diff --git a/DESCRIPTION b/DESCRIPTION index 8aca3aa39..87e5c4785 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: AMR Version: 3.0.1.9106 -Date: 2026-10-07 +Date: 2026-10-09 Title: Antimicrobial Resistance Data Analysis Description: Functions to simplify and standardise antimicrobial resistance (AMR) data analysis and to work with microbial and antimicrobial properties by diff --git a/NEWS.md b/NEWS.md index cb7ec1586..cbb0906c4 100644 --- a/NEWS.md +++ b/NEWS.md @@ -75,6 +75,7 @@ Planned as v3.1.0, mid October 2026. * Taxonomy: names that a source lists twice now take the correct record (e.g. *Eggerthella lenta*, *Gordonia amarae* and *Anisakis simplex* were synonyms without a current name) * Taxonomy: synonyms without a current name are linked via LPSN or removed, with their codes retired; the *M. tuberculosis* complex is always kept * Taxonomy: consistent higher taxonomy and parent records, and data sets refer only to current names (except `intrinsic_resistant`) +* `antimicrobials`: trade names of combinations (Tazocin, Timentin, Recarbrio, Exblifep) were listed under a single component, and names of screening libraries and suppliers (e.g. Prestwick, Spectrum) as synonyms (#315) ### Updated * Faster `as.ab()`, `as.mo()` and all `mo_*()` functions through one consistent session cache design, which is cleared when lookup tables change, e.g. after `add_custom_microorganisms()` (#313) diff --git a/R/sysdata.rda b/R/sysdata.rda index 5fb024cdc..ad8137d3c 100755 Binary files a/R/sysdata.rda and b/R/sysdata.rda differ diff --git a/data-raw/_reproduction_scripts/reproduction_of_antimicrobials.R b/data-raw/_reproduction_scripts/reproduction_of_antimicrobials.R index b044102af..640b2a220 100644 --- a/data-raw/_reproduction_scripts/reproduction_of_antimicrobials.R +++ b/data-raw/_reproduction_scripts/reproduction_of_antimicrobials.R @@ -673,7 +673,23 @@ antimicrobials[which(antimicrobials$ab == "RFI"), "synonyms"][[1]] <- list(sort( old_sym <- antimicrobials[which(antimicrobials$ab == "SMX"), "synonyms"][[1]] old_sym <- old_sym[!old_sym %in% c("Cotrimoxazole", "Bactrimel")] antimicrobials[which(antimicrobials$ab == "SMX"), "synonyms"][[1]] <- list(old_sym) -antimicrobials[which(antimicrobials$ab == "SXT"), "synonyms"][[1]] <- list(sort(unique(c(antimicrobials[which(antimicrobials$ab == "COL"), "synonyms"][[1]], "Cotrimoxazole", "Bactrimel", "Septra", "Bactrim", "Cotrimazole")))) +antimicrobials[which(antimicrobials$ab == "SXT"), "synonyms"][[1]] <- list(sort(unique(c(antimicrobials[which(antimicrobials$ab == "SXT"), "synonyms"][[1]], "Cotrimoxazole", "Bactrimel", "Septra", "Bactrim", "Cotrimazole")))) +# trade names of combinations must not be filed under a single agent (PubChem similarity also returns mixtures, and +# components sort before their combinations), and names of screening libraries, suppliers and chemical fragments are +# no synonyms; both found in October 2026, a structural solution is discussed in #315 +synonym_moves <- data.frame( + synonym = c("Tazocin", "Timentin", "Recarbrio", "Exblifep"), + from = c("PIP", "TIC", "IPM", "TAZ"), + to = c("TZP", "TCC", "IMR", "FPE"), + stringsAsFactors = FALSE +) +not_synonyms <- c("lopac", "nbleomycinamide", "pharmakon", "prestwick", "spectrum", "spiro", "tocris") +for (i in seq_len(nrow(antimicrobials))) { + syn <- unlist(antimicrobials$synonyms[i]) + syn <- syn[!is.na(syn) & !tolower(syn) %in% c(not_synonyms, tolower(synonym_moves$synonym[synonym_moves$from == antimicrobials$ab[i]]))] + syn <- c(syn, synonym_moves$synonym[synonym_moves$to == antimicrobials$ab[i]]) + antimicrobials$synonyms[i] <- list(if (length(syn) == 0) NA_character_ else sort(unique(syn))) +} # Fix penicillins antimicrobials[which(antimicrobials$ab == "PEN"), "abbreviations"][[1]] <- list(c("bepe", "pg", "pen", "peni", "peni g", "penicillin", "penicillin g")) diff --git a/data-raw/ab.md5 b/data-raw/ab.md5 index 985903b74..94f4fdbd2 100644 --- a/data-raw/ab.md5 +++ b/data-raw/ab.md5 @@ -1 +1 @@ -11aade8a39bfdff02d01fb52b04eacdc +07d2d9bd1acc925b809a8ddff2ef977f diff --git