# Get Properties of a Microorganism Use these functions to return a specific property of a microorganism based on the latest accepted taxonomy. All input values will be evaluated internally with [`as.mo()`](https://amr-for-r.org/reference/as.mo.md), which makes it possible to use microbial abbreviations, codes and names as input. See *Examples*. ## Usage ``` r mo_name(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) mo_fullname(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) mo_shortname(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) mo_subspecies(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) mo_species(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) mo_genus(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) mo_family(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) mo_order(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) mo_class(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) mo_phylum(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) mo_kingdom(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) mo_domain(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) mo_type(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) mo_status(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) mo_pathogenicity(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) mo_gramstain(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) mo_is_gram_negative(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) mo_is_gram_positive(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) mo_is_yeast(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) mo_is_intrinsic_resistant(x, ab, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) mo_oxygen_tolerance(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) mo_is_anaerobic(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) mo_snomed(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) mo_ref(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) mo_authors(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) mo_year(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) mo_lpsn(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) mo_mycobank(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) mo_gbif(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) mo_rank(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) mo_taxonomy(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) mo_synonyms(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) mo_current(x, language = get_AMR_locale(), ...) mo_group_members(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) mo_info(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) mo_url(x, open = FALSE, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) mo_property(x, property = "fullname", language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) ``` ## Arguments - x: Any [character](https://rdrr.io/r/base/character.html) (vector) that can be coerced to a valid microorganism code with [`as.mo()`](https://amr-for-r.org/reference/as.mo.md). Can be left blank for auto-guessing the column containing microorganism codes if used in a data set, see *Examples*. - language: Language to translate text like "no growth", which defaults to the system language (see [`get_AMR_locale()`](https://amr-for-r.org/reference/translate.md)). - keep_synonyms: A [logical](https://rdrr.io/r/base/logical.html) to indicate if old, previously valid taxonomic names must be preserved and not be corrected to currently accepted names. The default is `FALSE`, which will return a note if old taxonomic names were processed. The default can be set with the package option [`AMR_keep_synonyms`](https://amr-for-r.org/reference/AMR-options.md), i.e. `options(AMR_keep_synonyms = TRUE)` or `options(AMR_keep_synonyms = FALSE)`. - ...: Other arguments passed on to [`as.mo()`](https://amr-for-r.org/reference/as.mo.md), such as 'minimum_matching_score', 'ignore_pattern', and 'remove_from_input'. - ab: Any (vector of) text that can be coerced to a valid antibiotic drug code with [`as.ab()`](https://amr-for-r.org/reference/as.ab.md). - open: Browse the URL using [`browseURL()`](https://rdrr.io/r/utils/browseURL.html). - property: One of the column names of the [microorganisms](https://amr-for-r.org/reference/microorganisms.md) data