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@@ -10,115 +10,270 @@ possible to use microbial abbreviations, codes and names as input. See
## Usage
``` r
mo_name(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_name(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_fullname(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_fullname(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_shortname(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_shortname(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_subspecies(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_subspecies(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_species(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_species(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_genus(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_genus(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_family(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_family(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_order(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_order(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_class(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_class(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_phylum(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_phylum(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_kingdom(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_kingdom(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_domain(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_domain(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_type(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_type(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_status(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_status(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_pathogenicity(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_pathogenicity(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_gramstain(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_gramstain(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
add_morphology = FALSE,
...
)
mo_is_gram_negative(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_is_gram_negative(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_is_gram_positive(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_is_gram_positive(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_is_yeast(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_is_yeast(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_is_intrinsic_resistant(x, ab, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_is_intrinsic_resistant(
x,
ab,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_oxygen_tolerance(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_oxygen_tolerance(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_is_anaerobic(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_is_anaerobic(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_snomed(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_morphology(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_ref(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_snomed(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_authors(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_ref(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_year(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_authors(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_lpsn(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_year(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_mycobank(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_lpsn(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_gbif(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_mycobank(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_rank(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_gbif(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_taxonomy(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_rank(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_synonyms(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_taxonomy(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_synonyms(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_current(x, language = get_AMR_locale(), ...)
mo_group_members(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_group_members(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_info(x, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_info(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_url(x, open = FALSE, language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_url(
x,
open = FALSE,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_property(x, property = "fullname", language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
mo_property(
x,
property = "fullname",
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
```
## Arguments
@@ -160,6 +315,13 @@ mo_property(x, property = "fullname", language = get_AMR_locale(),
[`as.mo()`](https://amr-for-r.org/reference/as.mo.md), such as
'minimum_matching_score', 'ignore_pattern', and 'remove_from_input'.
- add_morphology:
a [logical](https://rdrr.io/r/base/logical.html) to indicate whether
the morphology (from `mo_morphology()`) should be added to the Gram
stain result, e.g. `"Gram-negative rods"` instead of
`"Gram-negative"`. The default is `FALSE`.
- ab:
Any (vector of) text that can be coerced to a valid antibiotic drug
@@ -174,126 +336,160 @@ mo_property(x, property = "fullname", language = get_AMR_locale(),
One of the column names of the
[microorganisms](https://amr-for-r.org/reference/microorganisms.md)
data set: `"mo"`, `"fullname"`, `"status"`, `"kingdom"`, `"phylum"`,
`"class"`, `"order"`, `"family"`, `"genus"`, `"species"`,
`"subspecies"`, `"rank"`, `"ref"`, `"oxygen_tolerance"`, `"source"`,
`"lpsn"`, `"lpsn_parent"`, `"lpsn_renamed_to"`, `"mycobank"`,
`"mycobank_parent"`, `"mycobank_renamed_to"`, `"gbif"`,
`"gbif_parent"`, `"gbif_renamed_to"`, `"prevalence"`, or `"snomed"`,
or must be `"shortname"`.
data set: `"mo"`, `"fullname"`, `"status"`, `"domain"`, `"kingdom"`,
`"phylum"`, `"class"`, `"order"`, `"family"`, `"genus"`, `"species"`,
`"subspecies"`, `"rank"`, `"ref"`, `"oxygen_tolerance"`,
`"morphology"`, `"source"`, `"lpsn"`, `"lpsn_parent"`,
`"lpsn_renamed_to"`, `"mycobank"`, `"mycobank_parent"`,
`"mycobank_renamed_to"`, `"gbif"`, `"gbif_parent"`,
`"gbif_renamed_to"`, `"prevalence"`, or `"snomed"`, or must be
`"shortname"`.
