diff --git a/DESCRIPTION b/DESCRIPTION index 881700da..bf08955d 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: AMR -Version: 2.0.0.9019 -Date: 2023-05-24 +Version: 2.0.0.9020 +Date: 2023-05-26 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 f7b2bf3f..cb2d27c0 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,9 +1,9 @@ -# AMR 2.0.0.9019 +# AMR 2.0.0.9020 ## Changed -* Added oxygen tolerance to over 25,000 bacteria in the `microorganisms` data set +* Added oxygen tolerance from BacDive to over 25,000 bacteria in the `microorganisms` data set * Added `mo_oxygen_tolerance()` to retrieve the values - * Added `mo_is_anaerobic()` to determine which species are obligate anaerobic bacteria + * Added `mo_is_anaerobic()` to determine which genera/species are obligate anaerobic bacteria * Added LPSN and GBIF identifiers, and oxygen tolerance to `mo_info()` * Added SAS Transport files (file extension `.xpt`) to [our download page](https://msberends.github.io/AMR/articles/datasets.html) to use in SAS software * Added microbial codes for Gram-negative/positive anaerobic bacteria @@ -13,6 +13,7 @@ * Fixed a bug for `as.mo()` that led to coercion of `NA` values when using custom microorganism codes * Fixed usage of `icu_exclude` in `first_isolates()` * Improved `as.mo()` algorithm for searching on only species names +* Updated the code table in `microorganisms.codes` # AMR 2.0.0 diff --git a/R/aa_globals.R b/R/aa_globals.R index 0ec7c8ae..32eed3f0 100755 --- a/R/aa_globals.R +++ b/R/aa_globals.R @@ -81,6 +81,11 @@ TAXONOMY_VERSION <- list( citation = "Parte, AC *et al.* (2020). **List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ.** International Journal of Systematic and Evolutionary Microbiology, 70, 5607-5612; \\doi{10.1099/ijsem.0.004332}.", url = "https://lpsn.dsmz.de" ), + BacDive = list( + accessed_date = as.Date("2023-05-12"), + citation = "Reimer, LC *et al.* (2022). ***BacDive* in 2022: the knowledge base for standardized bacterial and archaeal data.** Nucleic Acids Res., 50(D1):D741-D74; \\doi{10.1093/nar/gkab961}.", + url = "https://bacdive.dsmz.de" + ), SNOMED = list( accessed_date = as.Date("2021-07-01"), citation = "Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS). US Edition of SNOMED CT from 1 September 2020. Value Set Name 'Microoganism', OID 2.16.840.1.114222.4.11.1009 (v12).", diff --git a/R/aa_helper_functions.R b/R/aa_helper_functions.R index 4a530ec6..a4f58c3f 100755 --- a/R/aa_helper_functions.R +++ b/R/aa_helper_functions.R @@ -629,7 +629,12 @@ dataset_UTF8_to_ASCII <- function(df) { } documentation_date <- function(d) { - paste0(trimws(format(d, "%e")), " ", month.name[as.integer(format(d, "%m"))], ", ", format(d, "%Y")) + day <- as.integer(format(d, "%e")) + suffix <- rep("th", length(day)) + suffix[day %in% c(1, 21, 31)] <- "st" + suffix[day %in% c(2, 22)] <- "nd" + suffix[day %in% c(3, 23)] <- "rd" + paste0(month.name[as.integer(format(d, "%m"))], " ", day, suffix, ", ", format(d, "%Y")) } format_included_data_number <- function(data) { diff --git a/R/data.R b/R/data.R index 88649552..2743d765 100755 --- a/R/data.R +++ b/R/data.R @@ -141,13 +141,13 @@ #' #' * `r TAXONOMY_VERSION$GBIF$citation` Accessed from <`r TAXONOMY_VERSION$GBIF$url`> on `r documentation_date(TAXONOMY_VERSION$GBIF$accessed_date)`. #' +#' * `r TAXONOMY_VERSION$BacDive$citation` Accessed from <`r TAXONOMY_VERSION$BacDive$url`> on `r documentation_date(TAXONOMY_VERSION$BacDive$accessed_date)`. +#' #' * `r TAXONOMY_VERSION$SNOMED$citation` URL: <`r TAXONOMY_VERSION$SNOMED$url`> #' #' * Grimont *et al.