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Implement extensive support for antiviral agents support (#77)
This commit is contained in:
Dr. Matthijs Berends
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GitHub
GitHub
parent
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commit
496c08d851
@ -267,17 +267,19 @@ AB_BETALACTAMS <- c(AB_PENICILLINS, AB_CEPHALOSPORINS, AB_CARBAPENEMS)
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# this will be used for documentation:
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DEFINED_AB_GROUPS <- ls(envir = globalenv())
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DEFINED_AB_GROUPS <- DEFINED_AB_GROUPS[!DEFINED_AB_GROUPS %in% globalenv_before_ab]
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create_AB_lookup <- function() {
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AMR_env$AB_lookup <- AMR::antibiotics
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AMR_env$AB_lookup$generalised_name <- generalise_antibiotic_name(AMR_env$AB_lookup$name)
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AMR_env$AB_lookup$generalised_synonyms <- lapply(AMR_env$AB_lookup$synonyms, generalise_antibiotic_name)
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AMR_env$AB_lookup$generalised_abbreviations <- lapply(AMR_env$AB_lookup$abbreviations, generalise_antibiotic_name)
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AMR_env$AB_lookup$generalised_loinc <- lapply(AMR_env$AB_lookup$loinc, generalise_antibiotic_name)
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AMR_env$AB_lookup$generalised_all <- unname(lapply(
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as.list(as.data.frame(t(AMR_env$AB_lookup[,
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create_AB_AV_lookup <- function(df) {
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new_df <- df
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new_df$generalised_name <- generalise_antibiotic_name(new_df$name)
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new_df$generalised_synonyms <- lapply(new_df$synonyms, generalise_antibiotic_name)
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if ("abbreviations" %in% colnames(df)) {
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new_df$generalised_abbreviations <- lapply(new_df$abbreviations, generalise_antibiotic_name)
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}
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new_df$generalised_loinc <- lapply(new_df$loinc, generalise_antibiotic_name)
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new_df$generalised_all <- unname(lapply(
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as.list(as.data.frame(t(new_df[,
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c(
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"ab", "atc", "cid", "name",
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colnames(AMR_env$AB_lookup)[colnames(AMR_env$AB_lookup) %like% "generalised"]
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colnames(new_df)[colnames(new_df) %in% c("ab", "av", "atc", "cid", "name")],
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colnames(new_df)[colnames(new_df) %like% "generalised"]
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),
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drop = FALSE
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]),
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@ -288,9 +290,10 @@ create_AB_lookup <- function() {
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x[x != ""]
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}
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))
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AMR_env$AB_lookup[, colnames(AMR_env$AB_lookup)[colnames(AMR_env$AB_lookup) %like% "^generalised"]]
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new_df[, colnames(new_df)[colnames(new_df) %like% "^generalised"]]
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}
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AB_LOOKUP <- create_AB_lookup()
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AB_LOOKUP <- create_AB_AV_lookup(AMR::antibiotics)
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AV_LOOKUP <- create_AB_AV_lookup(AMR::antivirals)
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# Export to package as internal data ----
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usethis::ui_info(paste0("Updating internal package data"))
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@ -304,6 +307,7 @@ suppressMessages(usethis::use_data(EUCAST_RULES_DF,
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MO_FULLNAME_LOWER,
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MO_PREVALENT_GENERA,
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AB_LOOKUP,
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AV_LOOKUP,
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AB_AMINOGLYCOSIDES,
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AB_AMINOPENICILLINS,
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AB_ANTIFUNGALS,
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@ -1,103 +1,121 @@
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"atc" "cid" "name" "atc_group" "synonyms" "oral_ddd" "oral_units" "iv_ddd" "iv_units"
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"J05AF06" 441300 "Abacavir" "Nucleoside and nucleotide reverse transcriptase inhibitors" "Abacavir,Abacavir sulfate,Ziagen" 0.6 "g"
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"J05AB01" 135398513 "Aciclovir" "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "Acicloftal,Aciclovier,Aciclovir,Aciclovirum,Activir,AcycloFoam,Acycloguanosine,Acyclovir,Acyclovir Lauriad,ACYCLOVIR SODIUM,Avirax,Cargosil,Cyclovir,Genvir,Gerpevir,Hascovir,Herpevir,Maynar,Poviral,Sitavig,Sitavir,Vipral,Virolex,Viropump,Virorax,Zovirax,Zovirax topical,Zyclir" 4 "g" 4 "g"
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"J05AF08" 60871 "Adefovir dipivoxil" "Nucleoside and nucleotide reverse transcriptase inhibitors" "Adefovir di ester,Adefovir dipivoxil,Adefovir Dipivoxil,Adefovir dipivoxyl,Adefovir pivoxil,Adefovirdipivoxl,Bisadenine,BISADENINE,BisPMEA,Hepsera,Preveon,YouHeDing" 10 "mg"
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"J05AE05" 65016 "Amprenavir" "Protease inhibitors" "Agenerase,Amprenavir,Amprenavirum,Prozei,Vertex" 1.2 "g"
