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+# 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 <https://lpsn.dsmz.de> 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 <https://www.mycobank.org> on June 24th, 2024.
+
+- GBIF Secretariat (2023). GBIF Backbone Taxonomy. Checklist dataset
+  [doi:10.15468/39omei](https://doi.org/10.15468/39omei) . Accessed from
+  <https://www.gbif.org> 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 <https://bacdive.dsmz.de> 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: <https://www.cdc.gov/phin/php/phinvads/>
+
+- 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
+#>    <chr>           <int>
+#>  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
+#>    <chr>            <int>
+#>  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)
+#> 
+# }
+```