* (2007). Antigenic Formulae of the Salmonella Serovars, 9th Edition. WHO Collaborating Centre for Reference and Research on *Salmonella* (WHOCC-SALM). #' #' * Bartlett *et al.* (2022). **A comprehensive list of bacterial pathogens infecting humans** *Microbiology* 168:001269; \doi{10.1099/mic.0.001269} -#' -#' * Reimer *et al.* (2022). ***BacDive* in 2022: the knowledge base for standardized bacterial and archaeal data.** *Nucleic Acids Res.* 2022 Jan 7;50(D1):D741-D746; \doi{10.1093/nar/gkab961} #' @seealso [as.mo()], [mo_property()], [microorganisms.codes], [intrinsic_resistant] #' @examples #' microorganisms diff --git a/R/mo.R b/R/mo.R index bae76f10..696d7bcc 100755 --- a/R/mo.R +++ b/R/mo.R @@ -100,9 +100,9 @@ #' 6. Berends MS *et al.* (2022). **Trends in Occurrence and Phenotypic Resistance of Coagulase-Negative Staphylococci (CoNS) Found in Human Blood in the Northern Netherlands between 2013 and 2019/** *Micro.rganisms* 10(9), 1801; \doi{10.3390/microorganisms10091801} #' 7. `r TAXONOMY_VERSION$LPSN$citation` Accessed from <`r TAXONOMY_VERSION$LPSN$url`> on `r documentation_date(TAXONOMY_VERSION$LPSN$accessed_date)`. #' 8. `r TAXONOMY_VERSION$GBIF$citation` Accessed from <`r TAXONOMY_VERSION$GBIF$url`> on `r documentation_date(TAXONOMY_VERSION$GBIF$accessed_date)`. -#' 9. `r TAXONOMY_VERSION$SNOMED$citation` URL: <`r TAXONOMY_VERSION$SNOMED$url`> -#' 10. Bartlett A *et al.* (2022). **A comprehensive list of bacterial pathogens infecting humans** *Microbiology* 168:001269; \doi{10.1099/mic.0.001269} -#' 11. Reimer *et al.* (2022). ***BacDive* in 2022: the knowledge base for standardized bacterial and archaeal data.** *Nucleic Acids Res.* 2022 Jan 7;50(D1):D741-D746; \doi{10.1093/nar/gkab961} +#' 9. `r TAXONOMY_VERSION$BacDive$citation` Accessed from <`r TAXONOMY_VERSION$BacDive$url`> on `r documentation_date(TAXONOMY_VERSION$BacDive$accessed_date)`. +#' 10. `r TAXONOMY_VERSION$SNOMED$citation` URL: <`r TAXONOMY_VERSION$SNOMED$url`> +#' 11. Bartlett A *et al.* (2022). **A comprehensive list of bacterial pathogens infecting humans** *Microbiology* 168:001269; \doi{10.1099/mic.0.001269} #' @export #' @return A [character] [vector] with additional class [`mo`] #' @seealso [microorganisms] for the [data.frame] that is being used to determine ID's. @@ -281,16 +281,12 @@ as.mo <- function(x, x_parts <- strsplit(gsub("-", " ", x_out, fixed = TRUE), " ", fixed = TRUE)[[1]] # do a pre-match on first character (and if it contains a space, first chars of first two terms) - if (length(x_parts) == 1) { - # for genus or species or subspecies - filtr <- which(AMR_env$MO_lookup$full_first == substr(x_parts, 1, 1) | - AMR_env$MO_lookup$species_first == substr(x_parts, 1, 1) | - AMR_env$MO_lookup$subspecies_first == substr(x_parts, 1, 1)) - } else if (length(x_parts) %in% c(2, 3)) { + if (length(x_parts) %in% c(2, 3)) { # for genus + species + subspecies - filtr <- which(AMR_env$MO_lookup$full_first == substr(x_parts[1], 1, 1) & - (AMR_env$MO_lookup$species_first == substr(x_parts[2], 1, 1) | - AMR_env$MO_lookup$subspecies_first == substr(x_parts[2], 1, 1))) + filtr <- which(AMR_env$MO_lookup$full_first == substr(x_parts[1], 