set: "mo", "fullname", "status", "kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies", "rank", "ref", "oxygen_tolerance", "source", "lpsn", "lpsn_parent", "lpsn_renamed_to", "mycobank", "mycobank_parent", "mycobank_renamed_to", "gbif", "gbif_parent", "gbif_renamed_to", "prevalence", or "snomed", or must be `"shortname"`. ## Value - An [integer](https://rdrr.io/r/base/integer.html) in case of `mo_year()` - An [ordered factor](https://rdrr.io/r/base/factor.html) in case of `mo_pathogenicity()` - A [list](https://rdrr.io/r/base/list.html) in case of `mo_taxonomy()`, `mo_synonyms()`, `mo_snomed()`, and `mo_info()` - A [logical](https://rdrr.io/r/base/logical.html) in case of `mo_is_anaerobic()`, `mo_is_gram_negative()`, `mo_is_gram_positive()`, `mo_is_intrinsic_resistant()`, and `mo_is_yeast()` - A named [character](https://rdrr.io/r/base/character.html) in case of `mo_synonyms()` and `mo_url()` - A [character](https://rdrr.io/r/base/character.html) in all other cases ## Details All functions will, at default, **not** keep old taxonomic properties, as synonyms are automatically replaced with the current taxonomy. Take for example *Enterobacter aerogenes*, which was initially named in 1960 but renamed to *Klebsiella aerogenes* in 2017: - `mo_genus("Enterobacter aerogenes")` will return `"Klebsiella"` (with a note about the renaming) - `mo_genus("Enterobacter aerogenes", keep_synonyms = TRUE)` will return `"Enterobacter"` (with a once-per-session warning that the name is outdated) - `mo_ref("Enterobacter aerogenes")` will return `"Tindall et al., 2017"` (with a note about the renaming) - `mo_ref("Enterobacter aerogenes", keep_synonyms = TRUE)` will return `"Hormaeche et al., 1960"` (with a once-per-session warning that the name is outdated) The short name (`mo_shortname()`) returns the first character of the genus and the full species, such as `"E. coli"`, for species and subspecies. Exceptions are abbreviations of staphylococci (such as *"CoNS"*, Coagulase-Negative Staphylococci) and beta-haemolytic streptococci (such as *"GBS"*, Group B Streptococci). Please bear in mind that e.g. *E. coli* could mean *Escherichia coli* (kingdom of Bacteria) as well as *Entamoeba coli* (kingdom of Protozoa). Returning to the full name will be done using [`as.mo()`](https://amr-for-r.org/reference/as.mo.md) internally, giving priority to bacteria and human pathogens, i.e. `"E. coli"` will be considered *Escherichia coli*. As a result, `mo_fullname(mo_shortname("Entamoeba coli"))` returns `"Escherichia coli"`. Since the top-level of the taxonomy is sometimes referred to as 'kingdom' and sometimes as 'domain', the functions `mo_kingdom()` and `mo_domain()` return the exact same results. Determination of human pathogenicity (`mo_pathogenicity()`) is strongly based on Bartlett *et al.* (2022, [doi:10.1099/mic.0.001269](https://doi.org/10.1099/mic.0.001269) ). This function returns a [factor](https://rdrr.io/r/base/factor.html) with the levels *Pathogenic*, *Potentially pathogenic*, *Non-pathogenic*, and *Unknown*. Determination of the Gram stain (`mo_gramstain()`) will be based on the taxonomic kingdom and phylum. Originally, Cavalier-Smith defined the so-called subkingdoms Negibacteria and Posibacteria (2002, [PMID 11837318](https://pubmed.ncbi.nlm.nih.gov/11837318/)), and only considered these phyla as Posibacteria: Actinobacteria, Chloroflexi, Firmicutes, and Tenericutes. These phyla were later renamed to Actinomycetota, Chloroflexota, Bacillota, and Mycoplasmatota (2021, [PMID 34694987](https://pubmed.ncbi.nlm.nih.gov/34694987/)). Bacteria in these phyla are considered Gram-positive in this `AMR` package, except for members of the class Negativicutes (within phylum Bacillota) which are Gram-negative. All other bacteria are considered Gram-negative. Species outside the kingdom of Bacteria will return a value `NA`. Functions `mo_is_gram_negative()` and `mo_is_gram_positive()` always return `TRUE` or `FALSE` (or `NA` when the input is `NA` or the MO code is `UNKNOWN`), thus always return `FALSE` for species outside the taxonomic kingdom of Bacteria. Determination of yeasts (`mo_is_yeast()`) will be based on the taxonomic kingdom and class. *Budding yeasts* are yeasts that reproduce asexually through a process