|
||||
# other species from a genus in either group
|
||||
genus %in% nonbacterial_genera & rank %in% c("genus", "species", "subspecies") ~ 1.5,
|
||||
# we keep track of prevalent genera too of non-bacterial species
|
||||
genus %in% AMR:::MO_PREVALENT_GENERA & kingdom != "Bacteria" & rank %in% c("genus", "species", "subspecies") ~ 1.5,
|
||||
genus %in% AMR:::MO_PREVALENT_GENERA & kingdom != "Bacteria" & rank %in% c("genus", "species", "subspecies") ~ 1.25,
|
||||
|
||||
# all others
|
||||
TRUE ~ 2.0
|
||||
@ -1298,6 +1298,15 @@ AMR::microorganisms %>%
|
||||
View()
|
||||
|
||||
|
||||
# Some manual fixes -------------------------------------------------------
|
||||
|
||||
# Candida haemulonis and C. duobushaemulonis should be Candida haemulonii and C. duobushaemulonii
|
||||
# not sure how this can be, but GBIF contained spelling errors?
|
||||
# see https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3486233/
|
||||
taxonomy$species[which(taxonomy$fullname %like% "^Candida .*haemulonis")] <- gsub("nis$", "nii", taxonomy$species[which(taxonomy$fullname %like% "^Candida .*haemulonis")])
|
||||
taxonomy$fullname[which(taxonomy$fullname %like% "^Candida .*haemulonis")] <- gsub("nis$", "nii", taxonomy$fullname[which(taxonomy$fullname %like% "^Candida .*haemulonis")])
|
||||
|
||||
|
||||
# Add SNOMED CT -----------------------------------------------------------
|
||||
|
||||
# we will use Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS)
|
||||
|
||||
175
data-raw/reproduction_of_microorganisms.groups.R
Normal file
175
data-raw/reproduction_of_microorganisms.groups.R
Normal file
@ -0,0 +1,175 @@
|
||||
# ==================================================================== #
|
||||
# TITLE: #
|
||||
# AMR: An R Package for Working with Antimicrobial Resistance Data #
|
||||
# #
|
||||
# SOURCE CODE: #
|
||||
# https://github.com/msberends/AMR #
|
||||
# #
|
||||
# PLEASE CITE THIS SOFTWARE AS: #
|
||||
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
|
||||
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# https://doi.org/10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen and the University Medical #