1, 1) | + AMR_env$MO_lookup$species_first == substr(x_parts[2], 1, 1) | + AMR_env$MO_lookup$subspecies_first == substr(x_parts[2], 1, 1) | + AMR_env$MO_lookup$subspecies_first == substr(x_parts[3], 1, 1)) } else if (length(x_parts) > 3) { first_chars <- paste0("(^| )", "[", paste(substr(x_parts, 1, 1), collapse = ""), "]") filtr <- which(AMR_env$MO_lookup$full_first %like_case% first_chars) @@ -305,7 +301,10 @@ as.mo <- function(x, msg <- c(msg, paste0("Input \"", x_search, "\" was assumed to be a microorganism code - tried to match on ", vector_and(c(gsub("[a-z]*", "(...)", first_part, fixed = TRUE), second_part), sort = FALSE))) filtr <- which(AMR_env$MO_lookup$fullname_lower %like_case% paste0("(^| )", first_part, ".* ", second_part)) } else { - filtr <- which(AMR_env$MO_lookup$full_first == substr(x_out, 1, 1)) + # for genus or species or subspecies + filtr <- which(AMR_env$MO_lookup$full_first == substr(x_parts, 1, 1) | + AMR_env$MO_lookup$species_first == substr(x_parts, 1, 1) | + AMR_env$MO_lookup$subspecies_first == substr(x_parts, 1, 1)) } if (length(filtr) == 0) { mo_to_search <- AMR_env$MO_lookup$fullname @@ -807,9 +806,13 @@ rep.mo <- function(x, ...) { #' @export #' @noRd print.mo_uncertainties <- function(x, n = 10, ...) { + more_than_50 <- FALSE if (NROW(x) == 0) { cat(word_wrap("No uncertainties to show. Only uncertainties of the last call of `as.mo()` or any `mo_*()` function are stored.\n\n", add_fn = font_blue)) return(invisible(NULL)) + } else if (NROW(x) > 50) { + more_than_50 <- TRUE + x <- x[1:50, , drop = FALSE] } cat(word_wrap("Matching scores are based on the resemblance between the input and the full taxonomic name, and the pathogenicity in humans. See `?mo_matching_score`.\n\n", add_fn = font_blue)) @@ -917,6 +920,9 @@ print.mo_uncertainties <- function(x, n = 10, ...) { if (isTRUE(any_maxed_out)) { cat(font_blue(word_wrap("\nOnly the first ", n, " other matches of each record are shown. Run `print(mo_uncertainties(), n = ...)` to view more entries, or save `mo_uncertainties()` to an object."))) } + if (isTRUE(more_than_50)) { + cat(font_blue(word_wrap("\nOnly the first 50 uncertainties are shown. Run `View(mo_uncertainties())` to view all entries, or save `mo_uncertainties()` to an object."))) + } } #' @method print mo_renamed diff --git a/_pkgdown.yml b/_pkgdown.yml index 14571e68..085f5215 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -116,19 +116,19 @@ navbar: icon: "fa-capsules" href: "reference/av_property.html" # reference instead of an article - text: "With other pkgs" - icon: "fa-circles-overlap" + icon: "fa-layer-plus" menu: - text: "AMR & dplyr/tidyverse" - icon: "fa-circles-overlap" + icon: "fa-layer-plus" href: "articles/other_pkg.html" - text: "AMR & data.table" - icon: "fa-circles-overlap" + icon: "fa-layer-plus" href: "articles/other_pkg.html" - text: "AMR & tidymodels" - icon: "fa-circles-overlap" + icon: "fa-layer-plus" href: "articles/other_pkg.html" - text: "AMR & base R" - icon: "fa-circles-overlap" + icon: "fa-layer-plus" href: "articles/other_pkg.html" - text: "Manual" icon: "fa-book-open" diff --git a/data/microorganisms.codes.rda b/data/microorganisms.codes.rda index cbd17463..fb7f6f1f 100644 Binary files a/data/microorganisms.codes.rda and b/data/microorganisms.codes.rda differ diff --git a/man/antibiotics.Rd b/man/antibiotics.Rd index 