called budding, where a new cell develops from a small protrusion on the parent cell. Taxonomically, these are members of the phylum Ascomycota, class Saccharomycetes (also called Hemiascomycetes) or Pichiomycetes. *True yeasts* quite specifically refers to yeasts in the underlying order Saccharomycetales (such as *Saccharomyces cerevisiae*). Thus, for all microorganisms that are member of the taxonomic class Saccharomycetes or Pichiomycetes, the function will return `TRUE`. It returns `FALSE` otherwise (or `NA` when the input is `NA` or the MO code is `UNKNOWN`). Determination of intrinsic resistance (`mo_is_intrinsic_resistant()`) will be based on the [intrinsic_resistant](https://amr-for-r.org/reference/intrinsic_resistant.md) data set, which is based on ['EUCAST Expected Resistant Phenotypes' v1.2](https://www.eucast.org/expert_rules_and_expected_phenotypes) (2023). The `mo_is_intrinsic_resistant()` function can be vectorised over both argument `x` (input for microorganisms) and `ab` (input for antimicrobials). Determination of bacterial oxygen tolerance (`mo_oxygen_tolerance()`) will be based on BacDive, see *Source*. The function `mo_is_anaerobic()` only returns `TRUE` if the oxygen tolerance is `"anaerobe"`, indicting an obligate anaerobic species or genus. It always returns `FALSE` for species outside the taxonomic kingdom of Bacteria. The function `mo_url()` will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species. [This MycoBank URL](https://www.mycobank.org) will be used for fungi wherever available , [this LPSN URL](https://www.mycobank.org) for bacteria wherever available, and [this GBIF link](https://www.gbif.org) otherwise. SNOMED codes (`mo_snomed()`) was last updated on July 16th, 2024. See *Source* and the [microorganisms](https://amr-for-r.org/reference/microorganisms.md) data set for more info. Old taxonomic names (so-called 'synonyms') can be retrieved with `mo_synonyms()` (which will have the scientific reference as [name](https://rdrr.io/r/base/names.html)), the current taxonomic name can be retrieved with `mo_current()`. Both functions return full names. All output [will be translated](https://amr-for-r.org/reference/translate.md) where possible. ## Matching Score for Microorganisms This function uses [`as.mo()`](https://amr-for-r.org/reference/as.mo.md) internally, which uses an advanced algorithm to translate arbitrary user input to valid taxonomy using a so-called matching score. You can read about this public algorithm on the [MO matching score page](https://amr-for-r.org/reference/mo_matching_score.md). ## Source - Berends MS *et al.* (2022). **AMR: An R Package for Working with Antimicrobial Resistance Data**. *Journal of Statistical Software*, 104(3), 1-31; [doi:10.18637/jss.v104.i03](https://doi.org/10.18637/jss.v104.i03) - 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](https://doi.org/10.1099/ijsem.0.004332) . Accessed from on June 24th, 2024. - Vincent, R *et al* (2013). **MycoBank gearing up for new horizons.** IMA Fungus, 4(2), 371-9; [doi:10.5598/imafungus.2013.04.02.16](https://doi.org/10.5598/imafungus.2013.04.02.16) . Accessed from on June 24th, 2024. - GBIF Secretariat (2023). GBIF Backbone Taxonomy. Checklist dataset [doi:10.15468/39omei](https://doi.org/10.15468/39omei) . Accessed from on June 24th, 2024. - 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](https://doi.org/10.1093/nar/gkab961) . Accessed from on July 16th, 2024. - Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS). US Edition of SNOMED CT from 1 September 2020. Value Set Name 'Microorganism', OID 2.16.840.1.114222.4.11.1009 (v12). URL: - Bartlett A *et al.* (2022). **A comprehensive list of bacterial pathogens infecting humans** *Microbiology* 168:001269; [doi:10.1099/mic.0.001269](https://doi.org/10.1099/mic.0.001269) ## Download Our Reference Data All reference data sets in the AMR package - including information on microorganisms, antimicrobials, and clinical breakpoints - are freely available for download in multiple formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata. For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems. Visit [our website for direct download links](https://amr-for-r.org/articles/datasets.html), or explore the actual files in [our GitHub