a/data-raw/datasets/antimicrobials.dta b/data-raw/datasets/antimicrobials.dta index a2481f7d0..6bfa6add1 100644 Binary files a/data-raw/datasets/antimicrobials.dta and b/data-raw/datasets/antimicrobials.dta differ diff --git a/data-raw/datasets/antimicrobials.feather b/data-raw/datasets/antimicrobials.feather index 49d0d53e1..d92cdaab9 100644 Binary files a/data-raw/datasets/antimicrobials.feather and b/data-raw/datasets/antimicrobials.feather differ diff --git a/data-raw/datasets/antimicrobials.parquet b/data-raw/datasets/antimicrobials.parquet index 866100ada..a73362469 100644 Binary files a/data-raw/datasets/antimicrobials.parquet and b/data-raw/datasets/antimicrobials.parquet differ diff --git a/data-raw/datasets/antimicrobials.rds b/data-raw/datasets/antimicrobials.rds index 5d94a84ae..9d9941f75 100644 Binary files a/data-raw/datasets/antimicrobials.rds and b/data-raw/datasets/antimicrobials.rds differ diff --git a/data-raw/datasets/antimicrobials.sav b/data-raw/datasets/antimicrobials.sav index e088f6bca..0c187eba3 100644 Binary files a/data-raw/datasets/antimicrobials.sav and b/data-raw/datasets/antimicrobials.sav differ diff --git a/data-raw/datasets/antimicrobials.txt b/data-raw/datasets/antimicrobials.txt index b3680a643..345c24015 100644 --- a/data-raw/datasets/antimicrobials.txt +++ b/data-raw/datasets/antimicrobials.txt @@ -1,9 +1,9 @@ "ab" "cid" "name" "group" "atc" "atc_group1" "atc_group2" "abbreviations" "synonyms" "oral_ddd" "oral_units" "iv_ddd" "iv_units" "loinc" -"AMA" 4649 "4-aminosalicylic acid" "Antimycobacterials" "J04AA01" "Drugs for treatment of tuberculosis" "Aminosalicylic acid and derivatives" "NA" "aminacyl,aminopar,aminosalyl,aminox,apacil,deapasil,entepas,gabbropas,granupas,helipidyl,hellipidyl,nemasol,nippas,osacyl,pamacyl,pamisyl,paramisan,paramycin,parasal,parasalicil,parasalindon,pasade,pasalon,pasara,pascorbic,pasdium,pasem,paser,pasmed,pasnal,pasnodia,pasolac,passodico,pharmakon,propasa,rezipas,salvis,sanipirol,sanipriol,sodiopas,spectrum" 12 "g" "NA" +"AMA" 4649 "4-aminosalicylic acid" "Antimycobacterials" "J04AA01" "Drugs for treatment of tuberculosis" "Aminosalicylic acid and derivatives" "NA" "aminacyl,aminopar,aminosalyl,aminox,apacil,deapasil,entepas,gabbropas,granupas,helipidyl,hellipidyl,nemasol,nippas,osacyl,pamacyl,pamisyl,paramisan,paramycin,parasal,parasalicil,parasalindon,pasade,pasalon,pasara,pascorbic,pasdium,pasem,paser,pasmed,pasnal,pasnodia,pasolac,passodico,propasa,rezipas,salvis,sanipirol,sanipriol,sodiopas" 12 "g" "NA" "ACM" 6450012 "Acetylmidecamycin" "Macrolides" "NA" "NA" "NA" "NA" "ASP" 49787020 "Acetylspiramycin" "Macrolides" "NA" "NA" "espiramicin,espiramicina,foromacidin,provamycin,rovamicina,rovamycin,rovamycine,selectomycin,sequamycin,spiramycine,spiramycinum" "NA" "ALS" 8954 "Aldesulfone sodium" "Other" "J04BA03" "Drugs for treatment of lepra" "Drugs for treatment of lepra" "NA" "adesulfone,aldapsone,aldesulfone,aldesulphone,diamidin,diason,diasone,diasoneenterab,diazon,didimethanesulfinate,novotrone,sulfoxone" 0.33 "g" "NA" -"AMK" 37768 "Amikacin" "Aminoglycosides" "D06AX12,J01GB06,QD06AX12,QJ01GB06,QS01AA21,S01AA21" "Aminoglycoside antibacterials" "Other aminoglycosides" "ak,ami,amik,amikac,amk,an" "amikacillin,amikacina,amikacine,amikacinum,amikavet,amikin,amikozit,amukin,arikace,briclin,butirosins,kaminax,lukadin,mikavir,potentox,prestwick" 1 "g" "101493-5,11-7,12-5,13-3,13546-7,14-1,15098-7,17798-0,18860-7,20373-7,23624-0,25174-4,25175-1,25176-9,25177-7,25178-5,25179-3,31097-9,31098-7,31099-5,3319-1,3320-9,3321-7,35669-1,42642-9,48169-7,50802-8,50803-6,56628-1,59378-0,60564-2,60565-9,6975-7,80972-3,89484-0" +"AMK" 37768 "Amikacin" "Aminoglycosides" "D06AX12,J01GB06,QD06AX12,QJ01GB06,QS01AA21,S01AA21" "Aminoglycoside antibacterials" "Other aminoglycosides" "ak,ami,amik,amikac,amk,an" "amikacillin,amikacina,amikacine,amikacinum,amikavet,amikin,amikozit,amukin,arikace,briclin,butirosins,kaminax,lukadin,mikavir,potentox" 1 "g" "101493-5,11-7,12-5,13-3,13546-7,14-1,15098-7,17798-0,18860-7,20373-7,23624-0,25174-4,25175-1,25176-9,25177-7,25178-5,25179-3,31097-9,31098-7,31099-5,3319-1,3320-9,3321-7,35669-1,42642-9,48169-7,50802-8,50803-6,56628-1,59378-0,60564-2,60565-9,6975-7,80972-3,89484-0" "AKF" "Amikacin/fosfomycin" "Aminoglycosides,Phosphonics" "NA" "NA" "NA" "NA" "AMO" 54260 "Amorolfine" "Antifungals" "D01AE16,QD01AE16" "Antifungals for topical use" "Other antifungals for topical use" "amor" "amorolfina,amorolfinum,bekiron,corbel,curanail,fenpropemorph,fenpropimorph,fenpropimorphe,forbel,funbas,loceryl,locetar,mildofix,mistral,morpholine,odenil,omicur,pekiron" "NA" "AMX" 33613 "Amoxicillin" "Aminopenicillins,Penicillins,Beta-lactams" "J01CA04,QG51AA03,QJ01CA04" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "ac,amox,amoxic,amx" "acuotricina,alfamox,alfida,amitron,amoclen,amodex,amoksicillin,amolin,amopen,amopenixin,amophar,amoran,amoxi,amoxicaps,amoxicilina,amoxicilline,amoxicillinum,amoxidal,amoxiden,amoxil,amoxillat,amoxina,amoxine,amoxipen,amoxivet,amoxycillin,amoxycillinsalt,amoxyke,anemolin,aspenil,atoksilin,bristamox,cemoxin,ciblor,clamoxyl,damoxy,danoxillin,delacillin,demoksil,dispermox,efpenix,eupen,flemoxin,flemoxine,galenamox,gramidil,hiconcil,himinomax,histocillin,ibiamox,imacillin,izoltil,kentrocyllin,lamoxy,largopen,larotid,matasedrin,metifarma,moksilin,moxacin,moxal,moxaline,moxatag,neotetranase,novabritine,ospamox,pacetocin,pamocil,paradroxil,pasetocin,penamox,piramox,promoxil,quimiopen,remoxil,riotapen,robamox,sawacillin,siganopen,simplamox,sintopen,sumox,topramoxin,trifamox,trimox,unicillin,utimox,velamox,vetramox,wymox,zamocillin,zamocilline,zimox" 1.5 "g" 3 "g" "101498-4,15-8,16-6,16365-9,17-4,18-2,18861-5,18862-3,19-0,20-8,21-6,22-4,25274-2,25310-4,3344-9,55614-2,55615-9,55616-7,6976-5,6977-3,80133-2" @@ -42,7 +42,7 @@ "BLA-S" "Beta-lactamase screening test" "Other" "NA" "beta-lactamase,betalactamase,bl screen,blt screen" "NA" "NA" "BIA" 71339 "Biapenem" "Carbapenems,Beta-lactams" "J01DH05,QJ01DH05" "biapen" "biapenern,omegacin" 1.2 "g" "41665-1,41666-9,41667-7,41728-7" "BCZ" 65807 "Bicyclomycin" "Other" "NA" "bicozamycin" "aizumycin,bacfeed,bacteron,bicozamicina,bicozamycin,bicozamycine,bicozamycinum" "NA" -"BLM" 5360373 "Bleomycin" "Glycopeptides,Peptides" "L01DC01,QL01DC01" "NA" "blenamax,blenoxane,bleocin,bleomicin,bleomicina,bleomycine,bleomycins,bleomycinum,blexane,nbleomycinamide" "NA" +"BLM" 5360373 "Bleomycin" "Glycopeptides,Peptides" "L01DC01,QL01DC01" "NA" "blenamax,blenoxane,bleocin,bleomicin,bleomicina,bleomycine,bleomycins,bleomycinum,blexane" "NA" "BDP" 68760 "Brodimoprim" "Trimethoprims" "J01EA02,QJ01EA02" "Sulfonamides and trimethoprim" "Trimethoprim and derivatives" "NA" "brodimoprima,brodimoprime,brodimoprimum,bromdimoprim,hyprim,unitrim" 0.2 "g" "NA" "BUT" 47472 "Butoconazole" "Antifungals" "G01AF15,QG01AF15" "NA" "butaconazole,butoconazol,butoconazolum,gynofort" "NA" "CDZ" 44242317 "Cadazolid" "Oxazolidinones" "NA" "NA" "NA" "NA" @@ -53,7 +53,7 @@ "CAR" 6540466 "Carumonam" "Monobactams,Beta-lactams" "J01DF02,QJ01DF02" "NA" "carumonamum" 2 "g" "51694-8" "CAS" 2826718 "Caspofungin" "Antifungals" "J02AX04,QJ02AX04" "Antimycotics for systemic use" "Other antimycotics for systemic use" "casp,caspof" "cancidas,caspofungina" 50 "mg" "32378-2,54175-5,54176-3,54185-4,58419-3" "CAC" 91562 "Cefacetrile" "Cephalosporins (1st gen.),Cephalosporins,Beta-lactams" "J01DB10,QJ01DB10,QJ51DB10" "Other beta-lactam antibacterials" "First-generation cephalosporins" "cephac" "cefacetril,cefacetrilo,cefacetrilum,celospor,cephacetrile,vetrimast" "55624-1,55625-8,55626-6,55627-4" -"CEC" 51039 "Cefaclor" "Cephalosporins (2nd gen.),Cephalosporins,Beta-lactams" "J01DC04,QJ01DC04" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "ccl,cec,cefacl,cf,cfac,cfc,cfcl,cfr,fac" "alenfral,alfacet,alfatil,ceclor,cefachlor,cefaclorum,cefeaclor,cephaclor,compound,distaclor,keflor,kefolor,kefral,keftab,keftid,lilly,lopac,panacef,panoral,raniclor" 1 "g" "16564-7,18874-8,21149-0,6986-4,83-6,84-4,85-1,86-9" +"CEC" 51039 "Cefaclor" "Cephalosporins (2nd