## Value
\- An \[integer\] in case of \[mo_year()\] - An \[ordered
factor\]\[factor\] in case of \[mo_pathogenicity()\] - A \[list\] in
case of \[mo_taxonomy()\], \[mo_synonyms()\], \[mo_snomed()\], and
\[mo_info()\] - A \[logical\] in case of \[mo_is_anaerobic()\],
\[mo_is_gram_negative()\], \[mo_is_gram_positive()\],
\[mo_is_intrinsic_resistant()\], and \[mo_is_yeast()\] - A named
\[character\] in case of \[mo_synonyms()\] and \[mo_url()\] - A
\[character\] in all other cases
- An [integer](https://rdrr.io/r/base/integer.html) in case of
`mo_year()`
- An [ordered factor](https://rdrr.io/pkg/data.table/man/fctr.html) in
case of `mo_pathogenicity()`
- A [list](https://rdrr.io/r/base/list.html) in case of `mo_taxonomy()`,
`mo_synonyms()`, `mo_snomed()`, and `mo_info()`
- A [logical](https://rdrr.io/r/base/logical.html) in case of
`mo_is_anaerobic()`, `mo_is_gram_negative()`, `mo_is_gram_positive()`,
`mo_is_intrinsic_resistant()`, and `mo_is_yeast()`
- A named [character](https://rdrr.io/r/base/character.html) in case of
`mo_synonyms()` and `mo_url()`
- A [character](https://rdrr.io/r/base/character.html) in all other
cases
## Details
All functions will, at default, \*\*not\*\* keep old taxonomic
properties, as synonyms are automatically replaced with the current
taxonomy. Take for example \*Enterobacter aerogenes\*, which was
initially named in 1960 but renamed to \*Klebsiella aerogenes\* in
2017: - \`mo_genus("Enterobacter aerogenes")\` will return
\`"Klebsiella"\` (with a note about the renaming) -
\`mo_genus("Enterobacter aerogenes", keep_synonyms = TRUE)\` will return
\`"Enterobacter"\` (with a once-per-session warning that the name is
outdated) - \`mo_ref("Enterobacter aerogenes")\` will return \`"Tindall
et al., 2017"\` (with a note about the renaming) -
\`mo_ref("Enterobacter aerogenes", keep_synonyms = TRUE)\` will return
\`"Hormaeche et al., 1960"\` (with a once-per-session warning that the
name is outdated)
All functions will, at default, **not** keep old taxonomic properties,
as synonyms are automatically replaced with the current taxonomy. Take
for example *Enterobacter aerogenes*, which was initially named in 1960
but renamed to *Klebsiella aerogenes* in 2017:
The short name (\[mo_shortname()\]) returns the first character of the
genus and the full species, such as \`"E. coli"\`, for species and
- `mo_genus("Enterobacter aerogenes")` will return `"Klebsiella"` (with
a note about the renaming)
- `mo_genus("Enterobacter aerogenes", keep_synonyms = TRUE)` will return
`"Enterobacter"` (with a once-per-session warning that the name is
outdated)
- `mo_ref("Enterobacter aerogenes")` will return
`"Tindall et al., 2017"` (with a note about the renaming)
- `mo_ref("Enterobacter aerogenes", keep_synonyms = TRUE)` will return
`"Hormaeche et al., 1960"` (with a once-per-session warning that the
name is outdated)
`mo_ref()` returns the abbreviated authority of the nomenclatural act
that created the queried name combination. When `keep_synonyms = FALSE`
(default), this is the authority of the currently accepted name. When
`keep_synonyms = TRUE`, this is the authority under which the queried
(possibly outdated) name was published. Emendations (changes to the
species description without a name change) are not reflected; only the
combination or original description authority is returned.
The short name (`mo_shortname()`) returns the first character of the
genus and the full species, such as `"E. coli"`, for species and
subspecies. Exceptions are abbreviations of staphylococci (such as
\*"CoNS"\*, Coagulase-Negative Staphylococci) and beta-haemolytic
streptococci (such as \*"GBS"\*, Group B Streptococci). Please bear in
mind that e.g. \*E. coli\* could mean \*Escherichia coli\* (kingdom of
Bacteria) as well as \*Entamoeba coli\* (kingdom of Protozoa). Returning
to the full name will be done using \[as.mo()\] internally, giving
priority to bacteria and human pathogens, i.e. \`"E. coli"\` will be
considered \*Escherichia coli\*. As a result,
\`mo_fullname(mo_shortname("Entamoeba coli"))\` returns \`"Escherichia
coli"\`.
*"CoNS"*, Coagulase-Negative Staphylococci) and beta-haemolytic
streptococci (such as *"GBS"*, Group B Streptococci). Please bear in
mind that e.g. *E. coli* could mean *Escherichia coli* (kingdom of
Bacteria) as well as *Entamoeba coli* (kingdom of Protozoa). Returning
to the full name will be done using
[`as.mo()`](https://amr-for-r.org/reference/as.mo.md) internally, giving
priority to bacteria and human pathogens, i.e. `"E. coli"` will always
be considered *Escherichia coli*. As a result,
`mo_fullname(mo_shortname("Entamoeba coli"))` returns
`"Escherichia coli"`.
Since the top-level of the taxonomy is sometimes referred to as
'kingdom' and sometimes as 'domain', the functions \[mo_kingdom()\] and
\[mo_domain()\] return the exact same results.
