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Data Set with 4 972 Common Microorganism Codes

Source: R/data.R
microorganisms.codes.Rd

A data set containing commonly used codes for microorganisms, from laboratory systems and WHONET. Define your own with set_mo_source(). They will all be searched when using as.mo() and consequently all the mo_* functions.

Usage

microorganisms.codes

Format

A tibble with 4 972 observations and 2 variables:

  • code
    Commonly used code of a microorganism. This is a unique identifier.

  • mo
    ID of the microorganism in the microorganisms data set

Details

Like all data sets in this package, this data set is publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. Please visit our website for the download links. The actual files are of course available on our GitHub repository.

See also

as.mo() microorganisms

Examples

microorganisms.codes
#> # A tibble: 4,972 × 2
#>    code  mo               
#>    <chr> <mo>             
#>  1 1011  B_GRAMP          
#>  2 1012  B_GRAMP          
#>  3 1013  B_GRAMN          
#>  4 1014  B_GRAMN          
#>  5 1015  F_YEAST          
#>  6 103   B_ESCHR_COLI     
#>  7 104   B_SLMNL_ENTR_ENTR
#>  8 1100  B_STRPT          
#>  9 1101  B_STRPT_VIRI     
#> 10 1102  B_STRPT_HAEM     
#> # ℹ 4,962 more rows

# 'ECO' or 'eco' is the WHONET code for E. coli:
microorganisms.codes[microorganisms.codes$code == "ECO", ]
#> # A tibble: 1 × 2
#>   code  mo          
#>   <chr> <mo>        
#> 1 ECO   B_ESCHR_COLI

# and therefore, 'eco' will be understood as E. coli in this package:
mo_info("eco")
#> $mo
#> [1] "B_ESCHR_COLI"
#> 
#> $kingdom
#> [1] "Bacteria"
#> 
#> $phylum
#> [1] "Pseudomonadota"
#> 
#> $class
#> [1] "Gammaproteobacteria"
#> 
#> $order
#> [1] "Enterobacterales"
#> 
#> $family
#> [1] "Enterobacteriaceae"
#> 
#> $genus
#> [1] "Escherichia"
#> 
#> $species
#> [1] "coli"
#> 
#> $subspecies
#> [1] ""
#> 
#> $status
#> [1] "accepted"
#> 
#> $synonyms
#> NULL
#> 
#> $gramstain
#> [1] "Gram-negative"
#> 
#> $oxygen_tolerance
#> [1] "facultative anaerobe"
#> 
#> $url
#> [1] "https://lpsn.dsmz.de/species/escherichia-coli"
#> 
#> $ref
#> [1] "Castellani et al., 1919"
#> 
#> $snomed
#>  [1] "1095001000112106" "715307006"        "737528008"        "416989002"       
#>  [5] "116397003"        "414097009"        "414098004"        "414099007"       
#>  [9] "414100004"        "116395006"        "735270003"        "116396007"       
#> [13] "83285000"         "116394005"        "112283007"        "710886005"       
#> [17] "710887001"        "710888006"        "710889003"        "414132004"       
#> [21] "721892009"        "416812001"        "416740004"        "417216001"       
#> [25] "457541006"        "710253004"        "416530004"        "417189006"       
#> [29] "409800005"        "713925008"        "444771000124108"  "838549008"       
#> 
#> $lpsn
#> [1] "776057"
#> 
#> $gbif
#> [1] "11286021"
#> 
#> $group_members
#> character(0)
#> 

# works for all AMR functions:
mo_is_intrinsic_resistant("eco", ab = "vancomycin")
#> [1] TRUE