gen.),Cephalosporins,Beta-lactams" "J01DC04,QJ01DC04" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "ccl,cec,cefacl,cf,cfac,cfc,cfcl,cfr,fac" "alenfral,alfacet,alfatil,ceclor,cefachlor,cefaclorum,cefeaclor,cephaclor,compound,distaclor,keflor,kefolor,kefral,keftab,keftid,lilly,panacef,panoral,raniclor" 1 "g" "16564-7,18874-8,21149-0,6986-4,83-6,84-4,85-1,86-9" "CFR" 47965 "Cefadroxil" "Cephalosporins (1st gen.),Cephalosporins,Beta-lactams" "J01DB05,QJ01DB05" "Other beta-lactam antibacterials" "First-generation cephalosporins" "cefadr,cfdx,cfr,fad" "bidocel,cefadrops,cefadroxilo,cefadroxilum,cefradroxil,cefzil,cephadroxil,duracef,duricef,kefroxil,sumacef,ultracef" 2 "g" "16565-4,18875-5,55628-2,63-8,64-6,65-3,66-1" "LEX" 27447 "Cefalexin" "Cephalosporins (1st gen.),Cephalosporins,Beta-lactams" "J01DB01,QJ01DB01,QJ51DB01" "Other beta-lactam antibacterials" "First-generation cephalosporins" "cepale,cflx" "adcadina,alcephin,alsporin,ambal,amplex,aristosporin,azabort,bactopenor,beliam,biocef,carnosporin,cefablan,cefacet,cefadal,cefadin,cefadina,cefalekey,cefaleksin,cefalessina,cefalexgobens,cefalexina,cefalexine,cefalexinum,cefalin,cefalival,cefaloto,cefanex,cefaseptin,cefax,ceffanex,cefibacter,ceflax,ceforal,cefovit,celexin,cepastar,cepexin,cephacillin,cephalexine,cephalexinum,cephalobene,cephanasten,cephaxin,cephin,cepol,ceporex,ceporexin,ceporexine,cerexin,cerexins,check,cophalexin,domucef,doriman,durantel,efemida,erocetin,factagard,felexin,fexin,ibilex,ibrexin,inphalex,karilexina,kefalospes,keflet,keflex,kefolan,keforal,kekrinal,kidolex,lafarine,larixin,lenocef,lexibiotico,loisine,lonflex,lopilexin,losporal,madlexin,maksipor,mamalexin,mamlexin,medolexin,medoxine,neokef,neolexina,noveol,novolexin,nufex,optocef,oracef,oriphex,oroxin,ortisporina,ospexin,palitrex,panixine,pectril,prindex,pyassan,rilexine,roceph,rogevil,sanaxin,sartosona,sencephalin,sepexin,servicef,servispor,sialexin,sinthecillin,sintolexyn,sporicef,sporidex,syncl,syncle,synecl,taicelexin,tepaxin,theratrex,tokiolexin,uphalexin,viosporine,voxxim,winlex,zabytrex,zozarine" 2 "g" "NA" "RID" 5773 "Cefaloridine" "Cephalosporins (1st gen.),Cephalosporins,Beta-lactams" "J01DB02,QJ01DB02" "Other beta-lactam antibacterials" "First-generation cephalosporins" "cefa,ceplor" "aliporina,ampligram,cefaloridin,cefaloridina,cefaloridinum,cefalorizin,ceflorin,cepaloridin,cepalorin,cephalomycine,cephaloridin,cephaloridine,cephaloridinum,ceporan,ceporin,ceporine,cilifor,deflorin,faredina,floridin,glaxoridin,intrasporin,keflodin,keflordin,kefloridin,kefspor,lloncefal,sasperin,sefacin,verolgin,vioviantine" 3 "g" "NA" @@ -72,7 +72,7 @@ "FEP" 5479537 "Cefepime" "Cephalosporins (4th gen.),Cephalosporins,Beta-lactams" "J01DE01,QJ01DE01" "Other beta-lactam antibacterials" "Fourth-generation cephalosporins" "cefep4,cefepi,cfep,cfpi,cpe,cpm,fep,pm,xpm" "anticefepime,axepim,cefepima,cefepimum,maxipime,pyrrolidinium,renapime" 4 "g" "101502-3,18879-7,31142-3,31143-1,35763-2,38363-8,42350-9,42351-7,42353-3,50631-1,58412-8,6643-1,6644-9,6645-7,6646-5,6987-2,8272-7,8273-5" "CFA" "Cefepime/amikacin" "Cephalosporins (4th gen.),Cephalosporins,Beta-lactams" "J01DE51,QJ01DE51" "Combinations of antibacterials" "Combinations of antibacterials" "NA" "NA" "NA" "CPC" 9567559 "Cefepime/clavulanic acid" "Cephalosporins (4th gen.),Cephalosporins,Beta-lactams" "J01DE51,QJ01DE51" "cefcla,cicl,xpml" "NA" "NA" -"FPE" 23653540 "Cefepime/enmetazobactam" "Cephalosporins (4th gen.),Cephalosporins,Beta-lactams,Beta-lactamase inhibitors" "J01DE51,QJ01DE51" "NA" "NA" "NA" +"FPE" 23653540 "Cefepime/enmetazobactam" "Cephalosporins (4th gen.),Cephalosporins,Beta-lactams,Beta-lactamase inhibitors" "J01DE51,QJ01DE51" "NA" "exblifep" "NA" "FNC" "Cefepime/nacubactam" "Cephalosporins (4th gen.),Cephalosporins,Beta-lactams,Beta-lactamase inhibitors" "J01DE51,QJ01DE51" "NA" "NA" "NA" "FTA" "Cefepime/taniborbactam" "Cephalosporins (4th gen.),Cephalosporins,Beta-lactams,Beta-lactamase inhibitors" "J01DE51,QJ01DE51" "NA" "NA" "NA" "FPT" 9567558 "Cefepime/tazobactam" "Cephalosporins (4th gen.),Cephalosporins,Beta-lactams,Beta-lactamase