Following the formal introduction of the new kingdom rank into
prokaryotic nomenclature in 2024
([doi:10.1099/ijsem.0.006242](https://doi.org/10.1099/ijsem.0.006242) ),
`mo_kingdom()` and `mo_domain()` return different results for bacteria
and archaea: `mo_kingdom()` returns the new formal kingdom (e.g.
"Pseudomonadati", "Bacillati"), while `mo_domain()` returns the new
domain (e.g. "Bacteria", "Archaea"). For non-prokaryotic organisms, both
functions return identical results.
Determination of human pathogenicity (\[mo_pathogenicity()\]) is
strongly based on Bartlett \*et al.\* (2022,
Determination of human pathogenicity (`mo_pathogenicity()`) is strongly
based on Bartlett *et al.* (2022,
[doi:10.1099/mic.0.001269](https://doi.org/10.1099/mic.0.001269) ). This
function returns a \[factor\] with the levels \*Pathogenic\*,
\*Potentially pathogenic\*, \*Non-pathogenic\*, and \*Unknown\*.
function returns a
[factor](https://rdrr.io/pkg/data.table/man/fctr.html) with the levels
*Pathogenic*, *Potentially pathogenic*, *Non-pathogenic*, and *Unknown*.
Determination of the Gram stain (\[mo_gramstain()\]) will be based on
the taxonomic kingdom and phylum. Originally, Cavalier-Smith defined the
so-called subkingdoms Negibacteria and Posibacteria (2002, \[PMID
11837318\](https://pubmed.ncbi.nlm.nih.gov/11837318/)), and only
Determination of the Gram stain (`mo_gramstain()` is based on the
taxonomic kingdom and phylum. Originally, Cavalier-Smith defined the
so-called subkingdoms Negibacteria and Posibacteria (2002, [PMID
11837318](https://pubmed.ncbi.nlm.nih.gov/11837318/)), and only
considered these phyla as Posibacteria: Actinobacteria, Chloroflexi,
Firmicutes, and Tenericutes. These phyla were later renamed to
Actinomycetota, Chloroflexota, Bacillota, and Mycoplasmatota (2021,
\[PMID 34694987\](https://pubmed.ncbi.nlm.nih.gov/34694987/)). Bacteria
in these phyla are considered Gram-positive in this \`AMR\` package,
except for members of the class Negativicutes (within phylum Bacillota)
which are Gram-negative. All other bacteria are considered
Gram-negative. Species outside the kingdom of Bacteria will return a
value \`NA\`. Functions \[mo_is_gram_negative()\] and
\[mo_is_gram_positive()\] always return \`TRUE\` or \`FALSE\` (or \`NA\`
when the input is \`NA\` or the MO code is \`UNKNOWN\`), thus always
return \`FALSE\` for species outside the taxonomic kingdom of Bacteria.
[PMID 34694987](https://pubmed.ncbi.nlm.nih.gov/34694987/)). Bacteria in
these phyla are considered Gram-positive in this `AMR` package, except
for members of the class Negativicutes (within phylum Bacillota) which
are Gram-negative. All other bacteria are considered Gram-negative.
Species outside the kingdom of Bacteria will return a value `NA`.
Functions `mo_is_gram_negative()` and `mo_is_gram_positive()` always
return `TRUE` or `FALSE` (or `NA` when the input is `NA` or the MO code
is `UNKNOWN`), thus always return `FALSE` for species outside the
taxonomic kingdom of Bacteria.
Determination of yeasts (\[mo_is_yeast()\]) will be based on the
taxonomic kingdom and class. \*Budding yeasts\* are yeasts that
reproduce asexually through a process called budding, where a new cell
develops from a small protrusion on the parent cell. Taxonomically,
these are members of the phylum Ascomycota, class Saccharomycetes (also
called Hemiascomycetes) or Pichiomycetes. \*True yeasts\* quite
specifically refers to yeasts in the underlying order Saccharomycetales
(such as \*Saccharomyces cerevisiae\*). Thus, for all microorganisms
that are member of the taxonomic class Saccharomycetes or Pichiomycetes,
the function will return \`TRUE\`. It returns \`FALSE\` otherwise (or
\`NA\` when the input is \`NA\` or the MO code is \`UNKNOWN\`).