835f1421..1d2885aa 100644 --- a/man/antibiotics.Rd +++ b/man/antibiotics.Rd @@ -46,7 +46,7 @@ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) w \source{ \itemize{ \item World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology (WHOCC): \url{https://www.whocc.no/atc_ddd_index/} -\item Logical Observation Identifiers Names and Codes (LOINC), Version 2.73 (8 August, 2022). Accessed from \url{https://loinc.org} on 30 October, 2022. +\item Logical Observation Identifiers Names and Codes (LOINC), Version 2.73 (8 August, 2022). Accessed from \url{https://loinc.org} on October 30th, 2022. \item European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm} } } diff --git a/man/as.mo.Rd b/man/as.mo.Rd index 57df863d..7896aaeb 100644 --- a/man/as.mo.Rd +++ b/man/as.mo.Rd @@ -124,11 +124,11 @@ The coercion rules consider the prevalence of microorganisms in humans, which is \item Becker K \emph{et al.} (2020). \strong{Emergence of coagulase-negative staphylococci.} \emph{Expert Rev Anti Infect Ther.} 18(4):349-366; \doi{10.1080/14787210.2020.1730813} \item Lancefield RC (1933). \strong{A serological differentiation of human and other groups of hemolytic streptococci.} \emph{J Exp Med.} 57(4): 571-95; \doi{10.1084/jem.57.4.571} \item Berends MS \emph{et al.} (2022). \strong{Trends in Occurrence and Phenotypic Resistance of Coagulase-Negative Staphylococci (CoNS) Found in Human Blood in the Northern Netherlands between 2013 and 2019/} \emph{Micro.rganisms} 10(9), 1801; \doi{10.3390/microorganisms10091801} -\item Parte, AC \emph{et al.} (2020). \strong{List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ.} International Journal of Systematic and Evolutionary Microbiology, 70, 5607-5612; \doi{10.1099/ijsem.0.004332}. Accessed from \url{https://lpsn.dsmz.de} on 11 December, 2022. -\item GBIF Secretariat (2022). GBIF Backbone Taxonomy. Checklist dataset \doi{10.15468/39omei}. Accessed from \url{https://www.gbif.org} on 11 December, 2022. +\item Parte, AC \emph{et al.} (2020). \strong{List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ.} International Journal of Systematic and Evolutionary Microbiology, 70, 5607-5612; \doi{10.1099/ijsem.0.004332}. Accessed from \url{https://lpsn.dsmz.de} on December 11th, 2022. +\item GBIF Secretariat (2022). GBIF Backbone Taxonomy. Checklist dataset \doi{10.15468/39omei}. Accessed from \url{https://www.gbif.org} on December 11th, 2022. +\item Reimer, LC \emph{et al.} (2022). \strong{\emph{BacDive} in 2022: the knowledge base for standardized bacterial and archaeal data.} Nucleic Acids Res., 50(D1):D741-D74; \doi{10.1093/nar/gkab961}. Accessed from \url{https://bacdive.dsmz.de} on May 12th, 2023. \item Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS). US Edition of SNOMED CT from 1 September 2020. Value Set Name 'Microoganism', OID 2.16.840.1.114222.4.11.1009 (v12). URL: \url{https://phinvads.cdc.gov} \item Bartlett A \emph{et al.} (2022). \strong{A comprehensive list of bacterial pathogens infecting humans} \emph{Microbiology} 168:001269; \doi{10.1099/mic.0.001269} -\item Reimer \emph{et al.} (2022). \strong{\emph{BacDive} in 2022: the knowledge base for standardized bacterial and archaeal data.} \emph{Nucleic Acids Res.