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"J05AP06" 16076883 "Asunaprevir" "Antivirals for treatment of HCV infections" "Asunaprevir,Sunvepra"
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"J05AE08" 148192 "Atazanavir" "Protease inhibitors" "Atazanavir,Atazanavir Base,Latazanavir,Reyataz,Zrivada" 0.3 "g"
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"J05AR15" 86583336 "Atazanavir and cobicistat" "Antivirals for treatment of HIV infections, combinations" ""
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"J05AR23" "Atazanavir and ritonavir" "Antivirals for treatment of HIV infections, combinations" "" 0.3 "g"
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"J05AP03" 10324367 "Boceprevir" "Antivirals for treatment of HCV infections" "Bocepravir,Boceprevir,Victrelis" 2.4 "g"
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"J05AB15" 446727 "Brivudine" "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "Bridic,Brivox,Brivudin,Brivudina,Brivudine,Brivudinum,BrVdUrd,Helpin,Zerpex,Zostex" 0.125 "g"
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"J05AB12" 60613 "Cidofovir" "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "Cidofovir,Cidofovir anhydrous,Cidofovir gel,Cidofovirum,Forvade,Vistide" 25 "mg"
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"J05AF12" 73115 "Clevudine" "Nucleoside and nucleotide reverse transcriptase inhibitors" "Clevudine,Levovir,Revovir" 30 "mg"
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"J05AP07" 25154714 "Daclatasvir" "Antivirals for treatment of HCV infections" "Daclatasvir,Daklinza" 60 "mg"
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"J05AE10" 213039 "Darunavir" "Protease inhibitors" "Darunavir,Darunavirum,Prezista,Prezista Naive" 1.2 "g"
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"J05AR14" "Darunavir and cobicistat" "Antivirals for treatment of HIV infections, combinations" ""
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"J05AP09" 56640146 "Dasabuvir" "Antivirals for treatment of HCV infections" "Dasabuvir" 0.5 "g"
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"J05AP52" "Dasabuvir, ombitasvir, paritaprevir and ritonavir" "Antivirals for treatment of HCV infections" ""
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"J05AG02" 5625 "Delavirdine" "Non-nucleoside reverse transcriptase inhibitors" "BHAP der,Delavirdin,Delavirdina,Delavirdine,Delavirdinum,PIPERAZINE,Rescriptor" 1.2 "g"
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"J05AF02" 135398739 "Didanosine" "Nucleoside and nucleotide reverse transcriptase inhibitors" "Didanosina,Didanosine,Didanosinum,Dideoxyinosine,DIDEOXYINOSINE,Hypoxanthine ddN,Videx,Videx EC" 0.4 "g"
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"J05AX12" 54726191 "Dolutegravir" "Other antivirals" "Dolutegravir,Dolutegravir Sodium,Soltegravir,Tivicay" 50 "mg"
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"J05AR21" 131801472 "Dolutegravir and rilpivirine" "Antivirals for treatment of HIV infections, combinations" ""
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"J05AG06" 58460047 "Doravirine" "Non-nucleoside reverse transcriptase inhibitors" "Doravirine,Pifeltro"
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"J05AG03" 64139 "Efavirenz" "Non-nucleoside reverse transcriptase inhibitors" "Efavirenz,Efavirenzum,Eravirenz,Stocrin,Strocin,Sustiva" 0.6 "g"
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"J05AP54" 91669168 "Elbasvir and grazoprevir" "Antivirals for treatment of HCV infections" ""
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"J05AX11" 5277135 "Elvitegravir" "Other antivirals" "Elvitegravir,Vitekta"
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"J05AF09" 60877 "Emtricitabine" "Nucleoside and nucleotide reverse transcriptase inhibitors" "Coviracil,Emtricitabin,Emtricitabina,Emtricitabine,Emtricitabinum,Emtritabine,Emtriva,Racivir" 0.2 "g"
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"J05AR17" 90469070 "Emtricitabine and tenofovir alafenamide" "Antivirals for treatment of HIV infections, combinations" ""
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"J05AR20" "Emtricitabine, tenofovir alafenamide and bictegravir" "Antivirals for treatment of HIV infections, combinations" ""
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"J05AR19" "Emtricitabine, tenofovir alafenamide and rilpivirine" "Antivirals for treatment of HIV infections, combinations" ""
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"J05AR22" "Emtricitabine, tenofovir alafenamide, darunavir and cobicistat" "Antivirals for treatment of HIV infections, combinations" ""
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"J05AR18" "Emtricitabine, tenofovir alafenamide, elvitegravir and cobicistat" "Antivirals for treatment of HIV infections, combinations" ""
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"J05AR06" "Emtricitabine, tenofovir disoproxil and efavirenz" "Antivirals for treatment of HIV infections, combinations" ""
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"J05AR08" "Emtricitabine, tenofovir disoproxil and rilpivirine" "Antivirals for treatment of HIV infections, combinations" ""
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"J05AR09" "Emtricitabine, tenofovir disoproxil, elvitegravir and cobicistat" "Antivirals for treatment of HIV infections, combinations" ""
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"J05AX07" 16130199 "Enfuvirtide" "Other antivirals" "Enfurvitide,Enfuvirtide,Fuzeon,Pentafuside" 0.18 "g"
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"J05AX17" 10089466 "Enisamium iodide" "Other antivirals" "Enisamium iodide" 1.5 "g"
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"J05AF10" 135398508 "Entecavir" "Nucleoside and nucleotide reverse transcriptase inhibitors" "Baraclude,Entecavir,Entecavir anhydrous,Entecavirum" 0.5 "mg"
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"J05AG04" 193962 "Etravirine" "Non-nucleoside reverse transcriptase inhibitors" "DAPY deriv,Etravine,Etravirine,Intelence" 0.4 "g"
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"J05AP04" 42601552 "Faldaprevir" "Antivirals for treatment of HCV infections" "Faldaprevir"
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"J05AB09" 3324 "Famciclovir" "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "Famciclovir,Famciclovirum,Famvir,Oravir" 0.75 "g"