inhibitors" "J01DE51,QJ01DE51" "NA" "NA" "NA" @@ -219,16 +219,16 @@ "GEH" "Gentamicin-high" "Aminoglycosides" "NA" "gehi,gehl,genta high,gentamicin high" "NA" "18929-0,35817-6,7017-7,7018-5" "GEP" 25101874 "Gepotidacin" "Other" "J01XX13,QJ01XX13" "NA" "gepotidacina,gepotidacine" "NA" "GRX" 72474 "Grepafloxacin" "Fluoroquinolones,Quinolones" "J01MA11,QJ01MA11" "Quinolone antibacterials" "Fluoroquinolones" "grep,grepaf" "grepafloxacine,grepafloxacino,lungaskin,raxar,vaxar" 0.4 "g" "21316-5,23638-0,23639-8,35818-4" -"GRI" 441140 "Griseofulvin" "Antifungals" "D01AA08,D01BA01,QD01AA08,QD01BA01" "NA" "amudane,delmofulvina,epigriseofulvin,fulcin,fulcine,fulvicin,fulvidex,fulvina,fulvinil,fulvistatin,fungivin,greosin,gresfeed,gricin,grifulin,grifulvin,grisactin,griscofulvin,grisefuline,griseo,griseofulviin,griseofulvina,griseofulvine,griseofulvinum,griseomix,griseostatin,grisetin,grisofulvin,grisovin,grisowen,grizeofulvin,grysio,guservin,lamoryl,likuden,likunden,murfulvin,poncyl,spiro,spirofulvin,xuanjing" 0.5 "g" "12402-4,54200-1,54201-9,54202-7" +"GRI" 441140 "Griseofulvin" "Antifungals" "D01AA08,D01BA01,QD01AA08,QD01BA01" "NA" "amudane,delmofulvina,epigriseofulvin,fulcin,fulcine,fulvicin,fulvidex,fulvina,fulvinil,fulvistatin,fungivin,greosin,gresfeed,gricin,grifulin,grifulvin,grisactin,griscofulvin,grisefuline,griseo,griseofulviin,griseofulvina,griseofulvine,griseofulvinum,griseomix,griseostatin,grisetin,grisofulvin,grisovin,grisowen,grizeofulvin,grysio,guservin,lamoryl,likuden,likunden,murfulvin,poncyl,spirofulvin,xuanjing" 0.5 "g" "12402-4,54200-1,54201-9,54202-7" "HAB" 175989 "Habekacin" "Aminoglycosides" "NA" "NA" "amikafur,amikan,amitrex,arikayce,biklin,biodacyn,chemacin,fabianol,habekacinxsulfate,likacin,pierami" "NA" "HCH" 11979956 "Hachimycin" "Antifungals" "D01AA03,G01AA06,J02AA02,QD01AA03,QG01AA06,QJ02AA02" "Antimycotics for systemic use" "Antibiotics" "NA" "cabimicina,hachimicina,hachimycine,hachimycinum,trichomycinum,trichonat" "NA" "HET" 443387 "Hetacillin" "Penicillins,Beta-lactams" "J01CA18,QJ01CA18" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "hetaci" "etacillina,hetacilina,hetacilline,hetacillinum,natacillin,phenazacillin,versapen,versatrex" 2 "g" "18931-6,274-1,275-8,276-6,277-4" "HYG" 56928061 "Hygromycin" "Aminoglycosides" "NA" "NA" "antihelmycin,destomysin,hyanthelmix,hygromix,hygrovectine,hygrovetine" "NA" "IBX" "Ibrexafungerp" "Antifungals" "J02AX07,QJ02AX07" "NA" "NA" "NA" "ICL" 213043 "Iclaprim" "Trimethoprims" "J01EA03,QJ01EA03" "iclapr" "iclaprime,mersarex" "73597-7,73619-9,73642-1" -"IPM" 104838 "Imipenem" "Carbapenems,Beta-lactams" "J01DH51,QJ01DH51" "Other beta-lactam antibacterials" "Carbapenems" "imci,imi,imip,imip32,imipen,imp" "imipemide,imipenemum,imipenen,primaxin,recarbrio,tienam,tienamycin" 2 "g" "101487-7,17010-0,18932-4,18933-2,23613-3,25221-3,25257-7,27331-8,278-2,279-0,280-8,281-6,282-4,283-2,284-0,285-7,35819-2,3688-9,54170-6,54171-4,54172-2,7019-3,85424-0,93232-7,96372-8" +"IPM" 104838 "Imipenem" "Carbapenems,Beta-lactams" "J01DH51,QJ01DH51" "Other beta-lactam antibacterials" "Carbapenems" "imci,imi,imip,imip32,imipen,imp" "imipemide,imipenemum,imipenen,primaxin,tienam,tienamycin" 2 "g" "101487-7,17010-0,18932-4,18933-2,23613-3,25221-3,25257-7,27331-8,278-2,279-0,280-8,281-6,282-4,283-2,284-0,285-7,35819-2,3688-9,54170-6,54171-4,54172-2,7019-3,85424-0,93232-7,96372-8" "IPE" "Imipenem/EDTA" "Carbapenems,Beta-lactams" "NA" "NA" "NA" "35819-2,54170-6,54171-4,54172-2" -"IMR" "Imipenem/relebactam" "Carbapenems,Beta-lactams,Beta-lactamase inhibitors" "J01DH56,QJ01DH56" "NA" "NA" 2 "g" "85424-0,93232-7,96372-8" +"IMR" "Imipenem/relebactam" "Carbapenems,Beta-lactams,Beta-lactamase inhibitors" "J01DH56,QJ01DH56" "NA" "recarbrio" 2 "g" "85424-0,93232-7,96372-8" "ISV" 6918485 "Isavuconazole" "Antifungals" "J02AC05,QJ02AC05" "isav" "benzonitrile,ravuconazole" 0.2 "g" 0.2 "g" "85381-2,88887-5" "ISE" 3037209 "Isepamicin" "Aminoglycosides" "J01GB11,QJ01GB11" "Aminoglycoside antibacterials" "Other aminoglycosides" "isepam" "isepacin,isepalline,isepamicina,isepamicine,isepamicinsulphate,isepamicinum" 