|
||||
# Center Groningen in The Netherlands, in collaboration with many #
|
||||
# colleagues from around the world, see our website. #
|
||||
# #
|
||||
# This R package is free software; you can freely use and distribute #
|
||||
# it for both personal and commercial purposes under the terms of the #
|
||||
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
|
||||
# the Free Software Foundation. #
|
||||
# We created this package for both routine data analysis and academic #
|
||||
# research and it was publicly released in the hope that it will be #
|
||||
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
|
||||
# #
|
||||
# Visit our website for the full manual and a complete tutorial about #
|
||||
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
|
||||
# ==================================================================== #
|
||||
|
||||
# this data set is being used in the clinical_breakpoints data set, and thus by as.sir().
|
||||
# it prevents the breakpoints table from being extremely long for species that are part of a species group.
|
||||
|
||||
library(dplyr)
|
||||
library(readr)
|
||||
library(tidyr)
|
||||
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
|
||||
|
||||
# READ DATA ----
|
||||
|
||||
whonet_organisms <- read_tsv("data-raw/WHONET/Resources/Organisms.txt", na = c("", "NA", "-"), show_col_types = FALSE) %>%
|
||||
# remove old taxonomic names
|
||||
filter(TAXONOMIC_STATUS == "C") %>%
|
||||
mutate(ORGANISM_CODE = toupper(WHONET_ORG_CODE))
|
||||
|
||||
whonet_organisms <- whonet_organisms %>%
|
||||
select(ORGANISM_CODE, ORGANISM, SPECIES_GROUP, GBIF_TAXON_ID) %>%
|
||||
mutate(
|
||||
# this one was called Issatchenkia orientalis, but it should be:
|
||||
ORGANISM = if_else(ORGANISM_CODE == "ckr", "Candida krusei", ORGANISM)
|
||||
) %>%
|
||||
# try to match on GBIF identifier
|
||||
left_join(microorganisms %>% distinct(mo, gbif, status) %>% filter(!is.na(gbif)), by = c("GBIF_TAXON_ID" = "gbif")) %>%
|
||||
# remove duplicates
|
||||
arrange(ORGANISM_CODE, GBIF_TAXON_ID, status) %>%
|
||||
distinct(ORGANISM_CODE, .keep_all = TRUE) %>%
|
||||
# add Enterobacterales, which is a subkingdom code in their data
|
||||
bind_rows(data.frame(ORGANISM_CODE = "ebc", ORGANISM = "Enterobacterales", mo = as.mo("Enterobacterales"))) %>%
|
||||
arrange(ORGANISM)
|
||||
|
||||
# check non-existing species groups in the microorganisms table
|
||||
whonet_organisms %>%
|
||||
filter(!is.na(SPECIES_GROUP)) %>%
|
||||
group_by(SPECIES_GROUP) %>%
|
||||
summarise(complex = ORGANISM[ORGANISM %like% " (group|complex)"][1],
|
||||
organisms = paste0(n(), ": ", paste(sort(unique(ORGANISM)), collapse = ", "))) %>%
|
||||
filter(!SPECIES_GROUP %in% AMR::microorganisms.codes$code)
|
||||
|
||||
# create the species group data set ----
|
||||
microorganisms.groups <- whonet_organisms %>%
|
||||
# these will not be translated well
|
||||
filter(!ORGANISM %in% c("Trueperella pyogenes-like bacteria",
|
||||
"Mycobacterium suricattae",
|
||||
"Mycobacterium canetti")) %>%
|
||||
filter(!is.na(SPECIES_GROUP), SPECIES_GROUP != ORGANISM_CODE) %>%
|
||||
transmute(mo_group = as.mo(SPECIES_GROUP),
|
||||
mo = ifelse(is.na(mo),
|
||||
as.character(as.mo(ORGANISM, keep_synonyms = TRUE, minimum_matching_score = 0)),
|
||||
mo)) %>%
|
||||
# add our own CoNS and CoPS, WHONET does not strictly follow Becker et al (2014, 2019, 2020)
|
||||
filter(mo_group != as.mo("CoNS")) %>%
|
||||
bind_rows(tibble(mo_group = as.mo("CoNS"), mo = MO_CONS)) %>%
|
||||
filter(mo_group != as.mo("CoPS")) %>%
|
||||
bind_rows(tibble(mo_group = as.mo("CoPS"), mo = MO_COPS)) %>%
