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+# 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
+```