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mirror of https://github.com/msberends/AMR.git synced 2025-07-11 21:41:58 +02:00

(v2.1.1.9071) update veterinary SIR interpretation, add only_fungi

This commit is contained in:
2024-09-19 11:44:56 +02:00
parent 573c0346ed
commit ddb23b6e73
52 changed files with 290 additions and 162 deletions

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92d3e2f8deac335c92841d2ded974dee
5ad894790ad048110f8eb9207b89501f

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@ -468,7 +468,7 @@
"TOH" "Tobramycin-high" "Aminoglycosides" "NA" "tobra high,tobramycin high,tohl" "" ""
"TFX" 5517 "Tosufloxacin" "Quinolones" "J01MA22,S01AE09" "" "tosufloxacin" 0.45 "g" "100061-1,76146-0"
"TMP" 5578 "Trimethoprim" "Trimethoprims" "J01EA01" "Sulfonamides and trimethoprim" "Trimethoprim and derivatives" "t,tmp,tr,tri,trim,w" "abaprim,alprim,anitrim,antrima,antrimox,bacdan,bacidal,bacide,bacterial,bacticel,bactifor,bactin,bactoprim,bactramin,bactrim,bencole,bethaprim,biosulten,briscotrim,chemotrin,colizole,colizole ds,conprim,cotrimel,cotrimoxizole,deprim,dosulfin,duocide,esbesul,espectrin,euctrim,exbesul,fermagex,fortrim,idotrim,ikaprim,infectotrimet,instalac,kombinax,lagatrim,lagatrim forte,lastrim,lescot,methoprim,metoprim,monoprim,monotrim,monotrimin,novotrimel,omstat,oraprim,pancidim,polytrim,priloprim,primosept,primsol,proloprim,protrin,purbal,resprim,resprim forte,roubac,roubal,salvatrim,septrin ds,septrin forte,septrin s,setprin,sinotrim,stopan,streptoplus,sugaprim,sulfamar,sulfamethoprim,sulfoxaprim,sulthrim,sultrex,syraprim,tiempe,tmp smx,toprim,trimanyl,trimethioprim,trimethopim,trimethoprim,trimethoprime,trimethoprimum,trimethopriom,trimetoprim,trimetoprima,trimexazole,trimexol,trimezol,trimogal,trimono,trimopan,trimpex,triprim,trisul,trisulcom,trisulfam,trisural,uretrim,urobactrim,utetrin,velaten,wellcoprim,wellcoprin,xeroprim,zamboprim" 0.4 "g" 0.4 "g" "101495-0,11005-6,17747-7,18997-7,18998-5,20387-7,23614-1,23631-5,25273-4,32342-8,4079-0,4080-8,4081-6,511-6,512-4,513-2,514-0,515-7,516-5,517-3,518-1,55584-7,7056-5,7057-3,80552-3,80973-1"
"SXT" 358641 "Trimethoprim/sulfamethoxazole" "Trimethoprims" "J01EE01" "Sulfonamides and trimethoprim" "Combinations of sulfonamides and trimethoprim, incl. derivatives" "cot,cotrim,sxt,t/s,trsu,trsx,ts" "abacin,abactrim,agoprim,alfatrim,aposulfatrim,bacteral,bacterial forte,bactilen,bactiver,bacton,bactoreduct,bactrim,bactrim ds,bactrim forte,bactrim pediatric,bactrimel,bactrizol,bactromin,bactropin,baktar,belcomycine,berlocid,bibacrim,biseptol,chemitrim,chemotrim,ciplin,colimycin,colimycin sulphate,colisticin,colistimethate,colistimethate sodium,colistin sulfate,colistin sulphate,colomycin,coly-mycin,cotribene,cotrim d.s.,cotrim eu rho,cotrim holsen,cotrim.l.u.t.,cotrimaxazol,cotrimazole,cotrimhexal,cotrimoxazol,cotrimoxazol al,cotrimoxazole,cotrimstada,cotriver,dibaprim,drylin,duratrimet,eltrianyl,escoprim,esteprim,eusaprim,fectrim,gantaprim,gantaprin,gantrim,groprim,helveprim,imexim,jenamoxazol,kemoprim,kepinol,kepinol