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reference/microorganisms.md
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# Data Set with 96 982 Taxonomic Records of Microorganisms
A data set containing the full microbial taxonomy (**last updated: 7th
of May, 2026**) of 15 kingdoms. This data set is the backbone of this
of May, 2026**) of seven domains. 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
@@ -69,7 +69,7 @@ A [tibble](https://tibble.tidyverse.org/reference/tibble.html) with 96
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
1.3784 × 10⁶% of all 2 bacteria in the data set contain an oxygen
59.5% of all ~46 000 bacteria in the data set contain an oxygen
tolerance.
- `morphology`
@@ -81,8 +81,8 @@ A [tibble](https://tibble.tidyverse.org/reference/tibble.html) with 96
(the HACEK group and beyond, such as *Haemophilus* and
*Acinetobacter*) are classified as such regardless of BacDive majority
vote. Items that contain "likely" are missing from BacDive and were
extrapolated from other species within the same genus. Currently
1.3232 × 10⁶% of all 2 bacteria in the data set contain a morphology.
extrapolated from other species within the same genus. Currently 57.1%
of all ~46 000 bacteria in the data set contain a morphology.
- `source`
Either `"GBIF"`, `"LPSN"`, `"MycoBank"`, or `"manually added"` (see
@@ -159,7 +159,7 @@ Included taxonomic data from [LPSN](https://lpsn.dsmz.de),
[MycoBank](https://www.mycobank.org), and [GBIF](https://www.gbif.org)
are:
- All 2 (sub)species from the kingdoms of Archaea and Bacteria
- All ~46 000 (sub)species from the domains of Archaea and Bacteria
- ~36 000 species from the kingdom of Fungi. The kingdom of Fungi is a
very large taxon with almost 300,000 different (sub)species, of which
@@ -177,7 +177,7 @@ are:
- All ~31 000 previously accepted names of all included (sub)species
(these were taxonomically renamed)
- The complete taxonomic tree of all included (sub)species: from kingdom
- The complete taxonomic tree of all included (sub)species: from domain
to subspecies
- The identifier of the parent taxons