Property of a microorganism

Use these functions to return a specific property of a microorganism from the microorganisms data set. All input values will be evaluated internally with as.mo.

mo_fullname(x, language = get_locale(), ...)

mo_shortname(x, language = get_locale(), ...)

mo_subspecies(x, language = get_locale(), ...)

mo_species(x, language = get_locale(), ...)

mo_genus(x, language = get_locale(), ...)

mo_family(x, ...)

mo_order(x, ...)

mo_class(x, ...)

mo_phylum(x, ...)

mo_subkingdom(x, ...)

mo_kingdom(x, ...)

mo_type(x, language = get_locale(), ...)

mo_gramstain(x, language = get_locale(), ...)

mo_TSN(x, ...)

mo_ref(x, ...)

mo_authors(x, ...)

mo_year(x, ...)

mo_taxonomy(x, ...)

mo_property(x, property = "fullname", language = get_locale(), ...)

Arguments

x

any (vector of) text that can be coerced to a valid microorganism code with as.mo
language

language of the returned text, defaults to system language (see get_locale) and can also be set with getOption("AMR_locale"). Use language = NULL or language = "" to prevent translation.
...

other parameters passed on to as.mo
property

one of the column names of one of the microorganisms data set or "shortname"

Value

  • An integer in case of mo_TSN and mo_year

  • A list in case of mo_taxonomy

  • A character in all other cases

Details

All functions will return the most recently known taxonomic property according to ITIS, except for mo_ref, mo_authors and mo_year. This leads to the following results:

  • mo_fullname("Chlamydia psittaci") will return "Chlamydophila psittaci" (with a warning about the renaming)

  • mo_ref("Chlamydia psittaci") will return "Page, 1968" (with a warning about the renaming)

  • mo_ref("Chlamydophila psittaci") will return "Everett et al., 1999" (without a warning)

Supported languages

Supported languages are "en" (English), "de" (German), "nl" (Dutch), "es" (Spanish), "it" (Italian), "fr" (French), and "pt" (Portuguese).

ITIS


This package contains the complete microbial taxonomic data (with all nine taxonomic ranks - from kingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, https://www.itis.gov).

All (sub)species from the taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package, as well as all previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This allows users to use authoritative taxonomic information for their data analysis on any microorganism, not only human pathogens. It also helps to quickly determine the Gram stain of bacteria, since all bacteria are classified into subkingdom Negibacteria or Posibacteria.

ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3].

Source

[1] Becker K et al. Coagulase-Negative Staphylococci. 2014. Clin Microbiol Rev. 27(4): 870–926. https://dx.doi.org/10.1128/CMR.00109-13

[2] Lancefield RC A serological differentiation of human and other groups of hemolytic streptococci. 1933. J Exp Med. 57(4): 571–95. https://dx.doi.org/10.1084/jem.57.4.571

[3] Integrated Taxonomic Information System (ITIS). Retrieved September 2018. http://www.itis.gov

See also

microorganisms

Examples

# All properties of Escherichia coli
## taxonomic properties
mo_kingdom("E. coli")         # "Bacteria"
#> [1] "Bacteria"
mo_subkingdom("E. coli")      # "Negibacteria"
#> [1] "Negibacteria"
mo_phylum("E. coli")          # "Proteobacteria"
#> [1] "Proteobacteria"
mo_class("E. coli")           # "Gammaproteobacteria"
#> [1] "Gammaproteobacteria"
mo_order("E. coli")           # "Enterobacteriales"
#> [1] "Enterobacteriales"
mo_family("E. coli")          # "Enterobacteriaceae"
#> [1] "Enterobacteriaceae"
mo_genus("E. coli")           # "Escherichia"
#> [1] "Escherichia"
mo_species("E. coli")         # "coli"
#> [1] "coli"
mo_subspecies("E. coli")      # NA
#> [1] NA
mo_TSN("E. coli")             # 285 (Taxonomic Serial Number)
#> [1] 285

## colloquial properties
mo_fullname("E. coli")        # "Escherichia coli"
#> [1] "Escherichia coli"
mo_shortname("E. coli")       # "E. coli"
#> [1] "E. coli"

## other properties
mo_gramstain("E. coli")       # "Gram negative"
#> [1] "Gram-negatief"
mo_type("E. coli")            # "Bacteria" (equal to kingdom)
#> [1] "Bacteriën"