repository](https://github.com/msberends/AMR/tree/main/data-raw/datasets). ## See also Data set [microorganisms](https://amr-for-r.org/reference/microorganisms.md) ## Examples ``` r # taxonomic tree ----------------------------------------------------------- mo_kingdom("Klebsiella pneumoniae") #> [1] "Bacteria" mo_phylum("Klebsiella pneumoniae") #> [1] "Pseudomonadota" mo_class("Klebsiella pneumoniae") #> [1] "Gammaproteobacteria" mo_order("Klebsiella pneumoniae") #> [1] "Enterobacterales" mo_family("Klebsiella pneumoniae") #> [1] "Enterobacteriaceae" mo_genus("Klebsiella pneumoniae") #> [1] "Klebsiella" mo_species("Klebsiella pneumoniae") #> [1] "pneumoniae" mo_subspecies("Klebsiella pneumoniae") #> [1] "" # full names and short names ----------------------------------------------- mo_name("Klebsiella pneumoniae") #> [1] "Klebsiella pneumoniae" mo_fullname("Klebsiella pneumoniae") #> [1] "Klebsiella pneumoniae" mo_shortname("Klebsiella pneumoniae") #> [1] "K. pneumoniae" # other properties --------------------------------------------------------- mo_pathogenicity("Klebsiella pneumoniae") #> [1] Pathogenic #> Levels: Pathogenic < Potentially pathogenic < Non-pathogenic < Unknown mo_gramstain("Klebsiella pneumoniae") #> [1] "Gram-negative" mo_snomed("Klebsiella pneumoniae") #> [[1]] #> [1] "1098101000112102" "446870005" "1098201000112108" "409801009" #> [5] "56415008" "714315002" "713926009" #> mo_type("Klebsiella pneumoniae") #> [1] "Bacteria" mo_rank("Klebsiella pneumoniae") #> [1] "species" mo_url("Klebsiella pneumoniae") #> Klebsiella pneumoniae #> "https://lpsn.dsmz.de/species/klebsiella-pneumoniae" mo_is_yeast(c("Candida", "Trichophyton", "Klebsiella")) #> [1] TRUE FALSE FALSE mo_group_members(c( "Streptococcus group A", "Streptococcus group C", "Streptococcus group G", "Streptococcus group L" )) #> $`Streptococcus Group A` #> [1] "Streptococcus pyogenes" #> #> $`Streptococcus Group C` #> [1] "Streptococcus dysgalactiae" #> [2] "Streptococcus dysgalactiae dysgalactiae" #> [3] "Streptococcus dysgalactiae equisimilis" #> [4] "Streptococcus equi" #> [5] "Streptococcus equi equi" #> [6] "Streptococcus equi ruminatorum" #> [7] "Streptococcus equi zooepidemicus" #> #> $`Streptococcus Group G` #> [1] "Streptococcus canis" #> [2] "Streptococcus dysgalactiae" #> [3] "Streptococcus dysgalactiae dysgalactiae" #> [4] "Streptococcus dysgalactiae equisimilis" #> #> $`Streptococcus Group L` #> [1] "Streptococcus dysgalactiae" #> [2] "Streptococcus dysgalactiae dysgalactiae" #> [3] "Streptococcus dysgalactiae equisimilis" #> # scientific reference ----------------------------------------------------- mo_ref("Klebsiella aerogenes") #> [1] "Tindall et al., 2017" mo_authors("Klebsiella aerogenes") #> [1] "Tindall et al." mo_year("Klebsiella aerogenes") #> [1] 2017 mo_synonyms("Klebsiella aerogenes") #> Hormaeche et al., 1960 Bascomb et al., 1971 #> "Enterobacter aerogenes" "Klebsiella mobilis" mo_lpsn("Klebsiella aerogenes") #> [1] "777146" mo_gbif("Klebsiella aerogenes") #> [1] "9281703" mo_mycobank("Candida albicans") #> [1] "256187" mo_mycobank("Candida krusei") #> [1] "337013" mo_mycobank("Candida krusei", keep_synonyms = TRUE) #> Warning: Function `as.mo()` returned one old taxonomic name. Use `as.mo(..., #> keep_synonyms = FALSE)` to clean the input to currently accepted taxonomic #> names, or set the R option `AMR_keep_synonyms` to `FALSE`. This warning #> will be shown once per session. #> [1] "268707" # abbreviations known in the field ----------------------------------------- mo_genus("MRSA") #> [1] "Staphylococcus" mo_species("MRSA") #> [1] "aureus" mo_shortname("VISA") #> [1] "S. aureus" mo_gramstain("VISA") #> [1] "Gram-positive" mo_genus("EHEC") #> [1] "Escherichia" mo_species("EIEC") #> [1] "coli" mo_name("UPEC") #> [1] "Escherichia coli" # known subspecies --------------------------------------------------------- mo_fullname("K. pneu rh") #> [1] "Klebsiella pneumoniae rhinoscleromatis" mo_shortname("K. pneu rh") #> [1] "K. pneumoniae" # \donttest{ # Becker classification, see ?as.mo ---------------------------------------- mo_fullname("Staph epidermidis") #> [1] "Staphylococcus epidermidis" mo_fullname("Staph epidermidis", Becker = TRUE) #> [1] "Coagulase-negative Staphylococcus (CoNS)" mo_shortname("Staph epidermidis") #> [1] "S. epidermidis" mo_shortname("Staph