0.4 "g" "32381-6,35820-0,35821-8,55680-3" "ISO" 3760 "Isoconazole" "Antifungals" "D01AC05,G01AF07,QD01AC05,QG01AF07" "Antimycotics for topic use" "Triazole derivatives" "NA" "isoconazol,isoconazolum,travogen" "55681-1,55682-9,55683-7,55684-5" @@ -240,7 +240,7 @@ "KAH" "Kanamycin-high" "Aminoglycosides" "NA" "k_h,kahl" "NA" "18936-5,7023-5,7024-3" "KAC" "Kanamycin/cephalexin" "Aminoglycosides" "NA" "NA" "NA" "NA" "KAS" 65174 "Kasugamycin" "Aminoglycosides" "NA" "NA" "kasumin,kasuminl" "NA" -"KET" 456201 "Ketoconazole" "Antifungals" "D01AC08,G01AF11,H02CA03,J02AB02,QD01AC08,QG01AF11,QH02CA03,QJ02AB02" "Antimycotics for systemic use" "Imidazole derivatives" "keto,ketoco,ktc" "brizoral,ethanone,extina,fungarest,fungoral,ketaconazole,ketocanazole,ketoconazol,ketoconazolum,ketodan,ketoderm,ketoisdin,ketozole,kuric,levoketoconazole,nizoral,normocort,panfungol,piperazine,recorlev,sebazole,teryzolin,terzolin,tocris,xolegel" 0.6 "g" "10990-0,12393-5,18937-3,25259-3,294-9,295-6,296-4,297-2,60091-6,60092-4,7025-0" +"KET" 456201 "Ketoconazole" "Antifungals" "D01AC08,G01AF11,H02CA03,J02AB02,QD01AC08,QG01AF11,QH02CA03,QJ02AB02" "Antimycotics for systemic use" "Imidazole derivatives" "keto,ketoco,ktc" "brizoral,ethanone,extina,fungarest,fungoral,ketaconazole,ketocanazole,ketoconazol,ketoconazolum,ketodan,ketoderm,ketoisdin,ketozole,kuric,levoketoconazole,nizoral,normocort,panfungol,piperazine,recorlev,sebazole,teryzolin,terzolin,xolegel" 0.6 "g" "10990-0,12393-5,18937-3,25259-3,294-9,295-6,296-4,297-2,60091-6,60092-4,7025-0" "KIT" "Kitasamycin" "Macrolides" "QJ01FA93" "leucomycin" "NA" "NA" "LAS" 5360807 "Lasalocid" "Ionophores" "QP51BB02" "NA" "avatec,bovate,bovatec,lasalocide,lasalocido,lasalocidsalt,lasalocidum" "87598-9" "LSC" 71528768 "Lascufloxacin" "Fluoroquinolones,Quinolones" "J01MA25,QJ01MA25" "Quinolone antibacterials" "Fluoroquinolones" "NA" "lasvic" 75 "mg" "NA" @@ -343,9 +343,9 @@ "PHN" 6869 "Phenoxymethylpenicillin" "Penicillins,Beta-lactams" "J01CE02,QJ01CE02" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" "fepe,peni v,penicillin v,phepen,pnv,pv" "apopen,calcipen,fenacilin,fenospen,meropenin,oracillin,oracilline,oratren,orocillin,ospen,phenocillin,phenomycilline,phenopenicillin,rocilin,stabicillin,vebecillin" 2 "g" "NA" "PMR" 5284447 "Pimaricin" "Antifungals" "NA" "natamycin" "delvocid,delvolan,delvopos,mycophyt,myprozine,natacyn,natafucin,natajen,natamatrix,natamax,natamicina,natamycin,natamycine,natamycinum,pimafucin,pimaracin,pimaricine,pimarizin,synogil,tennecetin" "NA" "PPA" 4831 "Pipemidic acid" "Quinolones" "J01MB04,QJ01MB04" "Quinolone antibacterials" "Other quinolones" "pipaci,pipz,pizu" "deblaston,dolcol,filtrax,karunomazin,memento,nuril,palin,pipedac,pipemid,pipemidate,pipemidic,pipemidicacid,pipram,pipurin,tractur,uromidin,urosten,uroval" 0.8 "g" "NA" -"PIP" 43672 "Piperacillin" "Ureidopenicillins,Penicillins,Beta-lactams" "J01CA12,QJ01CA12" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "pi,pip,pipc,pipe,pipera,pp" "penmalin,pentcillin,peperacillin,peracin,piperacilina,piperacillina,piperacilline,piperacillinhydrate,piperacillinum,pipercillin,pipracil,tazocin" 14 "g" "101490-1,101491-9,18969-6,18970-4,25268-4,3972-7,407-7,408-5,409-3,410-1,411-9,412-7,413-5,414-3,54197-9,54198-7,54199-5,55704-1,7043-3,7044-1" +"PIP" 43672 "Piperacillin" "Ureidopenicillins,Penicillins,Beta-lactams" "J01CA12,QJ01CA12" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "pi,pip,pipc,pipe,pipera,pp" "penmalin,pentcillin,peperacillin,peracin,piperacilina,piperacillina,piperacilline,piperacillinhydrate,piperacillinum,pipercillin,pipracil" 14 "g" "101490-1,101491-9,18969-6,18970-4,25268-4,3972-7,407-7,408-5,409-3,410-1,411-9,412-7,413-5,414-3,54197-9,54198-7,54199-5,55704-1,7043-3,7044-1" "PIS" "Piperacillin/sulbactam" "Penicillins,Beta-lactams,Beta-lactamase inhibitors" "NA" "NA" "NA" 14 "g" "54197-9,54198-7,54199-5,55704-1" -"TZP" 461573 "Piperacillin/tazobactam" "Ureidopenicillins,Penicillins,Beta-lactams,Beta-lactamase inhibitors" "J01CR05,QJ01CR05" "Beta-lactam