forte,laratrim,linaris,maxtrim,microtrim,microtrim forte,mikrosid,momentol,oecotrim,oriprim,oxaprim,pantoprim,polymyxin e,polymyxin e. sulfate,primazole,promixin,septra,septra ds,septra grape,septrim,septrin,servitrim,sigaprim,sigaprin,sulfatrim pediatric,sulfotrim,sulfotrimin,sulmeprim pediatric,sulprim,sumetrolim,supracombin,suprim,tacumil,teleprim,teleprin,thiocuran,totazina,tribakin,trifen,trigonyl,trimesulf,trimetho comp,trimethoprimsulfa,trimetoger,trimexazol,trimforte,trimosulfa,uroplus,uroplus ds,uroplus ss" "101495-0,18998-5,20387-7,23631-5,25273-4,32342-8,4081-6,515-7,516-5,517-3,518-1,7057-3"
"SXT" 358641 "Trimethoprim/sulfamethoxazole" "Trimethoprims" "J01EE01" "Sulfonamides and trimethoprim" "Combinations of sulfonamides and trimethoprim, incl. derivatives" "cot,cotrim,sxt,t/s,tms,trsu,trsx,ts" "abacin,abactrim,agoprim,alfatrim,aposulfatrim,bacteral,bacterial forte,bactilen,bactiver,bacton,bactoreduct,bactrim,bactrim ds,bactrim forte,bactrim pediatric,bactrimel,bactrizol,bactromin,bactropin,baktar,belcomycine,berlocid,bibacrim,biseptol,chemitrim,chemotrim,ciplin,colimycin,colimycin sulphate,colisticin,colistimethate,colistimethate sodium,colistin sulfate,colistin sulphate,colomycin,coly-mycin,cotribene,cotrim d.s.,cotrim eu rho,cotrim holsen,cotrim.l.u.t.,cotrimaxazol,cotrimazole,cotrimhexal,cotrimoxazol,cotrimoxazol al,cotrimoxazole,cotrimstada,cotriver,dibaprim,drylin,duratrimet,eltrianyl,escoprim,esteprim,eusaprim,fectrim,gantaprim,gantaprin,gantrim,groprim,helveprim,imexim,jenamoxazol,kemoprim,kepinol,kepinol forte,laratrim,linaris,maxtrim,microtrim,microtrim forte,mikrosid,momentol,oecotrim,oriprim,oxaprim,pantoprim,polymyxin e,polymyxin e. sulfate,primazole,promixin,septra,septra ds,septra grape,septrim,septrin,servitrim,sigaprim,sigaprin,sulfatrim pediatric,sulfotrim,sulfotrimin,sulmeprim pediatric,sulprim,sumetrolim,supracombin,suprim,tacumil,teleprim,teleprin,thiocuran,totazina,tribakin,trifen,trigonyl,trimesulf,trimetho comp,trimethoprimsulfa,trimetoger,trimexazol,trimforte,trimosulfa,uroplus,uroplus ds,uroplus ss" "101495-0,18998-5,20387-7,23631-5,25273-4,32342-8,4081-6,515-7,516-5,517-3,518-1,7057-3"
"TRL" 202225 "Troleandomycin" "Macrolides/lincosamides" "J01FA08" "Macrolides, lincosamides and streptogramins" "Macrolides" "" "acetyloleandomycin,aovine,cyclamycin,evramicina,matromicina,matromycin t,micotil,oleandocetine,oleandomycin,t.a.o.,treolmicina,tribiocillina,triocetin,triolan,troleandomicina,troleandomycin,troleandomycine,troleandomycinum,viamicina,wytrion" 1 "g" "18999-3,519-9,520-7,521-5,522-3"
"TRO" 55886 "Trospectomycin" "Other antibacterials" "NA" "" "rubidiumnitrate,trospectinomycin,trospectomicina,trospectomycin,trospectomycine,trospectomycinum" ""
"TVA" 62959 "Trovafloxacin" "Quinolones" "J01MA13" "Quinolone antibacterials" "Fluoroquinolones" "trov" "trovafloxacin,trovan" 0.2 "g" 0.2 "g" "23642-2,23643-0,35855-6,7058-1"