} 2022 Jan 7;50(D1):D741-D746; \doi{10.1093/nar/gkab961} } } diff --git a/man/eucast_rules.Rd b/man/eucast_rules.Rd index 93f416ee..5bed8f5f 100644 --- a/man/eucast_rules.Rd +++ b/man/eucast_rules.Rd @@ -74,7 +74,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied \strong{Note:} This function does not translate MIC values to SIR values. Use \code{\link[=as.sir]{as.sir()}} for that. \cr \strong{Note:} When ampicillin (AMP, J01CA01) is not available but amoxicillin (AMX, J01CA04) is, the latter will be used for all rules where there is a dependency on ampicillin. These drugs are interchangeable when it comes to expression of antimicrobial resistance. \cr -The file containing all EUCAST rules is located here: \url{https://github.com/msberends/AMR/blob/main/data-raw/eucast_rules.tsv}. \strong{Note:} Old taxonomic names are replaced with the current taxonomy where applicable. For example, \emph{Ochrobactrum anthropi} was renamed to \emph{Brucella anthropi} in 2020; the original EUCAST rules v3.1 and v3.2 did not yet contain this new taxonomic name. The \code{AMR} package contains the full microbial taxonomy updated until 11 December, 2022, see \link{microorganisms}. +The file containing all EUCAST rules is located here: \url{https://github.com/msberends/AMR/blob/main/data-raw/eucast_rules.tsv}. \strong{Note:} Old taxonomic names are replaced with the current taxonomy where applicable. For example, \emph{Ochrobactrum anthropi} was renamed to \emph{Brucella anthropi} in 2020; the original EUCAST rules v3.1 and v3.2 did not yet contain this new taxonomic name. The \code{AMR} package contains the full microbial taxonomy updated until December 11th, 2022, see \link{microorganisms}. \subsection{Custom Rules}{ Custom rules can be created using \code{\link[=custom_eucast_rules]{custom_eucast_rules()}}, e.g.: diff --git a/man/microorganisms.Rd b/man/microorganisms.Rd index bf725a4c..00767a86 100644 --- a/man/microorganisms.Rd +++ b/man/microorganisms.Rd @@ -22,24 +22,24 @@ A \link[tibble:tibble]{tibble} with 52 151 observations and 23 variables: \item \code{gbif_renamed_to}\cr GBIF identifier of the currently valid taxon \item \code{source}\cr Either "GBIF", "LPSN", or "manually added" (see \emph{Source}) \item \code{prevalence}\cr Prevalence of the microorganism according to Bartlett \emph{et al.} (2022, \doi{10.1099/mic.0.001269}), see \code{\link[=mo_matching_score]{mo_matching_score()}} for the full explanation -\item \code{snomed}\cr Systematized Nomenclature of Medicine (SNOMED) code of the microorganism, version of 1 July, 2021 (see \emph{Source}). Use \code{\link[=mo_snomed]{mo_snomed()}} to retrieve it quickly, see \code{\link[=mo_property]{mo_property()}}. +\item \code{snomed}\cr Systematized Nomenclature of Medicine (SNOMED) code of the microorganism, version of July 1st, 2021 (see \emph{Source}). Use \code{\link[=mo_snomed]{mo_snomed()}} to retrieve it quickly, see \code{\link[=mo_property]{mo_property()}}. } } \source{ \itemize{ -\item Parte, AC \emph{et al.} (2020). \strong{List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ.} International Journal of Systematic and Evolutionary Microbiology, 70, 5607-5612; \doi{10.1099/ijsem.0.004332}. Accessed from \url{https://lpsn.dsmz.de} on 11 December, 2022. -\item GBIF Secretariat (2022). GBIF Backbone Taxonomy. Checklist dataset \doi{10.15468/39omei}. Accessed from \url{https://www.gbif.org} on 11 December, 2022. +\item Parte, AC \emph{et al.} (2020). \strong{List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ.} International Journal of Systematic and Evolutionary Microbiology, 70, 5607-5612; \doi{10.1099/ijsem.0.004332}. Accessed from \url{https://lpsn.dsmz.de} on December 11th, 2022. +\item GBIF Secretariat (2022). GBIF Backbone Taxonomy. Checklist dataset \doi{10.15468/39omei}. Accessed from \url{https://www.gbif.org} on December 11th, 2022. +\item Reimer, LC \emph{et al.} (2022). \strong{\emph{BacDive} in 2022: the knowledge base for standardized bacterial and archaeal data.} Nucleic Acids Res., 50(D1):D741-D74; \doi{10.1093/nar/gkab961}. Accessed from \url{https://bacdive.dsmz.de} on May 12th, 2023. \item Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS). US Edition of SNOMED CT from 1 September 2020. Value Set Name 'Microoganism', OID 2.16.840.1.114222.4.11.1009 (v12). URL: \url{https://phinvads.cdc.gov} \item Grimont \emph{et al.} (2007). Antigenic Formulae of the Salmonella Serovars, 9th Edition. WHO Collaborating Centre for Reference and Research on \emph{Salmonella} (WHOCC-SALM). \item Bartlett \emph{et al.} (2022). \strong{A comprehensive list of bacterial pathogens infecting humans} \emph{Microbiology} 168:001269; \doi{10.1099/mic.0.001269} -\item Reimer \emph{et al.} (2022). \strong{\emph{BacDive} in 2022: the knowledge base for standardized bacterial and archaeal data.} \emph{Nucleic Acids Res.} 2022 Jan 7;50(D1):D741-D746; \doi{10.1093/nar/gkab961} } } \usage{ microorganisms } \description{ -A data set containing the full microbial taxonomy (\strong{last updated: 11 December, 2022}) of five kingdoms from the List of Prokaryotic names with Standing in Nomenclature (LPSN) and the Global Biodiversity Information Facility (GBIF). This data set is the backbone of this \code{AMR} package. MO codes can be looked up using \code{\link[=as.mo]{as.mo()}}. +A data set containing the full microbial taxonomy (\strong{last updated: December 11th, 2022}) of five kingdoms from the List of Prokaryotic names with Standing in Nomenclature (LPSN) and the Global Biodiversity Information Facility (GBIF). This data set is the backbone of this \code{AMR} package. MO codes can be looked up using \code{\link[=as.mo]{as.mo()}}. } \details{ Please note that entries are only based on the List of Prokaryotic names with Standing in Nomenclature (LPSN) and the Global Biodiversity Information Facility (GBIF) (see below). Since these sources incorporate entries based on (recent) publications in the International Journal of Systematic and Evolutionary Microbiology (IJSEM), it can happen that the year of publication is sometimes later than one might expect. diff --git a/man/microorganisms.codes.Rd b/man/microorganisms.codes.Rd index a57a0ea7..b7adeb6b 100644 --- a/man/microorganisms.codes.Rd +++ b/man/microorganisms.codes.Rd @@ -3,9 +3,9 @@ \docType{data} \name{microorganisms.codes} \alias{microorganisms.codes} -\title{Data Set with 5 754 Common Microorganism Codes} +\title{Data Set with 4 909 Common Microorganism Codes} \format{ -A \link[tibble:tibble]{tibble} with 5 754 observations and 2 variables: +A \link[tibble:tibble]{tibble} with 4 909 observations and 2 variables: \itemize{ \item \code{code}\cr Commonly used code of a microorganism \item \code{mo}\cr ID of the microorganism in the \link{microorganisms} data set diff --git a/man/mo_property.Rd b/man/mo_property.Rd index 97beb35e..bcf364f3 100644 --- a/man/mo_property.Rd +++ b/man/mo_property.Rd @@ -333,7 +333,7 @@ Determination of bacterial oxygen tolerance (\code{\link[=mo_oxygen_tolerance]{m The function \code{\link[=mo_url]{mo_url()}} will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species. -SNOMED codes (\code{\link[=mo_snomed]{mo_snomed()}}) are from the version of 1 July, 2021. See \emph{Source} and the \link{microorganisms} data set for more info. +SNOMED codes (\code{\link[=mo_snomed]{mo_snomed()}}) are from the version of July 1st, 2021. See \emph{Source} and the \link{microorganisms} data set for more info. Old taxonomic names (so-called 'synonyms') can be retrieved with \code{\link[=mo_synonyms]{mo_synonyms()}} (which will have the scientific reference as \link[base:names]{name}), the current taxonomic name can be retrieved with \code{\link[=mo_current]{mo_current()}}. Both functions return full names. @@ -353,11 +353,11 @@ This function uses \code{\link[=as.mo]{as.mo()}} internally, which uses an advan \item Becker K \emph{et al.} (2020). \strong{Emergence of coagulase-negative staphylococci.} \emph{Expert Rev Anti Infect Ther.} 18(4):349-366; \doi{10.1080/14787210.2020.1730813} \item Lancefield RC (1933). \strong{A serological differentiation of human and other groups of hemolytic streptococci.} \emph{J Exp Med.} 57(4): 571-95; \doi{10.1084/jem.57.4.571} \item Berends MS \emph{et al.} (2022). \strong{Trends in Occurrence and Phenotypic Resistance of Coagulase-Negative Staphylococci (CoNS) Found in Human Blood in the Northern Netherlands between 2013 and 2019/} \emph{Micro.rganisms} 10(9), 1801; \doi{10.3390/microorganisms10091801} -\item Parte, AC \emph{et al.} (2020). \strong{List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ.} International Journal of Systematic and Evolutionary Microbiology, 70, 5607-5612; \doi{10.1099/ijsem.0.004332}. Accessed from \url{https://lpsn.dsmz.de} on 11 December, 2022. -\item GBIF Secretariat (2022). GBIF Backbone Taxonomy. Checklist dataset \doi{10.15468/39omei}. Accessed from \url{https://www.gbif.org} on 11 December, 2022. +\item Parte, AC \emph{et al.} (2020). \strong{List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ.} International Journal of Systematic and Evolutionary Microbiology, 70, 5607-5612; \doi{10.1099/ijsem.0.004332}. Accessed from \url{https://lpsn.dsmz.de} on December 11th, 2022. +\item GBIF Secretariat (2022). GBIF Backbone Taxonomy. Checklist dataset \doi{10.15468/39omei}. Accessed from \url{https://www.gbif.org} on December 11th, 2022. +\item Reimer, LC \emph{et al.} (2022). \strong{\emph{BacDive} in 2022: the knowledge base for standardized bacterial and archaeal data.} Nucleic Acids Res., 50(D1):D741-D74; \doi{10.1093/nar/gkab961}. Accessed from \url{https://bacdive.dsmz.de} on May 12th, 2023. \item Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS). US Edition of SNOMED CT from 1 September 2020. Value Set Name 'Microoganism', OID 2.16.840.1.114222.4.11.1009 (v12). URL: \url{https://phinvads.cdc.gov} \item Bartlett A \emph{et al.} (2022). \strong{A comprehensive list of bacterial pathogens infecting humans} \emph{Microbiology} 168:001269; \doi{10.1099/mic.0.001269} -\item Reimer \emph{et al.} (2022). \strong{\emph{BacDive} in 2022: the knowledge base for standardized bacterial and archaeal data.} \emph{Nucleic Acids Res.} 2022 Jan 7;50(D1):D741-D746; \doi{10.1093/nar/gkab961} } }