antibacterials, penicillins" "Combinations of penicillins, incl. beta-lactamase inhibitors" "p/t,piptaz,piptazo,pit,pita,pt,ptc,ptz,tzp" "piptazobactam,tazonam,zobactin,zosyn" 14 "g" "101491-9,18970-4,411-9,412-7,413-5,414-3,7044-1" +"TZP" 461573 "Piperacillin/tazobactam" "Ureidopenicillins,Penicillins,Beta-lactams,Beta-lactamase inhibitors" "J01CR05,QJ01CR05" "Beta-lactam antibacterials, penicillins" "Combinations of penicillins, incl. beta-lactamase inhibitors" "p/t,piptaz,piptazo,pit,pita,pt,ptc,ptz,tzp" "piptazobactam,tazocin,tazonam,zobactin,zosyn" 14 "g" "101491-9,18970-4,411-9,412-7,413-5,414-3,7044-1" "PRC" 71978 "Piridicillin" "Penicillins,Beta-lactams" "NA" "NA" "NA" "NA" "PRL" 157385 "Pirlimycin" "Lincosamides,Macrolides" "QJ51FF90" "pirlim" "pirlimycina,pirlimycine,pirlimycinum,pirsue" "35829-1,35830-9,35831-7" "PIR" 4855 "Piromidic acid" "Quinolones" "J01MB03,QJ01MB03" "Quinolone antibacterials" "Other quinolones" "NA" "bactramyl,enterol,gastrurol,panacid,pirodal,piromidate,reelon,septural,urisept,uropir,zaomeal" 2 "g" "NA" @@ -448,7 +448,7 @@ "TAL" 71447 "Talampicillin" "Penicillins,Beta-lactams" "J01CA15,QJ01CA15" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "NA" "aseocillin,phthalidyl,talampicilina,talampicilline,talampicillinum,talpen,yamacillin" 2 "g" "18988-6,479-6,480-4,481-2,482-0" "TLP" 163307 "Talmetoprim" "Other" "NA" "NA" "NA" "NA" "TAN" 76902493 "Taniborbactam" "Carbapenems,Beta-lactams,Beta-lactamase inhibitors" "NA" "vnrx-5133" "NA" "NA" -"TAZ" 123630 "Tazobactam" "Beta-lactamase inhibitors" "J01CG02,QJ01CG02" "Beta-lactam antibacterials, penicillins" "Beta-lactamase inhibitors" "tazo,tazoba" "exblifep,tazobactamsalt,tazobactamum,tazobactum" "41719-6,41720-4,41721-2,41740-2" +"TAZ" 123630 "Tazobactam" "Beta-lactamase inhibitors" "J01CG02,QJ01CG02" "Beta-lactam antibacterials, penicillins" "Beta-lactamase inhibitors" "tazo,tazoba" "tazobactamsalt,tazobactamum,tazobactum" "41719-6,41720-4,41721-2,41740-2" "TBP" 9800194 "Tebipenem" "Carbapenems,Beta-lactams" "NA" "NA" "NA" "NA" "TZD" 11234049 "Tedizolid" "Oxazolidinones" "J01XX11,QJ01XX11" "Other antibacterials" "Other antibacterials" "tedi" "torezolid" 0.2 "g" 0.2 "g" "73586-0,73608-2,73631-4" "TEC" 16131923 "Teicoplanin" "Glycopeptides,Peptides" "J01XA02,QJ01XA02" "Other antibacterials" "Glycopeptide antibacterials" "tec,tei,teic,teicop,tp,tpl,tpn" "NA" 0.4 "g" "18989-4,25534-9,25535-6,34378-0,34379-8,4043-6,483-8,484-6,485-3,486-1,7051-6,80968-1" @@ -468,10 +468,10 @@ "THI" 27200 "Thiamphenicol" "Phenicols" "J01BA02,QJ01BA02,QJ51BA02" "Amphenicols" "Amphenicols" "thiaph" "armai,dextrosulfenidol,dextrosulphenidol,igralin,racefenicol,racefenicolo,racefenicolum,raceophenidol,thiamphenicolum,thiocymetin,thiophenicol,tiamfenicol,tiamfenicolo,urfamycine" 1.5 "g" 1.5 "g" "41723-8,41724-6,41725-3,54169-8" "TAT" "Thioacetazone" "Antimycobacterials" "J04AK07,QJ04AK07" "Drugs for treatment of tuberculosis" "Other drugs for treatment of tuberculosis" "NA" "NA" "NA" "THI1" "Thioacetazone/isoniazid" "Antimycobacterials" "J04AM04,QJ04AM04" "Drugs for treatment of tuberculosis" "Combinations of drugs for treatment of tuberculosis" "NA" "NA" "NA" -"THS" 16129666 "Thiostrepton" "Peptides" "NA" "NA" "alaninamide,bryamycin,gargon,pharmakon,prestwick,sporangiomycin,thiactin,tiostrepton" "NA" +"THS" 16129666 "Thiostrepton" "Peptides" "NA" "NA" "alaninamide,bryamycin,gargon,sporangiomycin,thiactin,tiostrepton" "NA" "TIA" 656958 "Tiamulin" "Pleuromutilins" "QJ01XQ01" "tiamul" "denagard,thiamutilin,tiamulina,tiamuline,tiamulinum" "35846-5,35847-3,35848-1,87589-8" -"TIC" 36921 "Ticarcillin" "Penicillins,Beta-lactams" "J01CA13,QJ01CA13" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "tc,ti,tic,tica,ticarc" "ticar,ticarcilina,ticarcilline,ticarcillinum,timentin" 15 "g" "18994-4,18995-1,25254-4,4054-3,4055-0,499-4,500-9,501-7,502-5,503-3,504-1,505-8,506-6,55716-5,55717-3,55718-1,55719-9,7053-2,7054-0" -"TCC" 6437075 "Ticarcillin/clavulanic acid" "Penicillins,Beta-lactams,Beta-lactamase inhibitors" "J01CR03,QJ01CR03" "Beta-lactam