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"J05AE07" 131536 "Fosamprenavir" "Protease inhibitors" "Amprenavir phosphate,Fosamprenavir,Lexiva,Telzir" 1.4 "g"
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"J05AD01" 3415 "Foscarnet" "Phosphonic acid derivatives" "Forscarnet,Forscarnet sodium,Foscarmet,Foscarnet,Phosphonoformate,Phosphonoformic acid" 6.5 "g"
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"J05AD02" 546 "Fosfonet" "Phosphonic acid derivatives" "Fosfonet,Fosfonet sodium,Fosfonet Sodium,Fosfonoacetate,Fosfonoacetic acid,Phosphonacetate,Phosphonacetic acid"
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"J05AB06" 135398740 "Ganciclovir" "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "Citovirax,Cymevan,Cymeven,Cymevene,Cytovene,Cytovene IV,Ganciclovir,Ganciclovirum,Gancyclovir,Hydroxyacyclovir,Virgan,Vitrasert,Zirgan" 3 "g" 0.5 "g"
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"J05AP57" "Glecaprevir and pibrentasvir" "Antivirals for treatment of HCV infections" ""
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"J05AX23" "Ibalizumab" "Other antivirals" ""
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"J05AB02" 5905 "Idoxuridine" "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "Antizona,Dendrid,Emanil,Heratil,Herpesil,Herpid,Herpidu,Herplex,HERPLEX,Herplex liquifilm,Idexur,Idossuridina,Idoxene,Idoxuridin,Idoxuridina,Idoxuridine,Idoxuridinum,Idu Oculos,Iducher,Idulea,Iduoculos,Iduridin,Iduviran,Iododeoxyridine,Iododeoxyuridine,Iodoxuridine,Joddeoxiuridin,Kerecid,Kerecide,Ophthalmadine,Spectanefran,Stoxil,Synmiol,Virudox"
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"J05AE02" 5362440 "Indinavir" "Protease inhibitors" "Compound J,Crixivan,Indinavir,Indinavir anhydrous,Propolis+Indinavir" 2.4 "g"
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"J05AX05" 135449284 "Inosine pranobex" "Other antivirals" "Aviral,Delimmun,Immunovir,Imunovir,Inosine pranobex,Inosiplex,Isoprinosin,Isoprinosina,Isoprinosine,Isoviral,Methisoprinol,Methysoprinol,Metisoprinol,Viruxan" 3 "g"
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"J05AF05" 60825 "Lamivudine" "Nucleoside and nucleotide reverse transcriptase inhibitors" "Epivir,Hepitec,Heptivir,Heptodin,Heptovir,Lamivir,Lamivudin,Lamivudina,Lamivudine,Lamivudinum,Zeffix" 0.3 "g"
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"J05AR02" "Lamivudine and abacavir" "Antivirals for treatment of HIV infections, combinations" ""
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"J05AR16" 73386700 "Lamivudine and raltegravir" "Antivirals for treatment of HIV infections, combinations" ""
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"J05AR12" "Lamivudine and tenofovir disoproxil" "Antivirals for treatment of HIV infections, combinations" ""
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"J05AR13" "Lamivudine, abacavir and dolutegravir" "Antivirals for treatment of HIV infections, combinations" ""
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"J05AR24" "Lamivudine, tenofovir disoproxil and doravirine" "Antivirals for treatment of HIV infections, combinations" ""
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"J05AR11" "Lamivudine, tenofovir disoproxil and efavirenz" "Antivirals for treatment of HIV infections, combinations" ""
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"J05AX18" 45138674 "Letermovir" "Other antivirals" "Letermovir,Prevymis" 0.48 "g" 0.48 "g"
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"J05AR10" 11979606 "Lopinavir and ritonavir" "Antivirals for treatment of HIV infections, combinations" "Aluvia,Kaletra" 0.8 "g"
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"J05AX02" 24839946 "Lysozyme" "Other antivirals" "Lysozyme chloride,Lysozyme Chloride,Lysozyme G"
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"J05AX09" 3002977 "Maraviroc" "Other antivirals" "Celsentri,Maraviroc,Selzentry" 0.6 "g"
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"J05AX10" 471161 "Maribavir" "Other antivirals" "Benzimidavir,Camvia,Maribavir"
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"J05AA01" 667492 "Metisazone" "Thiosemicarbazones" "Kemoviran,Marboran,Marborane,Methisazon,Methisazone,Methsazone,Metisazon,Metisazona,Metisazone,Metisazonum,Viruzona"
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"J05AX01" 71655 "Moroxydine" "Other antivirals" "Bimolin,Flumidine,Influmine,Moroxidina,Moroxydine,Moroxydinum,Vironil,Virugon,Virumin,Wirumin" 0.3 "g"
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"J05AE04" 64143 "Nelfinavir" "Protease inhibitors" "Nelfinavir,Viracept" 2.25 "g"
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"J05AG01" 4463 "Nevirapine" "Non-nucleoside reverse transcriptase inhibitors" "Nevirapine,Nevirapine anhydrous,Viramune,Viramune IR,Viramune XR" 0.4 "g"
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"J05AP53" "Ombitasvir, paritaprevir and ritonavir" "Antivirals for treatment of HCV infections" ""
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"J05AH02" 65028 "Oseltamivir" "Neuraminidase inhibitors" "Agucort,Oseltamivir,Tamiflu,Tamvir" 0.15 "g"
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"J05AB13" 135398748 "Penciclovir" "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "Adenovir,Denavir,Penciceovir,Penciclovir,Penciclovirum,Pencyclovir,Vectavir"
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"J05AX21" 9942657 "Pentanedioic acid imidazolyl ethanamide" "Other antivirals" "Ingamine" 90 "mg"
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"J05AH03" 154234 "Peramivir" "Neuraminidase inhibitors" "PeramiFlu,Peramivir,Rapiacta,RAPIVAB"
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"J05AX06" 1684 "Pleconaril" "Other antivirals" "Picovir,Pleconaril,Pleconarilis"
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"J05AX08" 54671008 "Raltegravir" "Other antivirals" "Isentress,Raltegravir" 0.8 "g"
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"J05AP01" 37542 "Ribavirin" "Antivirals for treatment of HCV infections" "Copegus,Cotronak,Drug: Ribavirin,Ravanex,Rebetol,Rebetron,Rebretron,Ribacine,Ribamide,Ribamidil,Ribamidyl,Ribasphere,Ribavirin,Ribavirin Capsules,Ribavirina,Ribavirine,Ribavirinum,Ribovirin,Tribavirin,Varazid,Vilona,Viramid,Viramide,Virazid,Virazide,Virazole" 1 "g"