|
||||
# at least all our Lancefield-grouped streptococci must be in the beta-haemolytic group:
|
||||
bind_rows(tibble(mo_group = as.mo("Beta-haemolytic streptococcus"),
|
||||
mo = c(MO_LANCEFIELD,
|
||||
microorganisms %>% filter(fullname %like% "^Streptococcus Group") %>% pull(mo)))) %>%
|
||||
# and per Streptococcus group as well:
|
||||
# group A - S. pyogenes
|
||||
bind_rows(tibble(mo_group = as.mo("Streptococcus Group A"),
|
||||
mo = microorganisms$mo[which(microorganisms$mo %like% "^B_STRPT_PYGN(_|$)")])) %>%
|
||||
# group B - S. agalactiae
|
||||
bind_rows(tibble(mo_group = as.mo("Streptococcus Group B"),
|
||||
mo = microorganisms$mo[which(microorganisms$mo %like% "^B_STRPT_AGLC(_|$)")])) %>%
|
||||
# group C - all subspecies within S. dysgalactiae and S. equi (such as S. equi zooepidemicus)
|
||||
bind_rows(tibble(mo_group = as.mo("Streptococcus Group C"),
|
||||
mo = microorganisms$mo[which(microorganisms$mo %like% "^B_STRPT_(DYSG|EQUI)(_|$)")])) %>%
|
||||
# group F - S. anginosus, incl. S. anginosus anginosus and S. anginosus whileyi
|
||||
bind_rows(tibble(mo_group = as.mo("Streptococcus Group F"),
|
||||
mo = microorganisms$mo[which(microorganisms$mo %like% "^B_STRPT_ANGN(_|$)")])) %>%
|
||||
# group G - S. dysgalactiae and S. canis (though dysgalactiae is also group C and will be matched there)
|
||||
bind_rows(tibble(mo_group = as.mo("Streptococcus Group G"),
|
||||
mo = microorganisms$mo[which(microorganisms$mo %like% "^B_STRPT_(DYSG|CANS)(_|$)")])) %>%
|
||||
# group H - S. sanguinis
|
||||
bind_rows(tibble(mo_group = as.mo("Streptococcus Group H"),
|
||||
mo = microorganisms$mo[which(microorganisms$mo %like% "^B_STRPT_SNGN(_|$)")])) %>%
|
||||
# group K - S. salivarius, incl. S. salivarius salivariuss and S. salivarius thermophilus
|
||||
bind_rows(tibble(mo_group = as.mo("Streptococcus Group K"),
|
||||
mo = microorganisms$mo[which(microorganisms$mo %like% "^B_STRPT_SLVR(_|$)")])) %>%
|
||||
# and for EUCAST: Strep group A, B, C, G
|
||||
bind_rows(tibble(mo_group = as.mo("Streptococcus Group A, B, C, G"),
|
||||
mo = microorganisms$mo[which(microorganisms$mo %like% "^B_STRPT_(PYGN|AGLC|DYSG|EQUI|CANS)(_|$)")])) %>%
|
||||
# HACEK is:
|
||||
# - Haemophilus species
|
||||
# - Aggregatibacter species
|
||||
# - Cardiobacterium hominis
|
||||
# - Eikenella corrodens
|
||||
# - Kingella species
|
||||
# - and previously Actinobacillus actinomycetemcomitans
|
||||
# see https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3656887/
|
||||
filter(mo_group != as.mo("HACEK")) %>%
|
||||
bind_rows(tibble(mo_group = as.mo("HACEK"), mo = microorganisms %>% filter(genus == "Haemophilus") %>% pull(mo))) %>%
|
||||
bind_rows(tibble(mo_group = as.mo("HACEK"), mo = microorganisms %>% filter(genus == "Aggregatibacter") %>% pull(mo))) %>%
|
||||
bind_rows(tibble(mo_group = as.mo("HACEK"), mo = as.mo("Cardiobacterium hominis", keep_synonyms = TRUE))) %>%
|
||||
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))) %>%
|
||||
# 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"),
|
||||
mo = paste("Mycobacterium", c( "abscessus abscessus", "abscessus bolletii", "abscessus