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# Data Set with 78 679 Taxonomic Records of Microorganisms
A data set containing the full microbial taxonomy (**last updated: June
24th, 2024**) of six kingdoms. This data set is the backbone of this
`AMR` package. MO codes can be looked up using
[`as.mo()`](https://amr-for-r.org/reference/as.mo.md) and microorganism
properties can be looked up using any of the
[`mo_*`](https://amr-for-r.org/reference/mo_property.md) functions.
This data set is carefully crafted, yet made 100% reproducible from
public and authoritative taxonomic sources (using [this
script](https://github.com/msberends/AMR/blob/main/data-raw/_reproduction_scripts/reproduction_of_microorganisms.R)),
namely: *List of Prokaryotic names with Standing in Nomenclature (LPSN)*
for bacteria, *MycoBank* for fungi, and *Global Biodiversity Information
Facility (GBIF)* for all others taxons.
## Usage
``` r
microorganisms
```
## Format
A [tibble](https://tibble.tidyverse.org/reference/tibble.html) with 78
679 observations and 26 variables:
- `mo`
ID of microorganism as used by this package. ***This is a unique
identifier.***
- `fullname`
Full name, like `"Escherichia coli"`. For the taxonomic ranks genus,
species and subspecies, this is the 'pasted' text of genus, species,
and subspecies. For all taxonomic ranks higher than genus, this is the
name of the taxon. ***This is a unique identifier.***
- `status`
Status of the taxon, either "accepted", "not validly published",
"synonym", or "unknown"
- `kingdom`, `phylum`, `class`, `order`, `family`, `genus`, `species`,
`subspecies`
Taxonomic rank of the microorganism. Note that for fungi, *phylum* is
equal to their taxonomic *division*. Also, for fungi, *subkingdom* and
*subdivision* were left out since they do not occur in the bacterial
taxonomy.
- `rank`
Text of the taxonomic rank of the microorganism, such as `"species"`
or `"genus"`
- `ref`
Author(s) and year of related scientific publication. This contains
only the *first surname* and year of the *latest* authors, e.g.
"Wallis *et al.* 2006 *emend.* Smith and Jones 2018" becomes "Smith
*et al.*, 2018". This field is directly retrieved from the source
specified in the column `source`. Moreover, accents were removed to
comply with CRAN that only allows ASCII characters.
- `oxygen_tolerance`
Oxygen tolerance, either "aerobe", "anaerobe",
"anaerobe/microaerophile", "facultative anaerobe", "likely facultative
anaerobe", or "microaerophile". These data were retrieved from BacDive
(see *Source*). Items that contain "likely" are missing from BacDive
and were extrapolated from other species within the same genus to
guess the oxygen tolerance. Currently 68.3% of all ~39 000 bacteria in
the data set contain an oxygen tolerance.
- `source`
Either "GBIF", "LPSN", "Manually added", "MycoBank", or "manually
added" (see *Source*)
- `lpsn`
Identifier ('Record number') of List of Prokaryotic names with
Standing in Nomenclature (LPSN). This will be the first/highest LPSN
identifier to keep one identifier per row. For example, *Acetobacter
ascendens* has LPSN Record number 7864 and 11011. Only the first is
available in the `microorganisms` data set. ***This is a unique
identifier***, though available for only ~33 000 records.
- `lpsn_parent`
LPSN identifier of the parent taxon
- `lpsn_renamed_to`
LPSN identifier of the currently valid taxon
- `mycobank`
Identifier ('MycoBank \#') of MycoBank. ***This is a unique
identifier***, though available for only ~19 000 records.
- `mycobank_parent`
MycoBank identifier of the parent taxon
- `mycobank_renamed_to`
MycoBank identifier of the currently valid taxon
- `gbif`
Identifier ('taxonID') of Global Biodiversity Information Facility
(GBIF). ***This is a unique identifier***, though available for only
~49 000 records.
- `gbif_parent`
GBIF identifier of the parent taxon
- `gbif_renamed_to`
GBIF identifier of the currently valid taxon
- `prevalence`
Prevalence of the microorganism based on Bartlett *et al.* (2022,
[doi:10.1099/mic.0.001269](https://doi.org/10.1099/mic.0.001269) ),
see
[`mo_matching_score()`](https://amr-for-r.org/reference/mo_matching_score.md)
for the full explanation
- `snomed`
Systematized Nomenclature of Medicine (SNOMED) code of the
microorganism, version of July 16th, 2024 (see *Source*). Use
[`mo_snomed()`](https://amr-for-r.org/reference/mo_property.md) to
retrieve it quickly, see
[`mo_property()`](https://amr-for-r.org/reference/mo_property.md).
## Source
Taxonomic entries were imported in this order of importance:
1. List of Prokaryotic names with Standing in Nomenclature (LPSN):
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.
2. MycoBank:
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.
3. Global Biodiversity Information Facility (GBIF):
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.
Furthermore, these sources were used for additional details:
- BacDive:
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.
- Systematized Nomenclature of Medicine - Clinical Terms (SNOMED-CT):
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).
Accessed from <https://www.cdc.gov/phin/php/phinvads/> on July 16th,
2024.
- Grimont *et al.* (2007). Antigenic Formulae of the Salmonella
Serovars, 9th Edition. WHO Collaborating Centre for Reference and
Research on *Salmonella* (WHOCC-SALM).