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"J05AG05" 6451164 "Rilpivirine" "Non-nucleoside reverse transcriptase inhibitors" "Edurant,Rilpivirine" 25 "mg"
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"J05AC02" 5071 "Rimantadine" "Cyclic amines" "Remantadine,Riamantadine,Rimant,RIMANTADIN,Rimantadin A,Rimantadina,Rimantadine,Rimantadinum" 0.2 "g"
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"J05AE03" 392622 "Ritonavir" "Protease inhibitors" "Norvir,Norvir Sec,Norvir Softgel,Ritonavir,Ritonavire,Ritonavirum" 1.2 "g"
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"J05AE01" 441243 "Saquinavir" "Protease inhibitors" "Fortovase,Invirase,Saquinavir" 1.8 "g"
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"J05AP05" 24873435 "Simeprevir" "Antivirals for treatment of HCV infections" "Olysio,Simeprevir sodium" 0.15 "g"
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"J05AP08" 45375808 "Sofosbuvir" "Antivirals for treatment of HCV infections" "Hepcinat,Hepcvir,Sofosbuvir,Sovaldi,SOVALDI,SoviHep" 0.4 "g"
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"J05AP51" 72734365 "Sofosbuvir and ledipasvir" "Antivirals for treatment of HCV infections" ""
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"J05AP55" 91885554 "Sofosbuvir and velpatasvir" "Antivirals for treatment of HCV infections" "Epclusa Tablet"
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"J05AP56" "Sofosbuvir, velpatasvir and voxilaprevir" "Antivirals for treatment of HCV infections" ""
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"J05AF04" 18283 "Stavudine" "Nucleoside and nucleotide reverse transcriptase inhibitors" "Estavudina,Sanilvudine,Stavudin,Stavudine,Stavudinum,Zerit Xr,Zerut XR" 80 "mg"
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"J05AR07" 15979285 "Stavudine, lamivudine and nevirapine" "Antivirals for treatment of HIV infections, combinations" "STAVUDIINE"
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"J05AP02" 3010818 "Telaprevir" "Antivirals for treatment of HCV infections" "Incivek,Incivo,Telaprevir,Telavic" 2.25 "g"
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"J05AF11" 159269 "Telbivudine" "Nucleoside and nucleotide reverse transcriptase inhibitors" "Epavudine,Sebivo,Telbivudin,Telbivudine,Tyzeka" 0.6 "g"
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"J05AF13" 9574768 "Tenofovir alafenamide" "Nucleoside and nucleotide reverse transcriptase inhibitors" "Vemlidy" 25 "mg"
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"J05AF07" 5481350 "Tenofovir disoproxil" "Nucleoside and nucleotide reverse transcriptase inhibitors" "BisPMPA,PMPA prodrug,Tenofovir,Viread" 0.245 "g"
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"J05AR03" "Tenofovir disoproxil and emtricitabine" "Antivirals for treatment of HIV infections, combinations" ""
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"J05AX19" 5475 "Tilorone" "Other antivirals" "Amiksin,Amixin,Amixin IC,Amyxin,Tiloron,Tilorona,Tilorone,Tiloronum" 0.125 "g"
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"J05AE09" 54682461 "Tipranavir" "Protease inhibitors" "Aptivus,Tipranavir" 1 "g"
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"J05AC03" 64377 "Tromantadine" "Cyclic amines" "Tromantadina,Tromantadine,Tromantadinum,Viruserol"
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"J05AX13" 131411 "Umifenovir" "Other antivirals" "Arbidol,Arbidol base,Umifenovir" 0.8 "g"
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"J05AB11" 135398742 "Valaciclovir" "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "Talavir,Valaciclovir,Valaciclovirum,ValACV,Valcivir,Valcyclovir,Valtrex,Virval,Zelitrex" 3 "g"
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"J05AB14" 135413535 "Valganciclovir" "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "Cymeval,Valganciclovir" 0.9 "g"
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"J05AB03" 21704 "Vidarabine" "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "Adenine arabinoside,Araadenosine,Arabinoside adenine,Arabinosyl adenine,Arabinosyladenine,Spongoadenosine,Vidarabin,Vidarabina,Vidarabine,Vidarabine anhydrous,Vidarabinum,Vira A,Vira ATM"
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"J05AF03" 24066 "Zalcitabine" "Nucleoside and nucleotide reverse transcriptase inhibitors" "Dideoxycytidine,Interferon AD + ddC,Zalcitabine,Zalcitibine" 2.25 "mg"
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"J05AH01" 60855 "Zanamivir" "Neuraminidase inhibitors" "MODIFIED SIALIC ACID,Relenza,Zanamavir,Zanamir,Zanamivi,Zanamivir,Zanamivir hydrate"
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"J05AF01" 35370 "Zidovudine" "Nucleoside and nucleotide reverse transcriptase inhibitors" "Azidothymidine,AZT Antiviral,Beta interferon,Compound S,Propolis+AZT,Retrovir,Zidovudina,Zidovudine,ZIDOVUDINE,Zidovudine EP III,Zidovudinum" 0.6 "g" 0.6 "g"
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"J05AR01" "Zidovudine and lamivudine" "Antivirals for treatment of HIV infections, combinations" ""
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"J05AR04" "Zidovudine, lamivudine and abacavir" "Antivirals for treatment of HIV infections, combinations" ""
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"J05AR05" "Zidovudine, lamivudine and nevirapine" "Antivirals for treatment of HIV infections, combinations" ""
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"av" "name" "atc" "cid" "atc_group" "synonyms" "oral_ddd" "oral_units" "iv_ddd" "iv_units" "loinc"
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"ABA" "Abacavir" "J05AF06" 441300 "Nucleoside and nucleotide reverse transcriptase inhibitors" "abacavir sulfate,avacavir,ziagen" 0.6 "g" "29113-8,78772-1,78773-9,79134-3,80118-3"
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"ACI" "Aciclovir" "J05AB01" 135398513 "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "acicloftal,aciclovier,aciclovirum,activir,acyclofoam,acycloguanosine,acyclovir,acyclovir lauriad,avaclyr,cargosil,cyclovir,genvir,gerpevir,hascovir,maynar,novirus,poviral,sitavig,sitavir,vipral,viropump,virorax,zovirax,zyclir" 4 "g" 4 "g" ""
|
||||
"ADD" "Adefovir dipivoxil" "J05AF08" 60871 "Nucleoside and nucleotide reverse transcriptase inhibitors" "adefovir di,adefovir di ester,adefovir dipivoxyl,adefovir pivoxil,adefovirdipivoxl,bisadenine,bispmea,hepsera,preveon,youheding" 10 "mg" ""
|
||||