## scientific reference
mo_ref("E. coli")             # "Castellani and Chalmers, 1919"
#> [1] "Castellani and Chalmers, 1919"
mo_authors("E. coli")         # "Castellani and Chalmers"
#> [1] "Castellani and Chalmers"
mo_year("E. coli")            # 1919
#> [1] 1919


# Abbreviations known in the field
mo_genus("MRSA")              # "Staphylococcus"
#> [1] "Staphylococcus"
mo_species("MRSA")            # "aureus"
#> [1] "aureus"
mo_shortname("MRSA")          # "S. aureus"
#> [1] "S. aureus"
mo_gramstain("MRSA")          # "Gram positive"
#> [1] "Gram-positief"

mo_genus("VISA")              # "Staphylococcus"
#> [1] "Staphylococcus"
mo_species("VISA")            # "aureus"
#> [1] "aureus"


# Known subspecies
mo_genus("doylei")            # "Campylobacter"
#> Warning: These 1 values could not be coerced to a valid MO code: "doylei". See mo_failures() to review them.
#> [1] NA
mo_species("doylei")          # "jejuni"
#> Warning: These 1 values could not be coerced to a valid MO code: "doylei". See mo_failures() to review them.
#> [1] NA
mo_fullname("doylei")         # "Campylobacter jejuni doylei"
#> Warning: These 1 values could not be coerced to a valid MO code: "doylei". See mo_failures() to review them.
#> [1] NA

mo_fullname("K. pneu rh")     # "Klebsiella pneumoniae rhinoscleromatis"
#> [1] "Klebsiella pneumoniae rhinoscleromatis"
mo_shortname("K. pneu rh")    # "K. pneumoniae"
#> [1] "K. pneumoniae"


# Becker classification, see ?as.mo
mo_fullname("S. epi")                     # "Staphylococcus epidermidis"
#> [1] "Staphylococcus epidermidis"
mo_fullname("S. epi", Becker = TRUE)      # "Coagulase Negative Staphylococcus (CoNS)"
#> [1] "Coagulase-negatieve Staphylococcus (CNS)"
mo_shortname("S. epi")                    # "S. epidermidis"
#> [1] "S. epidermidis"
mo_shortname("S. epi", Becker = TRUE)     # "CoNS"
#> [1] "CNS"

# Lancefield classification, see ?as.mo
mo_fullname("S. pyo")                     # "Streptococcus pyogenes"
#> [1] "Streptococcus pyogenes"
mo_fullname("S. pyo", Lancefield = TRUE)  # "Streptococcus group A"
#> [1] "Streptococcus groep A"
mo_shortname("S. pyo")                    # "S. pyogenes"
#> [1] "S. pyogenes"
mo_shortname("S. pyo", Lancefield = TRUE) # "GAS" ('Group A streptococci')
#> [1] "GAS"


# Language support for German, Dutch, Spanish, Portuguese, Italian and French
mo_gramstain("E. coli", language = "de")  # "Gramnegativ"
#> [1] "Gramnegativ"
mo_gramstain("E. coli", language = "nl")  # "Gram-negatief"
#> [1] "Gram-negatief"
mo_gramstain("E. coli", language = "es")  # "Gram negativo"
#> [1] "Gram negativo"

# mo_type is equal to mo_kingdom, but mo_kingdom will remain official
mo_kingdom("E. coli")                     # "Bacteria" on a German system
#> [1] "Bacteria"
mo_type("E. coli")                        # "Bakterien" on a German system
#> [1] "Bacteriën"
mo_type("E. coli")                        # "Bacteria" on an English system
#> [1] "Bacteriën"

mo_fullname("S. pyogenes",
            Lancefield = TRUE,
            language = "de")              # "Streptococcus Gruppe A"
#> [1] "Streptococcus Gruppe A"
mo_fullname("S. pyogenes",
            Lancefield = TRUE,
            language = "nl")              # "Streptococcus groep A"
#> [1] "Streptococcus groep A"


# Get a list with the complete taxonomy (subkingdom to subspecies)
mo_taxonomy("E. coli")
#> $kingdom
#> [1] "Bacteria"
#> 
#> $subkingdom
#> [1] "Negibacteria"
#> 
#> $phylum
#> [1] "Proteobacteria"
#> 
#> $class
#> [1] "Gammaproteobacteria"
#> 
#> $order
#> [1] "Enterobacteriales"
#> 
#> $family
#> [1] "Enterobacteriaceae"
#> 
#> $genus
#> [1] "Escherichia"
#> 
#> $species
#> [1] "coli"
#> 
#> $subspecies
#> [1] NA
#>