Determination of yeasts (`mo_is_yeast()`) is based on the taxonomic
kingdom and class. *Budding yeasts* are yeasts that reproduce asexually
through a process called budding, where a new cell develops from a small
protrusion on the parent cell. Taxonomically, these are members of the
phylum Ascomycota, class Saccharomycetes (also called Hemiascomycetes)
or Pichiomycetes. *True yeasts* quite specifically refers to yeasts in
the underlying order Saccharomycetales (such as *Saccharomyces
cerevisiae*). Thus, for all microorganisms that are member of the
taxonomic class Saccharomycetes or Pichiomycetes, the function will
return `TRUE`. It returns `FALSE` otherwise (or `NA` when the input is
`NA` or the MO code is `UNKNOWN`).
Determination of intrinsic resistance (\[mo_is_intrinsic_resistant()\])
will be based on the \[intrinsic_resistant\] data set, which is based on
\`r
format_eucast_version_nr(names(EUCAST_VERSION_EXPECTED_PHENOTYPES\[1\]))\`.
The \[mo_is_intrinsic_resistant()\] function can be vectorised over both
argument \`x\` (input for microorganisms) and \`ab\` (input for
Determination of intrinsic resistance (`mo_is_intrinsic_resistant()`) is
based on the
[intrinsic_resistant](https://amr-for-r.org/reference/intrinsic_resistant.md)
data set, which is based on ['EUCAST Expected Resistant Phenotypes'
v1.2](https://www.eucast.org/bacteria/important-additional-information/expert-rules/)
(2023). The `mo_is_intrinsic_resistant()` function can be vectorised
over both argument `x` (input for microorganisms) and `ab` (input for
antimicrobials).
Determination of bacterial oxygen tolerance (\[mo_oxygen_tolerance()\])
will be based on BacDive, see \*Source\*. The function
\[mo_is_anaerobic()\] only returns \`TRUE\` if the oxygen tolerance is
\`"anaerobe"\`, indicting an obligate anaerobic species or genus. It
always returns \`FALSE\` for species outside the taxonomic kingdom of
Bacteria.
Determination of both bacterial oxygen tolerance
(`mo_oxygen_tolerance()`) and morphology (`mo_morphology()`) are based
on BacDive, see *Source*. The function `mo_is_anaerobic()` only returns
`TRUE` if the oxygen tolerance is `"anaerobe"`, indicating an obligate
anaerobic species or genus. It always returns `FALSE` for species
outside the taxonomic kingdom of Bacteria.
The function \[mo_url()\] will return the direct URL to the online
The function `mo_url()` will return the direct URL to the online
database entry, which also shows the scientific reference of the
concerned species. \[This MycoBank URL\](\`r
TAXONOMY_VERSION\$MycoBank\$url\`) will be used for fungi wherever
available , \[this LPSN URL\](\`r TAXONOMY_VERSION\$MycoBank\$url\`) for
bacteria wherever available, and \[this GBIF link\](\`r
TAXONOMY_VERSION\$GBIF\$url\`) otherwise.
concerned species. [This MycoBank URL](https://www.mycobank.org) is used
for fungi wherever available , [this LPSN URL](https://www.mycobank.org)
for bacteria wherever available, and [this GBIF
link](https://www.gbif.org) otherwise.
SNOMED codes (\[mo_snomed()\]) was last updated on \`r
documentation_date(TAXONOMY_VERSION\$SNOMED\$accessed_date)\`. See
\*Source\* and the \[microorganisms\] data set for more info.
SNOMED codes (`mo_snomed()`) was last updated on 16th of July, 2024. See
*Source* and the
[microorganisms](https://amr-for-r.org/reference/microorganisms.md) data
set for more info.
Old taxonomic names (so-called 'synonyms') can be retrieved with
\[mo_synonyms()\] (which will have the scientific reference as
\[name\]\[base::names()\]), the current taxonomic name can be retrieved
with \[mo_current()\]. Both functions return full names.
`mo_synonyms()` (which will have the scientific reference as
[name](https://rdrr.io/r/base/names.html)), the current taxonomic name
can be retrieved with `mo_current()`. Both functions return full names.
All output \[will be translated\]\[translate\] where possible.
All output [will be
translated](https://amr-for-r.org/reference/translate.md) where
possible.
## Matching Score for Microorganisms
@@ -310,26 +506,28 @@ page](https://amr-for-r.org/reference/mo_matching_score.md).
104(3), 1-31;
[doi:10.18637/jss.v104.i03](https://doi.org/10.18637/jss.v104.i03)
- 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.