"AME" "Amenamevir" "J05AX26" 11397521 "Other antivirals" "amenalief" 0.4 "g" ""
|
||||
"AMP" "Amprenavir" "J05AE05" 65016 "Protease inhibitors" "agenerase,carbamate,prozei" 1.2 "g" "29114-6,31028-4,78791-1"
|
||||
"ASU" "Asunaprevir" "J05AP06" 16076883 "Antivirals for treatment of HCV infections" "sunvepra,sunvepratrade" 0.2 "g" ""
|
||||
"ATA" "Atazanavir" "J05AE08" 148192 "Protease inhibitors" "atazanavir base,latazanavir,reyataz,zrivada" 0.3 "g" "41470-6,78796-0,78797-8,80142-3,80143-1"
|
||||
"ATA+COBI" "Atazanavir/cobicistat" "J05AR15" 86583336 "Antivirals for treatment of HIV infections, combinations" "" ""
|
||||
"ATA+RIT" "Atazanavir/ritonavir" "J05AR23" 25134325 "Antivirals for treatment of HIV infections, combinations" "" 0.3 "g" ""
|
||||
"BAM" "Baloxavir marboxil" "J05AX25" 124081896 "Other antivirals" "xofluza" 40 "mg" ""
|
||||
"BOC" "Boceprevir" "J05AP03" 10324367 "Antivirals for treatment of HCV infections" "victrelis" 2.4 "g" ""
|
||||
"BRIN" "Brincidofovir" "J05AB17" 483477 "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "cidofovir prodrug,tembexa" ""
|
||||
"BRIV" "Brivudine" "J05AB15" 446727 "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "bridic,brivox,brivudin,brivudina,brivudinum,brvdurd,helpin,zerpex,zostex" 0.125 "g" ""
|
||||
"BUL" "Bulevirtide" "J05AX28" "Other antivirals" "" ""
|
||||
"CAB" "Cabotegravir" "J05AJ04" 54713659 "Integrase inhibitors" "cabenuva" 30 "mg" 10 "mg" ""
|
||||
"CID" "Cidofovir" "J05AB12" 60613 "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "cidofovir anhydrous,cidofovir gel,cidofovir hydrate,cidofovirum,forvade,hpmpc dihydrate,phosphonic acid,vistide" 25 "mg" ""
|
||||
"CLE" "Clevudine" "J05AF12" 73115 "Nucleoside and nucleotide reverse transcriptase inhibitors" "levovir,revovir" 30 "mg" ""
|
||||
"COBL" "Coblopasvir" "J05AP12" 58316387 "Antivirals for treatment of HCV infections" "" ""
|
||||
"DAC" "Daclatasvir" "J05AP07" 25154714 "Antivirals for treatment of HCV infections" "daklinza" 60 "mg" ""
|
||||
"DAC+ASU+BEC" "Daclatasvir/asunaprevir/beclabuvir" "J05AP58" "Antivirals for treatment of HCV infections" "" ""
|
||||
"DAR" "Darunavir" "J05AE10" 213039 "Protease inhibitors" "carbamate,darunavirum,derunavir,prezista,prezista naive" 1.2 "g" "57954-0"
|
||||
"DAR+COBI" "Darunavir/cobicistat" "J05AR14" 57327017 "Antivirals for treatment of HIV infections, combinations" "" ""
|
||||
"DAR+RIT" "Darunavir/ritonavir" "J05AR26" "Antivirals for treatment of HIV infections, combinations" "" ""
|
||||
"DAS" "Dasabuvir" "J05AP09" 56640146 "Antivirals for treatment of HCV infections" "" 0.5 "g" ""
|
||||
"DAS+OMB+PAR+RIT" "Dasabuvir/ombitasvir/paritaprevir/ritonavir" "J05AP52" "Antivirals for treatment of HCV infections" "" ""
|
||||
"DEL" "Delavirdine" "J05AG02" 5625 "Non-nucleoside reverse transcriptase inhibitors" "piperazine,rescriptor" 1.2 "g" "27082-7,29115-3"
|
||||
"DID" "Didanosine" "J05AF02" 135398739 "Nucleoside and nucleotide reverse transcriptase inhibitors" "didanosina,didanosinum,dideoxyinosine,hypoxanthine ddn,videx ec" 0.4 "g" "29116-1,48307-3"
|
||||
"DOL" "Dolutegravir" "J05AJ03" 54726191 "Integrase inhibitors" "dolutegravir dtg,soltegravir,tivicay" 50 "mg" ""
|
||||
"DOL+RIL" "Dolutegravir/rilpivirine" "J05AR21" 131801472 "Antivirals for treatment of HIV infections, combinations" "" ""
|
||||
"DOR" "Doravirine" "J05AG06" 58460047 "Non-nucleoside reverse transcriptase inhibitors" "pifeltro" 0.1 "g" ""
|
||||
"EFA" "Efavirenz" "J05AG03" 64139 "Non-nucleoside reverse transcriptase inhibitors" "efavirenz teva,efavirenzum,eravirenz,stocrin,strocin,sustiva,viraday" 0.6 "g" "29117-9,33928-3,51907-4,51908-2"
|
||||
"ELB" "Elbasvir" "J05AP10" 71661251 "Antivirals for treatment of HCV infections" "methyl carbamate" 50 "mg" ""
|
||||
"ELB+GRA" "Elbasvir/grazoprevir" "J05AP54" 91669168 "Antivirals for treatment of HCV infections" "zepatier" ""
|
||||
"ELV" "Elvitegravir" "J05AJ02" 5277135 "Integrase inhibitors" "vitekta" "88986-5"
|
||||
"EMT" "Emtricitabine" "J05AF09" 60877 "Nucleoside and nucleotide reverse transcriptase inhibitors" "coviracil,emtricitabinum,emtritabine,emtriva,racivir" 0.2 "g" ""
|
||||
"EMT+TEA" "Emtricitabine/tenofovir alafenamide" "J05AR17" 90469070 "Antivirals for treatment of HIV infections, combinations" "descovy" ""
|
||||
"EMT+TEA+BIC" "Emtricitabine/tenofovir alafenamide/bictegravir" "J05AR20" "Antivirals for treatment of HIV infections, combinations" "" ""
|
||||
"EMT+TEA+RIL" "Emtricitabine/tenofovir alafenamide/rilpivirine" "J05AR19" "Antivirals for treatment of HIV infections, combinations" "" ""
|
||||
"EMT+TEA+DAR+COBI" "Emtricitabine/tenofovir alafenamide/darunavir/cobicistat" "J05AR22" "Antivirals for treatment of HIV infections, combinations" "" ""
|
||||
"EMT+TEA+ELV+COBI" "Emtricitabine/tenofovir alafenamide/elvitegravir/cobicistat" "J05AR18" "Antivirals for treatment of HIV infections, combinations" "" ""
|
||||
"EMT+TED+EFA" "Emtricitabine/tenofovir disoproxil/efavirenz" "J05AR06" "Antivirals for treatment of HIV infections, combinations" "" ""
|
||||
"EMT+TED+RIL" "Emtricitabine/tenofovir disoproxil/rilpivirine" "J05AR08" "Antivirals for treatment of HIV infections, combinations" "" ""
|
||||
"EMT+TED+ELV+COBI" "Emtricitabine/tenofovir disoproxil/elvitegravir/cobicistat" "J05AR09" "Antivirals for treatment of HIV infections, combinations" "" ""
|
||||
"ENF" "Enfuvirtide" "J05AX07" 16130199 "Other antivirals" "enfurvitide,fuzeon,pentafuside" 0.18 "g" ""
|
||||
"ENI" "Enisamium iodide" "J05AX17" 10089466 "Other antivirals" "amizon" 1.5 "g" ""
|
||||
"ENT" "Entecavir" "J05AF10" 135398508 "Nucleoside and nucleotide reverse transcriptase inhibitors" "baraclude,entecavir anhydrous" 0.5 "mg" ""
|
||||
"ETR" "Etravirine" "J05AG04" 193962 "Non-nucleoside reverse transcriptase inhibitors" "dapy deriv,etravine,intelence" 0.4 "g" "57961-5"
|
||||
"FAL" "Faldaprevir" "J05AP04" 42601552 "Antivirals for treatment of HCV infections" "" ""
|
||||
"FAM" "Famciclovir" "J05AB09" 3324 "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "famciclovirum,famvir,oravir" 0.75 "g" ""
|
||||
"FAV" "Favipiravir" "J05AX27" 492405 "Other antivirals" "avigan,fapilavir,favilavir" 1.6 "g" ""
|
||||
"FOSA" "Fosamprenavir" "J05AE07" 131536 "Protease inhibitors" "amprenavir phosphate,carbamate,lexiva,telzir" 1.4 "g" ""
|
||||
"FOSC" "Foscarnet" "J05AD01" 3415 "Phosphonic acid derivatives" "forscarnet,foscarmet,foscavir,phosphonoformate,phosphonoformic acid" 6.5 "g" ""
