# Data Set with 6 036 Common Microorganism Codes

A data set containing commonly used codes for microorganisms, from
laboratory systems and [WHONET](https://whonet.org). Define your own
with [`set_mo_source()`](https://amr-for-r.org/reference/mo_source.md).
They will all be searched when using
[`as.mo()`](https://amr-for-r.org/reference/as.mo.md) and consequently
all the [`mo_*`](https://amr-for-r.org/reference/mo_property.md)
functions.

## Usage

``` r
microorganisms.codes
```

## Format

A [tibble](https://tibble.tidyverse.org/reference/tibble.html) with 6
036 observations and 2 variables:

- `code`  
  Commonly used code of a microorganism. ***This is a unique
  identifier.***

- `mo`  
  ID of the microorganism in the
  [microorganisms](https://amr-for-r.org/reference/microorganisms.md)
  data set

## 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

[`as.mo()`](https://amr-for-r.org/reference/as.mo.md)
[microorganisms](https://amr-for-r.org/reference/microorganisms.md)

## Examples

``` r
microorganisms.codes
#> # A tibble: 6,036 × 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 6,026 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"
#> 
#> $rank
#> [1] "species"
#> 
#> $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"
#> 
#> $mycobank
#> [1] NA
#> 
#> $gbif
#> [1] "11286021"
#> 
#> $group_members
#> character(0)
#> 

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