antibacterials, penicillins" "Combinations of penicillins, incl. beta-lactamase inhibitors" "t/c,tcc,ticcla,ticl,tim,tlc" "augpenin" 15 "g" "NA" +"TIC" 36921 "Ticarcillin" "Penicillins,Beta-lactams" "J01CA13,QJ01CA13" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "tc,ti,tic,tica,ticarc" "ticar,ticarcilina,ticarcilline,ticarcillinum" 15 "g" "18994-4,18995-1,25254-4,4054-3,4055-0,499-4,500-9,501-7,502-5,503-3,504-1,505-8,506-6,55716-5,55717-3,55718-1,55719-9,7053-2,7054-0" +"TCC" 6437075 "Ticarcillin/clavulanic acid" "Penicillins,Beta-lactams,Beta-lactamase inhibitors" "J01CR03,QJ01CR03" "Beta-lactam antibacterials, penicillins" "Combinations of penicillins, incl. beta-lactamase inhibitors" "t/c,tcc,ticcla,ticl,tim,tlc" "augpenin,timentin" 15 "g" "NA" "TGC" 54686904 "Tigecycline" "Tetracyclines" "J01AA12,QJ01AA12" "Tetracyclines" "Tetracyclines" "tgc,tig,tige,tigecy" "tigeciclina,tigecyclin,tigecyclinehydrate,tigilcycline,tygacil" 0.1 "g" "101499-2,42354-1,42355-8,42356-6,42357-4,55158-0" "TMN" "Tigemonam" "Monobactams,Beta-lactams" "NA" "NA" "NA" "NA" "TBQ" 65592 "Tilbroquinol" "Fluoroquinolones,Quinolones" "P01AA05" "NA" "tilbroquinolum" "NA" @@ -502,5 +502,5 @@ "XER" 140830474 "Xeruborbactam" "Beta-lactamase inhibitors" "NA" "NA" "benzo,borate" "NA" "XBR" 72144 "Xibornol" "Other" "J01XX02,QJ01XX02" "Other antibacterials" "Other antibacterials" "NA" "bactacine,bracen,nanbacine,xibornolo,xibornolum" "NA" "ZID" 77846445 "Zidebactam" "Beta-lactamase inhibitors" "NA" "NA" "zidebactamsalt" "NA" -"ZFD" 76685216 "Zoliflodacin" "Spiropyrimidinetriones" "NA" "zol" "nuzolvence,spiro,zoliflodacina,zoliflodacine" "NA" -"ZOR" 70697970 "Zorbamycin" "Glycopeptides,Peptides" "NA" "NA" "bleomycetin,boanmycin,nbleomycinamide,pingyangmycin" "NA" +"ZFD" 76685216 "Zoliflodacin" "Spiropyrimidinetriones" "NA" "zol" "nuzolvence,zoliflodacina,zoliflodacine" "NA" +"ZOR" 70697970 "Zorbamycin" "Glycopeptides,Peptides" "NA" "NA" "bleomycetin,boanmycin,pingyangmycin" "NA" diff --git a/data-raw/datasets/antimicrobials.xlsx b/data-raw/datasets/antimicrobials.xlsx index 21bc7e64a..3854ae951 100644 Binary files a/data-raw/datasets/antimicrobials.xlsx and b/data-raw/datasets/antimicrobials.xlsx differ diff --git a/data/antibiotics.rda b/data/antibiotics.rda index a9f6b7b8e..1f1017eef 100644 Binary files a/data/antibiotics.rda and b/data/antibiotics.rda differ diff --git a/data/antimicrobials.rda b/data/antimicrobials.rda index 6c2873788..7b9d50ae9 100644 Binary files a/data/antimicrobials.rda and b/data/antimicrobials.rda differ diff --git a/tests/testthat/test-data.R b/tests/testthat/test-data.R index e455a1d47..1c37291ad 100644 --- a/tests/testthat/test-data.R +++ b/tests/testthat/test-data.R @@ -615,3 +615,21 @@ test_that("antimicrobials: unique and well-formed", { loinc <- loinc[!is.na(loinc) & loinc != ""] expect_true(all(loinc %like_case% "^[0-9]+-[0-9]$"), info = paste(utils::head(loinc[loinc %unlike_case% "^[0-9]+-[0-9]$"], 20), collapse = ", ")) }) + +test_that("antimicrobials: synonyms are unambiguous and filed under the right agent", { + skip_on_cran() + ab <- AMR::antimicrobials + syn <- data.frame(ab = rep(as.character(ab$ab), lengths(ab$synonyms)), synonym = unlist(ab$synonyms), stringsAsFactors = FALSE) + syn <- syn[!is.na(syn$synonym), , drop = FALSE] + # a synonym must not belong to more than one agent + dups <- unique(syn$synonym[duplicated(syn$synonym)]) + expect_identical(length(dups), 0L, info = paste(dups, collapse = ", ")) + # trade names of combinations belong to the combination, not to one of its components (#315) + expect_identical( + as.character(as.ab(c("Tazocin", "Zosyn", "Timentin", "Recarbrio", "Exblifep", "Augmentin", "Bactrim"))), + c("TZP", "TZP", "TCC", "IMR", "FPE", "AMC", "SXT") + ) + # names of screening libraries, suppliers and chemical fragments are no synonyms (#315) + expect_false(any(c("lopac", "nbleomycinamide", "pharmakon", "prestwick", "spectrum", "spiro", "tocris") %in% syn$synonym)) + expect_false("AMA" %in% as.character(unlist(ab_from_text("Patient started on broad spectrum antibiotics")))) +})