|
||||
"FOSF" "Fosfonet" "J05AD02" 546 "Phosphonic acid derivatives" "fosfonet sodium,fosfonoacetate,fosfonoacetic acid,phosphonacetate,phosphonacetic acid,phosphonoaceticacid" ""
|
||||
"FOST" "Fostemsavir" "J05AX29" 11319217 "Other antivirals" "rukobia" 1.2 "g" ""
|
||||
"GAN" "Ganciclovir" "J05AB06" 135398740 "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "citovirax,cymevan,cymeven,cymevene,cytovene,ganciclovirum,gancyclovir,hydroxyacyclovir,virgan,vitrasert,zirgan" 3 "g" 0.5 "g" "15367-6,25256-9,59798-9,59799-7,60077-5,60078-3"
|
||||
"GLE+PIB" "Glecaprevir/pibrentasvir" "J05AP57" 85471918 "Antivirals for treatment of HCV infections" "" ""
|
||||
"GRA" "Grazoprevir" "J05AP11" 44603531 "Antivirals for treatment of HCV infections" "" 0.1 "g" ""
|
||||
"IBA" "Ibalizumab" "J05AX23" "Other antivirals" "" ""
|
||||
"IDO" "Idoxuridine" "J05AB02" 5905 "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "antizona,dendrid,heratil,herplex,idossuridina,idoxene,idoxuridin,idoxuridina,idoxuridinum,iduoculos,iduridin,iododeoxyridine,iododeoxyuridine,iodoxuridine,joddeoxiuridin,kerecid,stoxil,virudox" ""
|
||||
"IND" "Indinavir" "J05AE02" 5362440 "Protease inhibitors" "compound j,crixivan,indinavir anhydrous,propolis+indinavir" 2.4 "g" "29118-7,31033-4,51918-1"
|
||||
"INP" "Inosine pranobex" "J05AX05" 135449284 "Other antivirals" "aviral,delimmun,groprinosin,immunovir,imunovir,imunoviral,inosiplex,isoprinosin,isoprinosina,isoprinosine,isoviral,methisoprinol,modimmunal,pranosina,pranosine,viruxan" 3 "g" ""
|
||||
"LAM" "Lamivudine" "J05AF05" 60825 "Nucleoside and nucleotide reverse transcriptase inhibitors" "epivir,hepitec,heptivir,heptodin,heptovir,lamivir,lamivudeine,lamivudine teva,lamivudinum,virolam,zeffix" 0.3 "g" "29119-5,49226-4"
|
||||
"LAM+ABA" "Lamivudine/abacavir" "J05AR02" "Antivirals for treatment of HIV infections, combinations" "" ""
|
||||
"LAM+DOL" "Lamivudine/dolutegravir" "J05AR25" "Antivirals for treatment of HIV infections, combinations" "" ""
|
||||
"LAM+RAL" "Lamivudine/raltegravir" "J05AR16" 73386700 "Antivirals for treatment of HIV infections, combinations" "" ""
|
||||
"LAM+TED" "Lamivudine/tenofovir disoproxil" "J05AR12" "Antivirals for treatment of HIV infections, combinations" "" ""
|
||||
"LAM+ABA+DOL" "Lamivudine/abacavir/dolutegravir" "J05AR13" "Antivirals for treatment of HIV infections, combinations" "" ""
|
||||
"LAM+TED+DOL" "Lamivudine/tenofovir disoproxil/dolutegravir" "J05AR27" "Antivirals for treatment of HIV infections, combinations" "" ""
|
||||
"LAM+TED+DOR" "Lamivudine/tenofovir disoproxil/doravirine" "J05AR24" "Antivirals for treatment of HIV infections, combinations" "" ""
|
||||
"LAM+TED+EFA" "Lamivudine/tenofovir disoproxil/efavirenz" "J05AR11" "Antivirals for treatment of HIV infections, combinations" "" ""
|
||||
"LAN" "Laninamivir" "J05AH04" 502272 "Neuraminidase inhibitors" "" ""
|
||||
"LEN" "Lenacapavir" "J05AX31" 133082658 "Other antivirals" "" ""
|
||||
"LET" "Letermovir" "J05AX18" 45138674 "Other antivirals" "acetic acid,prevymis" 0.48 "g" 0.48 "g" ""
|
||||
"LOP+RIT" "Lopinavir/ritonavir" "J05AR10" 11979606 "Antivirals for treatment of HIV infections, combinations" "aluvia,kaletra,lopimune" 0.8 "g" ""
|
||||
"LYS" "Lysozyme" "J05AX02" 16130991 "Other antivirals" "" ""
|
||||
"MARA" "Maraviroc" "J05AX09" 3002977 "Other antivirals" "celsentri,selzentry" 0.6 "g" "88987-3"
|
||||
"MARI" "Maribavir" "J05AX10" 471161 "Other antivirals" "benzimidavir,camvia" ""
|
||||
"MET" "Metisazone" "J05AA01" 667492 "Thiosemicarbazones" "kemoviran,marboran,marborane,methisazon,methisazone,methsazone,metisazon,metisazona,metisazonum,viruzona" ""
|
||||
"MOR" "Moroxydine" "J05AX01" 71655 "Other antivirals" "bimolin,moroxidina,moroxydinum,virugon,virumin,wirumin" 0.3 "g" ""
|
||||
"NEL" "Nelfinavir" "J05AE04" 64143 "Protease inhibitors" "viracept" 2.25 "g" "29120-3,32647-0,35113-0,51923-1"
|
||||
"NEV" "Nevirapine" "J05AG01" 4463 "Non-nucleoside reverse transcriptase inhibitors" "nevirapine anhydrous,nevirapine teva,nevirapine),viramune,viramune ir,viramune xr" 0.4 "g" "29121-1,32646-2,51925-6"
|
||||
"OMB+PAR+RIT" "Ombitasvir/paritaprevir/ritonavir" "J05AP53" "Antivirals for treatment of HCV infections" "" ""
|
||||
"OSE" "Oseltamivir" "J05AH02" 65028 "Neuraminidase inhibitors" "agucort,tamiflu,tamvir" 0.15 "g" ""
|
||||
"PEN" "Penciclovir" "J05AB13" 135398748 "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "adenovir,denavir,penciceovir,penciclovirum,pencyclovir,vectavir" "60140-1,60141-9"
|
||||
"PAIE" "Pentanedioic acid imidazolyl ethanamide" "J05AX21" 9942657 "Other antivirals" "ingamine" 90 "mg" ""
|
||||
"PER" "Peramivir" "J05AH03" 154234 "Neuraminidase inhibitors" "peramiflu,peramivir anhydrous,rapiacta,rapivab" 0.6 "g" ""
|
||||
"PLE" "Pleconaril" "J05AX06" 1684 "Other antivirals" "picovir,pleconarilis" ""
|
||||
"RAL" "Raltegravir" "J05AJ01" 54671008 "Integrase inhibitors" "isentress" 0.8 "g" "72835-2"
|
||||
"REM" "Remdesivir" "J05AB16" 121304016 "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "veklury" 0.1 "g" ""
|
||||
"RIB" "Ribavirin" "J05AP01" 37542 "Antivirals for treatment of HCV infections" "copegus,cotronak,ravanex,rebetol,rebetron,rebretron,ribacine,ribamide,ribamidil,ribamidyl,ribasphere,ribavirin capsules,ribavirin mylan,ribavirin teva,ribavirina,ribavirine,ribavirinum,tribavirin,varazid,vilona,viramid,virazid,virazide,virazole" 1 "g" "41469-8"
|
||||
"RIL" "Rilpivirine" "J05AG05" 6451164 "Non-nucleoside reverse transcriptase inhibitors" "edurant,rilpivirina" 25 "mg" 15 "mg" "80547-3"
|
||||
"RIM" "Rimantadine" "J05AC02" 5071 "Cyclic amines" "ethanamine,rimant,rimantadin,rimantadin a,rimantadina,rimantadinum" 0.2 "g" ""
|
||||
"RIT" "Ritonavir" "J05AE03" 392622 "Protease inhibitors" "empetus,norvir,norvir softgel,ritomune,ritonavirum,ritovir,viekirax,viriton" 1.2 "g" "29122-9,31027-6,51929-8,51930-6"
|
||||
"SAQ" "Saquinavir" "J05AE01" 441243 "Protease inhibitors" "fortovase,invirase,saquinavirum" 1.8 "g" "19051-2,29123-7,51932-2"
|
||||
"SIM" "Simeprevir" "J05AP05" 24873435 "Antivirals for treatment of HCV infections" "olysio,simeprevir sodium" 0.15 "g" ""
|
||||
"SOF" "Sofosbuvir" "J05AP08" 45375808 "Antivirals for treatment of HCV infections" "hepcinat,hepcvir,sovaldi,sovihep" 0.4 "g" ""
|
||||
"SOF+LED" "Sofosbuvir/ledipasvir" "J05AP51" 72734365 "Antivirals for treatment of HCV infections" "harvoni" ""