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@ -736,6 +736,8 @@ taxonomy_mycobank <- taxonomy_mycobank %>%
# Combine the datasets ----------------------------------------------------
# TODO !! check why e.g. Clavispora lusitaniae is gotten from GBIF, not MycoBank !!
taxonomy <- taxonomy_lpsn %>%
# add fungi
bind_rows(taxonomy_mycobank) %>%
@ -1237,9 +1239,9 @@ saveRDS(taxonomy, "data-raw/taxonomy2.rds")
# taxonomy <- readRDS("data-raw/taxonomy2.rds")
# Remove unwanted taxonomic entries from Protoza/Fungi --------------------
# Remove unwanted taxonomic entries ---------------------------------------
taxonomy <- taxonomy %>%
part1 <- taxonomy %>%
filter(
# keep all we added ourselves:
source == "manually added" |
@ -1259,10 +1261,7 @@ taxonomy <- taxonomy %>%
# kingdom of Protozoa:
(phylum %in% c("Choanozoa", "Mycetozoa") & prevalence < 2) |
# Fungi:
(kingdom == "Fungi" & (!rank %in% c("genus", "species", "subspecies") | prevalence < 2)) |
# !(phylum %in% c("Ascomycota", "Zygomycota", "Basidiomycota") & prevalence == 2 & rank %in% c("genus", "species", "subspecies")),
# !(genus %in% c("Leptosphaeria", "Physarum") & rank %in% c("species", "subspecies")), # keep only genus of this rare fungus, with resp. 850 and 500 species
# # (leave Alternaria in there, part of human mycobiome and opportunistic pathogen)
(kingdom == "Fungi" & (!rank %in% c("genus", "species", "subspecies") | prevalence < 2 | class == "Pichiomycetes")) |
# Animalia:
genus %in% c("Lucilia", "Lumbricus") |
(class == "Insecta" & !rank %in% c("species", "subspecies")) | # keep only genus of insects, not all of their (sub)species
@ -1272,6 +1271,29 @@ taxonomy <- taxonomy %>%
filter(kingdom != "Plantae",
!(genus %in% c("Aedes", "Anopheles") & rank %in% c("species", "subspecies")))
# now get the parents and old names
part2 <- taxonomy %>%
filter(gbif %in% c(part1$gbif_parent[!is.na(part1$gbif_parent)], part1$gbif_renamed_to[!is.na(part1$gbif_renamed_to)]) |
mycobank %in% c(part1$mycobank_parent[!is.na(part1$mycobank_parent)], part1$mycobank_renamed_to[!is.na(part1$mycobank_renamed_to)]) |
lpsn %in% c(part1$lpsn_parent[!is.na(part1$lpsn_parent)], part1$lpsn_renamed_to[!is.na(part1$lpsn_renamed_to)]))
parts <- bind_rows(part1, part2)
part3 <- taxonomy %>%
filter(gbif %in% c(parts$gbif_parent[!is.na(parts$gbif_parent)], parts$gbif_renamed_to[!is.na(parts$gbif_renamed_to)]) |
mycobank %in% c(parts$mycobank_parent[!is.na(parts$mycobank_parent)], parts$mycobank_renamed_to[!is.na(parts$mycobank_renamed_to)]) |
lpsn %in% c(parts$lpsn_parent[!is.na(parts$lpsn_parent)], parts$lpsn_renamed_to[!is.na(parts$lpsn_renamed_to)]))
parts <- bind_rows(part1, part2, part3)
part4 <- taxonomy %>%
filter(gbif %in% c(parts$gbif_parent[!is.na(parts$gbif_parent)], parts$gbif_renamed_to[!is.na(parts$gbif_renamed_to)]) |
mycobank %in% c(parts$mycobank_parent[!is.na(parts$mycobank_parent)], parts$mycobank_renamed_to[!is.na(parts$mycobank_renamed_to)]) |
lpsn %in% c(parts$lpsn_parent[!is.na(parts$lpsn_parent)], parts$lpsn_renamed_to[!is.na(parts$lpsn_renamed_to)]))
parts <- bind_rows(part1, part2, part3, part4)
taxonomy <- bind_rows(part1, part2, part3, part4) %>%
arrange(fullname) %>%
distinct(fullname, .keep_all = TRUE)
# no ghost families, orders classes, phyla
taxonomy <- taxonomy %>%
group_by(kingdom, family) %>%
@ -2005,7 +2027,7 @@ taxonomy <- taxonomy %>%
filter(!mo %in% groups$mo) %>%
bind_rows(groups)
# we added MO code, so make sure everything is still unique
# we added an MO code, so make sure everything is still unique
any(duplicated(taxonomy$mo))
any(duplicated(taxonomy$fullname))
@ -2018,13 +2040,17 @@ AMR::clinical_breakpoints %>% filter(!mo %in% taxonomy$mo)
AMR::example_isolates %>% filter(!mo %in% taxonomy$mo)
AMR::intrinsic_resistant %>% filter(!mo %in% taxonomy$mo)
# all our previously manually added names should be in it
all(microorganisms$fullname[microorganisms$source == "manually added"] %in% taxonomy$fullname)
microorganisms$fullname[!microorganisms$fullname[microorganisms$source == "manually added"] %in% taxonomy$fullname]
# put this one back
taxonomy <- taxonomy %>%
bind_rows(microorganisms %>%
filter(fullname == "Blastocystis hominis") %>%
mutate(mo = as.character(mo)))
# we added MO code, so make sure everything is still unique
# we added an MO code, so make sure everything is still unique
any(duplicated(taxonomy$mo))
any(duplicated(taxonomy$fullname))