massiliense", "agri", "aichiense", "algericum", "alvei", "anyangense", "arabiense", "aromaticivorans", "aubagnense", "aubagnense", "aurum", "austroafricanum", "bacteremicum", "boenickei", "bourgelatii", "brisbanense", "brumae", "canariasense", "celeriflavum", "chelonae", "chitae", "chlorophenolicum", "chubuense", "confluentis", "cosmeticum", "crocinum", "diernhoferi", "duvalii", "elephantis", "fallax", "flavescens", "fluoranthenivorans", "fortuitum", "franklinii", "frederiksbergense", "gadium", "gilvum", "goodii", "hassiacum", "hippocampi", "hodleri", "holsaticum", "houstonense", "immunogenum", "insubricum", "iranicum", "komossense", "litorale", "llatzerense", "madagascariense", "mageritense", "monacense", "moriokaense", "mucogenicum", "mucogenicum", "murale", "neoaurum", "neworleansense", "novocastrense", "obuense", "pallens", "parafortuitum", "peregrinum", "phlei", "phocaicum", "phocaicum", "porcinum", "poriferae", "psychrotolerans", "pyrenivorans", "rhodesiae", "rufum", "rutilum", "salmoniphilum", "sediminis", "senegalense", "septicum", "setense", "smegmatis", "sphagni", "thermoresistibile", "tokaiense", "vaccae", "vanbaalenii", "wolinskyi")) %>% as.mo(keep_synonyms = TRUE))) %>%
|
||||
# add full names
|
||||
mutate(mo_group_name = mo_name(mo_group, keep_synonyms = TRUE),
|
||||
mo_name = mo_name(mo, keep_synonyms = TRUE)) %>%
|
||||
arrange(mo_group_name, mo_name) %>%
|
||||
filter(mo_group != mo) %>%
|
||||
distinct() %>%
|
||||
dataset_UTF8_to_ASCII()
|
||||
mo_uncertainties()
|
||||
|
||||
class(microorganisms.groups$mo_group) <- c("mo", "character")
|
||||
class(microorganisms.groups$mo) <- c("mo", "character")
|
||||
usethis::use_data(microorganisms.groups, internal = FALSE, overwrite = TRUE, compress = "xz", version = 2)
|
||||
rm(microorganisms.groups)
|
||||
devtools::load_all()
|
||||
|
||||
|
||||
#
|
||||
# microorganisms <- microorganisms %>%
|
||||
# mutate(mo = as.character(mo)) %>%
|
||||
# bind_rows(
|
||||
# microorganisms %>% filter(mo == "B_STRPT_HAEM") %>%
|
||||
# mutate(mo = as.character(mo),
|
||||
# mo = "B_STRPT_ABCG",
|
||||
# fullname = "Streptococcus Group A, B, C, G",
|
||||
# species = "Group A, B, C, G")) %>%
|
||||
# arrange(fullname) %>%
|
||||
# dataset_UTF8_to_ASCII()
|
||||
#
|
||||
# microorganisms$rank[which(microorganisms$fullname %like% "^Streptococcus Group")] <- "species group"
|
||||
# microorganisms$lpsn_parent[which(microorganisms$fullname %like% "^Streptococcus Group")] <- 517118
|
||||
# microorganisms$gbif_parent[which(microorganisms$fullname %like% "^Streptococcus Group")] <- 3223465
|
||||
# microorganisms$ref[which(microorganisms$fullname %like% "^Streptococcus Group")] <- "Lancefield, 1933"
|
||||
# microorganisms$prevalence[which(microorganisms$fullname %like% "^Streptococcus Group")] <- 1.5
|
||||
# microorganisms$oxygen_tolerance[which(microorganisms$fullname %like% "^Streptococcus Group")] <- "likely facultative anaerobe"
|
||||
#
|
||||
|
||||
|
||||
class(microorganisms$mo) <- c("mo", "character")
|
||||
usethis::use_data(microorganisms, internal = FALSE, overwrite = TRUE, compress = "xz", version = 2)
|
||||
rm(microorganisms)
|
||||
devtools::load_all()
|
||||
18
data-raw/species groups.R
Normal file
18
data-raw/species groups.R
Normal file
@ -0,0 +1,18 @@
|
||||
g <- certetoolbox::import_clipboard()
|
||||
g <- g %>% as_tibble()
|
||||
g
|
||||
for (i in seq_len(nrow(g))) {
|
||||
if (is.na(g$taxonomy_from[i])) next
|
||||
mo <- as.mo(g$taxonomy_from[i])
|
||||
g$phylum[i] <- mo_phylum(mo)
|
||||
g$class[i] <- mo_class(mo)
|
||||
g$order[i] <- mo_order(mo)
|
||||
g$family[i] <- mo_family(mo)
|
||||
g$genus[i] <- mo_genus(mo)
|
||||
g$species[i] <- paste(mo_species(mo), "complex")
|
||||
g$lpsn_parent[i] <- mo_property(mo, property = "lpsn_parent")
|
||||
g$gbif_parent[i] <- mo_property(mo, property = "gbif_parent")
|
||||
g$oxygen_tolerance[i] <- mo_property(mo, property = "oxygen_tolerance")
|
||||
g$prevalence[i] <- mo_property(mo, property = "prevalence")
|
||||
}
|
||||
certetoolbox::export_clipboard(g)
|
||||
Reference in New Issue
Block a user