|
||||
"SOF+VEL" "Sofosbuvir/velpatasvir" "J05AP55" 91885554 "Antivirals for treatment of HCV infections" "epclusa,epclusa tablet" ""
|
||||
"SOF+VEL+VOX" "Sofosbuvir/velpatasvir/voxilaprevir" "J05AP56" "Antivirals for treatment of HCV infections" "" ""
|
||||
"STA" "Stavudine" "J05AF04" 18283 "Nucleoside and nucleotide reverse transcriptase inhibitors" "estavudina,sanilvudine,stavudinum,zerit xr,zerut xr" 80 "mg" "29124-5,49227-2"
|
||||
"STA+LAM+NEV" "Stavudine/lamivudine/nevirapine" "J05AR07" 15979285 "Antivirals for treatment of HIV infections, combinations" "" ""
|
||||
"TEC" "Tecovirimat" "J05AX24" 16124688 "Other antivirals" "" ""
|
||||
"TELA" "Telaprevir" "J05AP02" 3010818 "Antivirals for treatment of HCV infections" "incivek,incivo,telavic" 2.25 "g" ""
|
||||
"TELB" "Telbivudine" "J05AF11" 159269 "Nucleoside and nucleotide reverse transcriptase inhibitors" "epavudine,sebivo,telbivudin,tyzeka" 0.6 "g" ""
|
||||
"TEA" "Tenofovir alafenamide" "J05AF13" 9574768 "Nucleoside and nucleotide reverse transcriptase inhibitors" "vemlidy" 25 "mg" ""
|
||||
"TED" "Tenofovir disoproxil" "J05AF07" 5481350 "Nucleoside and nucleotide reverse transcriptase inhibitors" "bispmpa,pmpa prodrug,tenofovir,tenofovir bis,tenofovirdisoproxil,viread" 0.245 "g" ""
|
||||
"TED+EMT" "Tenofovir disoproxil/emtricitabine" "J05AR03" "Antivirals for treatment of HIV infections, combinations" "" ""
|
||||
"TIL" "Tilorone" "J05AX19" 5475 "Other antivirals" "amixin ic,tiloron,tilorona,tiloronum" 0.125 "g" ""
|
||||
"TIP" "Tipranavir" "J05AE09" 54682461 "Protease inhibitors" "aptivus" 1 "g" "57383-2"
|
||||
"TRO" "Tromantadine" "J05AC03" 64377 "Cyclic amines" "tromantadina,tromantadinum" ""
|
||||
"UMI" "Umifenovir" "J05AX13" 131411 "Other antivirals" "arbidol,arbidol base" 0.8 "g" ""
|
||||
"VALA" "Valaciclovir" "J05AB11" 135398742 "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "talavir,valacv,valacyclovir,valcivir,valcyclovir,valtrex,virval,zelitrex" 3 "g" ""
|
||||
"VALG" "Valganciclovir" "J05AB14" 135413535 "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "cymeval" 0.9 "g" "74960-6"
|
||||
"VID" "Vidarabine" "J05AB03" 21704 "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "adenine arabinoside,araadenosine,arabinoside adenine,arabinosyl adenine,arabinosyladenine,spongoadenosine,vidarabin,vidarabina,vidarabine anhydrous,vidarabinum,vira a,vira atm" 0.7 "g" ""
|
||||
"ZAL" "Zalcitabine" "J05AF03" 24066 "Nucleoside and nucleotide reverse transcriptase inhibitors" "dideoxycytidine,interferon ad + ddc,zalcitibine" 2.25 "mg" "29125-2"
|
||||
"ZAN" "Zanamivir" "J05AH01" 60855 "Neuraminidase inhibitors" "modified sialic acid,relenza,zanamavir,zanamivi,zanamivirhydrate" 1.2 "g" ""
|
||||
"ZID" "Zidovudine" "J05AF01" 35370 "Nucleoside and nucleotide reverse transcriptase inhibitors" "azidothymidine,beta interferon,compound s,propolis+azt,retrovir,trizivir,zidovudina,zidovudinum" 0.6 "g" 0.6 "g" "29126-0,6894-0"
|
||||
"ZID+LAM" "Zidovudine/lamivudine" "J05AR01" "Antivirals for treatment of HIV infections, combinations" "" ""
|
||||
"ZID+LAM+ABA" "Zidovudine/lamivudine/abacavir" "J05AR04" "Antivirals for treatment of HIV infections, combinations" "" ""
|
||||
"ZID+LAM+NEV" "Zidovudine/lamivudine/nevirapine" "J05AR05" "Antivirals for treatment of HIV infections, combinations" "" ""
|
||||
|
||||
Binary file not shown.
@ -1 +1 @@
|
||||
246da79545e045edac7c3ec445b3a04e
|
||||
009fea3738cdb6390dccd470cb27f015
|
||||
|
||||
@ -62,7 +62,7 @@ for (i in seq_len(nrow(antibiotics))) {
|
||||
# sort and fix for empty values
|
||||
for (i in 1:nrow(antibiotics)) {
|
||||
loinc <- as.character(sort(unique(tolower(antibiotics[i, "loinc"][[1]]))))
|
||||
antibiotics[i, "loinc"][[1]] <- ifelse(length(syn[!syn == ""]) == 0, list(""), list(loinc))
|
||||
antibiotics[i, "loinc"][[1]] <- ifelse(length(loinc[!loinc == ""]) == 0, list(""), list(loinc))
|
||||
}
|
||||
|
||||
# remember to update R/aa_globals.R for the documentation
|
||||
|
||||
@ -192,7 +192,7 @@ abx2$abbr <- lapply(as.list(abx2$abbr), function(x) unlist(strsplit(x, "|", fixe
|
||||
# vector with official names, returns vector with CIDs
|
||||
get_CID <- function(ab) {
|
||||
CID <- rep(NA_integer_, length(ab))
|
||||
p <- progress_ticker(n = length(ab), min_time = 0)
|
||||
p <- AMR:::progress_ticker(n = length(ab), min_time = 0)
|
||||
for (i in 1:length(ab)) {
|
||||
p$tick()
|
||||
|
||||
@ -248,7 +248,7 @@ antibiotics[is.na(CIDs), ] %>% View()
|
||||
# returns list with synonyms (brand names), with CIDs as names
|
||||
get_synonyms <- function(CID, clean = TRUE) {
|
||||
synonyms <- rep(NA_character_, length(CID))
|
||||
p <- progress_ticker(n = length(CID), min_time = 0)
|
||||
p <- AMR:::progress_ticker(n = length(CID), min_time = 0)
|
||||
|
||||
for (i in 1:length(CID)) {
|
||||
p$tick()
|
||||
|
||||
@ -27,14 +27,18 @@
|
||||
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
|
||||
# ==================================================================== #
|
||||
|
||||
# get all data from the WHOCC website
|
||||
library(dplyr)
|
||||
library(tidyr)
|
||||
library(rvest)
|
||||
|
||||
# get all data from the WHOCC website
|
||||
get_atc_table <- function(atc_group) {
|
||||
# give as input J0XXX, like atc_group = "J05AB"
|
||||
downloaded <- read_html(paste0("https://www.whocc.no/atc_ddd_index/?code=", atc_group, "&showdescription=no"))
|
||||
table_title <- downloaded %>%
|
||||
html_nodes(paste0('a[href="./?code=', atc_group, '"]')) %>%
|
||||
html_nodes(paste0('a[href^="./?code=', atc_group, '&"]')) %>%
|
||||
html_text()
|
||||
table_title <- table_title[tolower(table_title) != "show text from guidelines"][1]
|
||||
table_content <- downloaded %>%
|
||||
html_nodes("table") %>%
|
||||
html_table(header = TRUE) %>%
|
||||
@ -59,12 +63,13 @@ get_atc_table <- function(atc_group) {
|
||||
}
|
||||
|
||||
# these are the relevant groups for input: https://www.whocc.no/atc_ddd_index/?code=J05A (J05 only contains J05A)
|
||||
atc_groups <- c("J05AA", "J05AB", "J05AC", "J05AD", "J05AE", "J05AF", "J05AG", "J05AH", "J05AP", "J05AR", "J05AX")
|
||||
atc_groups <- c("J05AA", "J05AB", "J05AC", "J05AD", "J05AE", "J05AF", "J05AG", "J05AH", "J05AJ", "J05AP", "J05AR", "J05AX")
|
||||
|
||||
# get the first
|
||||
antivirals <- get_atc_table(atc_groups[1])
|
||||
# bind all others to it
|
||||
for (i in 2:length(atc_groups)) {
|
||||
message(atc_groups[i], "...")