epidermidis", Becker = TRUE) #> [1] "CoNS" # Lancefield classification, see ?as.mo ------------------------------------ mo_fullname("Strep agalactiae") #> [1] "Streptococcus agalactiae" mo_fullname("Strep agalactiae", Lancefield = TRUE) #> [1] "Streptococcus Group B" mo_shortname("Strep agalactiae") #> [1] "S. agalactiae" mo_shortname("Strep agalactiae", Lancefield = TRUE) #> [1] "GBS" # language support -------------------------------------------------------- mo_gramstain("Klebsiella pneumoniae", language = "de") # German #> [1] "Gramnegativ" mo_gramstain("Klebsiella pneumoniae", language = "nl") # Dutch #> [1] "Gram-negatief" mo_gramstain("Klebsiella pneumoniae", language = "es") # Spanish #> [1] "Gram negativo" mo_gramstain("Klebsiella pneumoniae", language = "el") # Greek #> [1] "Αρνητικό κατά Gram" mo_gramstain("Klebsiella pneumoniae", language = "uk") # Ukrainian #> [1] "Грамнегативні" # mo_type is equal to mo_kingdom, but mo_kingdom will remain untranslated mo_kingdom("Klebsiella pneumoniae") #> [1] "Bacteria" mo_type("Klebsiella pneumoniae") #> [1] "Bacteria" mo_kingdom("Klebsiella pneumoniae", language = "zh") # Chinese, no effect #> [1] "Bacteria" mo_type("Klebsiella pneumoniae", language = "zh") # Chinese, translated #> [1] "细菌" mo_fullname("S. pyogenes", Lancefield = TRUE, language = "de") #> [1] "Streptococcus Gruppe A" mo_fullname("S. pyogenes", Lancefield = TRUE, language = "uk") #> [1] "Streptococcus Група A" # other -------------------------------------------------------------------- # gram stains and intrinsic resistance can be used as a filter in dplyr verbs if (require("dplyr")) { example_isolates %>% filter(mo_is_gram_positive()) %>% count(mo_genus(), sort = TRUE) } #> ℹ Using column 'mo' as input for `mo_is_gram_positive()` #> ℹ Using column 'mo' as input for `mo_genus()` #> # A tibble: 18 × 2 #> `mo_genus()` n #> #> 1 Staphylococcus 840 #> 2 Streptococcus 275 #> 3 Enterococcus 83 #> 4 Corynebacterium 17 #> 5 Micrococcus 6 #> 6 Gemella 3 #> 7 Aerococcus 2 #> 8 Cutibacterium 1 #> 9 Dermabacter 1 #> 10 Fusibacter 1 #> 11 Globicatella 1 #> 12 Granulicatella 1 #> 13 Lactobacillus 1 #> 14 Leuconostoc 1 #> 15 Listeria 1 #> 16 Paenibacillus 1 #> 17 Rothia 1 #> 18 Schaalia 1 if (require("dplyr")) { example_isolates %>% filter(mo_is_intrinsic_resistant(ab = "vanco")) %>% count(mo_genus(), sort = TRUE) } #> ℹ Using column 'mo' as input for `mo_is_intrinsic_resistant()` #> ℹ Using column 'mo' as input for `mo_genus()` #> # A tibble: 19 × 2 #> `mo_genus()` n #> #> 1 Escherichia 467 #> 2 Klebsiella 77 #> 3 Proteus 39 #> 4 Pseudomonas 30 #> 5 Serratia 25 #> 6 Enterobacter 23 #> 7 Citrobacter 11 #> 8 Haemophilus 9 #> 9 Acinetobacter 6 #> 10 Morganella 6 #> 11 Pantoea 4 #> 12 Salmonella 3 #> 13 Neisseria 2 #> 14 Stenotrophomonas 2 #> 15 Campylobacter 1 #> 16 Enterococcus 1 #> 17 Hafnia 1 #> 18 Leuconostoc 1 #> 19 Pseudescherichia 1 # get a list with the complete taxonomy (from kingdom to subspecies) mo_taxonomy("Klebsiella pneumoniae") #> $kingdom #> [1] "Bacteria" #> #> $phylum #> [1] "Pseudomonadota" #> #> $class #> [1] "Gammaproteobacteria" #> #> $order #> [1] "Enterobacterales" #> #> $family #> [1] "Enterobacteriaceae" #> #> $genus #> [1] "Klebsiella" #> #> $species #> [1] "pneumoniae" #> #> $subspecies #> [1] "" #> # get a list with the taxonomy, the authors, Gram-stain, # SNOMED codes, and URL to the online database mo_info("Klebsiella pneumoniae") #> $mo #> [1] "B_KLBSL_PNMN" #> #> $rank #> [1] "species" #> #> $kingdom #> [1] "Bacteria" #> #> $phylum #> [1] "Pseudomonadota" #> #> $class #> [1] "Gammaproteobacteria" #> #> $order #> [1] "Enterobacterales" #> #> $family #> [1] "Enterobacteriaceae" #> #> $genus #> [1] "Klebsiella" #> #> $species #> [1] "pneumoniae" #> #> $subspecies #> [1] "" #> #> $status #> [1] "accepted" #> #> $synonyms #> NULL #> #> $gramstain #> [1] "Gram-negative" #> #> $oxygen_tolerance #> [1] "facultative anaerobe" #> #> $url #> [1] "https://lpsn.dsmz.de/species/klebsiella-pneumoniae" #> #> $ref #> [1] "Trevisan, 1887" #> #> $snomed #> [1] "1098101000112102" "446870005" "1098201000112108" "409801009" #> [5] "56415008" "714315002" "713926009" #> #> $lpsn #> [1] "777151" #> #> $mycobank #> [1] NA #> #> $gbif #> [1] "3221874" #> #> $group_members #> character(0) #> # } ```