- Bartlett *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)
## Details
Please note that entries are only based on LPSN, MycoBank, and GBIF (see
below). Since these sources incorporate entries based on (recent)
publications in the International Journal of Systematic and Evolutionary
Microbiology (IJSEM), it can happen that the year of publication is
sometimes later than one might expect.
For example, *Staphylococcus pettenkoferi* was described for the first
time in Diagnostic Microbiology and Infectious Disease in 2002
([doi:10.1016/s0732-8893(02)00399-1](https://doi.org/10.1016/s0732-8893%2802%2900399-1)
), but it was not until 2007 that a publication in IJSEM followed
([doi:10.1099/ijs.0.64381-0](https://doi.org/10.1099/ijs.0.64381-0) ).
Consequently, the `AMR` package returns 2007 for
`mo_year("S. pettenkoferi")`.
## Included Taxa
Included taxonomic data from [LPSN](https://lpsn.dsmz.de),
[MycoBank](https://www.mycobank.org), and [GBIF](https://www.gbif.org)
are:
- All ~39 000 (sub)species from the kingdoms of Archaea and Bacteria
- ~28 000 species from the kingdom of Fungi. The kingdom of Fungi is a
very large taxon with almost 300,000 different (sub)species, of which
most are not microbial (but rather macroscopic, like mushrooms).
Because of this, not all fungi fit the scope of this package. Only
relevant fungi are covered (such as all species of *Aspergillus*,
*Candida*, *Cryptococcus*, *Histoplasma*, *Pneumocystis*,
*Saccharomyces* and *Trichophyton*).
- ~8 100 (sub)species from the kingdom of Protozoa
- ~1 600 (sub)species from 39 other relevant genera from the kingdom of
Animalia (such as *Strongyloides* and *Taenia*)
- All ~26 000 previously accepted names of all included (sub)species
(these were taxonomically renamed)
- The complete taxonomic tree of all included (sub)species: from kingdom
to subspecies
- The identifier of the parent taxons
- The year and first author of the related scientific publication
### Manual additions
For convenience, some entries were added manually:
- ~1 500 entries of *Salmonella*, such as the city-like serovars and
groups A to H
- 37 species groups (such as the beta-haemolytic *Streptococcus* groups
A to K, coagulase-negative *Staphylococcus* (CoNS), *Mycobacterium
tuberculosis* complex, etc.), of which the group compositions are
stored in the
[microorganisms.groups](https://amr-for-r.org/reference/microorganisms.groups.md)
data set
- 1 entry of *Blastocystis* (*B. hominis*), although it officially does
not exist (Noel *et al.* 2005, PMID 15634993)
- 1 entry of *Moraxella* (*M. catarrhalis*), which was formally named
*Branhamella catarrhalis* (Catlin, 1970) though this change was never
accepted within the field of clinical microbiology
- 8 other 'undefined' entries (unknown, unknown Gram-negatives, unknown
Gram-positives, unknown yeast, unknown fungus, and unknown anaerobic
Gram-pos/Gram-neg bacteria)
The syntax used to transform the original data to a cleansed R format,
can be [found
here](https://github.com/msberends/AMR/blob/main/data-raw/_reproduction_scripts/reproduction_of_microorganisms.R).
## 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),
[`mo_property()`](https://amr-for-r.org/reference/mo_property.md),
[microorganisms.groups](https://amr-for-r.org/reference/microorganisms.groups.md),
[microorganisms.codes](https://amr-for-r.org/reference/microorganisms.codes.md),
[intrinsic_resistant](https://amr-for-r.org/reference/intrinsic_resistant.md)
## Examples
``` r
microorganisms
#> # A tibble: 78,679 × 26
#> mo fullname status kingdom phylum class order family genus species
#> <mo> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 B_GRAMN (unknown … unkno… Bacter… (unkn… (unk… (unk… "(unk… (unk… "(unkn…
#> 2 B_GRAMP (unknown … unkno… Bacter… (unkn… (unk… (unk… "(unk… (unk… "(unkn…
#> 3 B_ANAER-NEG (unknown … unkno… Bacter… (unkn… (unk… (unk… "(unk… (unk… "(unkn…
#> 4 B_ANAER-POS (unknown … unkno… Bacter… (unkn… (unk… (unk… "(unk… (unk… "(unkn…
#> 5 B_ANAER (unknown … unkno… Bacter… (unkn… (unk… (unk… "(unk… (unk… "(unkn…
#> 6 F_FUNGUS (unknown … unkno… Fungi (unkn… (unk… (unk… "(unk… (unk… "(unkn…
#> 7 UNKNOWN (unknown … unkno… (unkno… (unkn… (unk… (unk… "(unk… (unk… "(unkn…
#> 8 P_PROTOZOAN (unknown … unkno… Protoz… (unkn… (unk… (unk… "(unk… (unk… "(unkn…
#> 9 F_YEAST (unknown … unkno… Fungi (unkn… (unk… (unk… "(unk… (unk… "(unkn…
#> 10 F_AABRN Aabaarnia unkno… Fungi Ascom… Leca… Ostr… "" Aaba… ""
#> # ℹ 78,669 more rows
#> # ℹ 16 more variables: subspecies <chr>, rank <chr>, ref <chr>,
#> # oxygen_tolerance <chr>, source <chr>, lpsn <chr>, lpsn_parent <chr>,
#> # lpsn_renamed_to <chr>, mycobank <chr>, mycobank_parent <chr>,
#> # mycobank_renamed_to <chr>, gbif <chr>, gbif_parent <chr>,
#> # gbif_renamed_to <chr>, prevalence <dbl>, snomed <list>
```
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