|
||||
antivirals <- rbind(antivirals, get_atc_table(atc_groups[i]))
|
||||
}
|
||||
|
||||
@ -73,7 +78,8 @@ antivirals <- antivirals %>%
|
||||
arrange(name) %>%
|
||||
as.data.frame(stringsAsFactors = FALSE)
|
||||
|
||||
# add PubChem Compound ID (cid) and their trade names - functions are in file to create `antibiotics` data set
|
||||
# add PubChem Compound ID (cid) and their trade names
|
||||
# see `data-raw/reproduction_of_antibiotics` for get_CID() and get_synonyms()
|
||||
CIDs <- get_CID(antivirals$name)
|
||||
# these could not be found:
|
||||
antivirals[is.na(CIDs), ] %>% View()
|
||||
@ -92,7 +98,7 @@ synonyms <- lapply(
|
||||
|
||||
antivirals <- antivirals %>%
|
||||
transmute(atc,
|
||||
cid = CIDs,
|
||||
cid = as.double(CIDs),
|
||||
name,
|
||||
atc_group,
|
||||
synonyms = unname(synonyms),
|
||||
@ -100,7 +106,79 @@ antivirals <- antivirals %>%
|
||||
oral_units,
|
||||
iv_ddd,
|
||||
iv_units
|
||||
)
|
||||
) %>%
|
||||
AMR:::dataset_UTF8_to_ASCII()
|
||||
|
||||
av_codes <- tibble(name = antivirals$name %>%
|
||||
strsplit("(, | and )") %>%
|
||||
unlist() %>%
|
||||
unique() %>%
|
||||
sort()) %>%
|
||||
mutate(av_1st = toupper(abbreviate(name, minlength = 3, use.classes = FALSE))) %>%
|
||||
filter(!name %in% c("acid", "dipivoxil", "disoproxil", "marboxil", "alafenamide"))
|
||||
|
||||
replace_with_av_code <- function(name) {
|
||||
unname(av_codes$av_1st[match(name, av_codes$name)])
|
||||
}
|
||||
|
||||
names_codes <- antivirals %>%
|
||||
separate(name,
|
||||
into = paste0("name", c(1:7)),
|
||||
sep = "(, | and )",
|
||||
remove = FALSE,
|
||||
fill = "right") %>%
|
||||
# remove empty columns
|
||||
select(!where(function(x) all(is.na(x)))) %>%
|
||||
mutate_at(vars(matches("name[1-9]")), replace_with_av_code) %>%
|
||||
unite(av, matches("name[1-9]"), sep = "+", na.rm = TRUE) %>%
|
||||
mutate(name = gsub("(, | and )", "/", name))
|
||||
substr(names_codes$name, 1, 1) <- toupper(substr(names_codes$name, 1, 1))
|
||||
|
||||
antivirals <- bind_cols(
|
||||
names_codes %>% select(av, name),
|
||||
antivirals %>% select(-name)
|
||||
)
|
||||
class(antivirals$av) <- c("av", "character")
|
||||
antivirals <- antivirals %>% AMR:::dataset_UTF8_to_ASCII()
|
||||
|
||||
# add loinc, see 'data-raw/loinc.R'
|
||||
loinc_df <- read.csv("data-raw/Loinc.csv",
|
||||
row.names = NULL,
|
||||
stringsAsFactors = FALSE)
|
||||
|
||||
loinc_df <- loinc_df %>% filter(CLASS == "DRUG/TOX")
|
||||
av_names <- antivirals %>%
|
||||
pull(name) %>%
|
||||
paste0(collapse = "|") %>%
|
||||
paste0("(", ., ")")
|
||||
|
||||
antivirals$loinc <- as.list(rep(NA_character_, nrow(antivirals)))
|
||||
for (i in seq_len(nrow(antivirals))) {
|
||||
message(i)
|
||||
loinc_ab <- loinc_df %>%
|
||||
filter(COMPONENT %like% paste0("^", antivirals$name[i])) %>%
|
||||
pull(LOINC_NUM)
|
||||
if (length(loinc_ab) > 0) {
|
||||
antivirals$loinc[i] <- list(loinc_ab)
|
||||
}
|
||||
}
|
||||
# sort and fix for empty values
|
||||
for (i in 1:nrow(antivirals)) {
|
||||
loinc <- as.character(sort(unique(tolower(antivirals[i, "loinc", drop = TRUE][[1]]))))
|
||||
antivirals[i, "loinc"][[1]] <- ifelse(length(loinc[!loinc == ""]) == 0, list(""), list(loinc))
|
||||
}
|
||||
|
||||
# de-duplicate synonyms
|
||||
for (i in 1:nrow(antivirals)) {
|
||||
syn <- as.character(sort(unique(tolower(antivirals[i, "synonyms", drop = TRUE][[1]]))))
|
||||
syn <- syn[!syn %in% tolower(antivirals[i, "name", drop = TRUE])]
|
||||
antivirals[i, "synonyms"][[1]] <- ifelse(length(syn[!syn == ""]) == 0, list(""), list(syn))
|
||||
}
|
||||
|
||||
antivirals <- antivirals %>% AMR:::dataset_UTF8_to_ASCII()
|
||||
|
||||
# check it
|
||||
antivirals
|
||||
|
||||
# save it
|
||||
usethis::use_data(antivirals, overwrite = TRUE)
|
||||
usethis::use_data(antivirals, overwrite = TRUE, internal = FALSE, compress = "xz", version = 2)
|
||||
|
||||
Reference in New Issue
Block a user