- Freese, HM *et al.* (2026). **TYGS and LPSN in 2025: a Global Core
Biodata Resource for genome-based classification and nomenclature of
prokaryotes within DSMZ Digital Diversity.** Nucleic Acids Research,
54, D884–D891;
[doi:10.1093/nar/gkaf1110](https://doi.org/10.1093/nar/gkaf1110) .
Accessed from <https://lpsn.dsmz.de> on 7th of May, 2026.
- 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.
. Accessed from <https://www.mycobank.org> on 7th of May, 2026.
- 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.
- Banki, O. *et al.* (2026). Catalogue of Life (2026-04-18 XR).
Catalogue of Life Foundation, Amsterdam, Netherlands.
[doi:10.48580/dgxjw](https://doi.org/10.48580/dgxjw) . Accessed from
<https://www.gbif.org> on 7th of May, 2026.
- 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.
Accessed from <https://bacdive.dsmz.de> on 7th of May, 2026.
- Public Health Information Network Vocabulary Access and Distribution
System (PHIN VADS). US Edition of SNOMED CT from 1 September 2020.
@@ -367,7 +565,7 @@ Data set
# taxonomic tree -----------------------------------------------------------
mo_kingdom("Klebsiella pneumoniae")
#> [1] "Bacteria"
#> [1] "Pseudomonadati"
mo_phylum("Klebsiella pneumoniae")
#> [1] "Pseudomonadota"
mo_class("Klebsiella pneumoniae")
@@ -396,11 +594,15 @@ mo_shortname("Klebsiella pneumoniae")
# other properties ---------------------------------------------------------
mo_morphology("Klebsiella pneumoniae")
#> [1] "Rods"
mo_gramstain("Klebsiella pneumoniae")
#> [1] "Gram-negative"
mo_gramstain("Klebsiella pneumoniae", add_morphology = TRUE)
#> [1] "Gram-negative rods"
mo_pathogenicity("Klebsiella pneumoniae")
#> [1] Pathogenic
#> Levels: Pathogenic < Potentially pathogenic < Non-pathogenic < Unknown
mo_gramstain("Klebsiella pneumoniae")
#> [1] "Gram-negative"
mo_snomed("Klebsiella pneumoniae")
#> [[1]]
#> [1] "1098101000112102" "446870005" "1098201000112108" "409801009"
@@ -461,7 +663,7 @@ mo_synonyms("Klebsiella aerogenes")
mo_lpsn("Klebsiella aerogenes")
#> [1] "777146"
mo_gbif("Klebsiella aerogenes")
#> [1] "9281703"
#> [1] "CSHB4"
mo_mycobank("Candida albicans")
#> [1] "256187"
mo_mycobank("Candida krusei")
@@ -539,11 +741,11 @@ mo_gramstain("Klebsiella pneumoniae", language = "uk") # Ukrainian
# mo_type is equal to mo_kingdom, but mo_kingdom will remain untranslated
mo_kingdom("Klebsiella pneumoniae")
#> [1] "Bacteria"
#> [1] "Pseudomonadati"
mo_type("Klebsiella pneumoniae")
#> [1] "Bacteria"
mo_kingdom("Klebsiella pneumoniae", language = "zh") # Chinese, no effect
#> [1] "Bacteria"
#> [1] "Pseudomonadati"
mo_type("Klebsiella pneumoniae", language = "zh") # Chinese, translated
#> [1] "细菌"
@@ -616,9 +818,12 @@ if (require("dplyr")) {
# get a list with the complete taxonomy (from kingdom to subspecies)
mo_taxonomy("Klebsiella pneumoniae")
#> $kingdom
#> $domain
#> [1] "Bacteria"
#>
#> $kingdom
#> [1] "Pseudomonadati"
#>
#> $phylum
#> [1] "Pseudomonadota"
#>
@@ -650,9 +855,12 @@ mo_info("Klebsiella pneumoniae")
#> $rank
#> [1] "species"
#>
#> $kingdom
#> $domain
#> [1] "Bacteria"
#>
#> $kingdom
#> [1] "Pseudomonadati"
#>
#> $phylum
#> [1] "Pseudomonadota"
#>
@@ -683,6 +891,9 @@ mo_info("Klebsiella pneumoniae")
#> $gramstain
#> [1] "Gram-negative"
#>
#> $morphology
#> [1] "Rods"
#>
#> $oxygen_tolerance
#> [1] "facultative anaerobe"
#>
@@ -703,7 +914,7 @@ mo_info("Klebsiella pneumoniae")
#> [1] NA
#>
#> $gbif
#> [1] "3221874"
#> [1] "CSHCH"
#>
#> $group_members
#> character(0)