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@@ -1,7 +1,7 @@
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# Data Set with 78 679 Taxonomic Records of Microorganisms
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# Data Set with 96 982 Taxonomic Records of Microorganisms
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A data set containing the full microbial taxonomy (**last updated: June
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24th, 2024**) of six kingdoms. This data set is the backbone of this
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A data set containing the full microbial taxonomy (**last updated: 7th
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of May, 2026**) of 15 kingdoms. This data set is the backbone of this
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`AMR` package. MO codes can be looked up using
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[`as.mo()`](https://amr-for-r.org/reference/as.mo.md) and microorganism
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properties can be looked up using any of the
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@@ -12,7 +12,7 @@ public and authoritative taxonomic sources (using [this
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script](https://github.com/msberends/AMR/blob/main/data-raw/_reproduction_scripts/reproduction_of_microorganisms.R)),
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namely: *List of Prokaryotic names with Standing in Nomenclature (LPSN)*
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for bacteria, *MycoBank* for fungi, and *Global Biodiversity Information
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Facility (GBIF)* for all others taxons.
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Facility (GBIF), via Catalogue of Life (COL)* for all others taxons.
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## Usage
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@@ -22,8 +22,8 @@ microorganisms
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## Format
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A [tibble](https://tibble.tidyverse.org/reference/tibble.html) with 78
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679 observations and 26 variables:
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A [tibble](https://tibble.tidyverse.org/reference/tibble.html) with 96
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982 observations and 28 variables:
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- `mo`
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ID of microorganism as used by this package. ***This is a unique
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@@ -36,27 +36,31 @@ A [tibble](https://tibble.tidyverse.org/reference/tibble.html) with 78
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name of the taxon. ***This is a unique identifier.***
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- `status`
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Status of the taxon, either `"accepted"`, `"not validly published"`,
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`"synonym"`, or `"unknown"`
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Status of the taxon, either `"accepted"`, `"synonym"`, or `"unknown"`
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- `kingdom`, `phylum`, `class`, `order`, `family`, `genus`, `species`,
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`subspecies`
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- `domain`, `kingdom`, `phylum`, `class`, `order`, `family`, `genus`,
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`species`, `subspecies`
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Taxonomic rank of the microorganism. Note that for fungi, *phylum* is
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equal to their taxonomic *division*. Also, for fungi, *subkingdom* and
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used for their taxonomic *division*. Also, for fungi, *subkingdom* and
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*subdivision* were left out since they do not occur in the bacterial
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taxonomy.
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taxonomy. For all species outside the domains of Bacteria and Archaea,
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the `domain` and `kingdom` are identical.
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- `rank`
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Text of the taxonomic rank of the microorganism, such as `"species"`
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or `"genus"`
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- `ref`
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Author(s) and year of related scientific publication. This contains
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only the *first surname* and year of the *latest* authors, e.g.
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"Wallis *et al.* 2006 *emend.* Smith and Jones 2018" becomes "Smith
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*et al.*, 2018". This field is directly retrieved from the source
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specified in the column `source`. Moreover, accents were removed to
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comply with CRAN that only allows ASCII characters.
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Abbreviated authority citation for the nomenclatural act that
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established the current name combination, following ICNP conventions.
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For species described in their current genus (*sp. nov.*), this is the
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original description author(s) and year. For species transferred to a
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different genus (*comb. nov.*), this is the reclassification author(s)
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and year. Emendations are excluded. For synonyms, this is the
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authority under which the synonym was originally published. This field
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is directly retrieved from the source specified in the column
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`source`. Diacritics were removed to comply with CRAN, that only
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allows ASCII characters.
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- `oxygen_tolerance`
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Oxygen tolerance, either `"aerobe"`, `"anaerobe"`,
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@@ -65,12 +69,24 @@ A [tibble](https://tibble.tidyverse.org/reference/tibble.html) with 78
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were retrieved from BacDive (see *Source*). Items that contain
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"likely" are missing from BacDive and were extrapolated from other
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species within the same genus to guess the oxygen tolerance. Currently
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68.3% of all ~39 000 bacteria in the data set contain an oxygen
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1.3784 × 10⁶% of all 2 bacteria in the data set contain an oxygen
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tolerance.
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- `morphology`
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Morphology (cell shape), either `"cocci"`, `"coccobacilli"`,
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`"filamentous"`, `"likely cocci"`, `"likely coccobacilli"`,
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`"likely filamentous"`, `"likely rods"`, `"likely spirilla"`,
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`"rods"`, `"spirilla"`, or NA. These data were retrieved from BacDive
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(see *Source*). Genera that are clinically established as coccobacilli
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(the HACEK group and beyond, such as *Haemophilus* and
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*Acinetobacter*) are classified as such regardless of BacDive majority
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vote. Items that contain "likely" are missing from BacDive and were
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extrapolated from other species within the same genus. Currently
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1.3232 × 10⁶% of all 2 bacteria in the data set contain a morphology.
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- `source`
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Either `"GBIF"`, `"LPSN"`, `"Manually added"`, `"MycoBank"`, or
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`"manually added"` (see *Source*)
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Either `"GBIF"`, `"LPSN"`, `"MycoBank"`, or `"manually added"` (see
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*Source*)
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- `lpsn`
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Identifier ('Record number') of List of Prokaryotic names with
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@@ -78,7 +94,7 @@ A [tibble](https://tibble.tidyverse.org/reference/tibble.html) with 78
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identifier to keep one identifier per row. For example, *Acetobacter
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ascendens* has LPSN Record number 7864 and 11011. Only the first is
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available in the `microorganisms` data set. ***This is a unique
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identifier***, though available for only ~33 000 records.
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identifier***, though available for only ~36 000 records.
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- `lpsn_parent`
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LPSN identifier of the parent taxon
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@@ -88,7 +104,7 @@ A [tibble](https://tibble.tidyverse.org/reference/tibble.html) with 78
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- `mycobank`
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Identifier ('MycoBank \#') of MycoBank. ***This is a unique
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identifier***, though available for only ~19 000 records.
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identifier***, though available for only ~25 000 records.
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- `mycobank_parent`
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MycoBank identifier of the parent taxon
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@@ -98,8 +114,8 @@ A [tibble](https://tibble.tidyverse.org/reference/tibble.html) with 78
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- `gbif`
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Identifier ('taxonID') of Global Biodiversity Information Facility
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(GBIF). ***This is a unique identifier***, though available for only
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~49 000 records.
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(GBIF), via Catalogue of Life (COL). ***This is a unique
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identifier***, though available for only ~79 000 records.
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- `gbif_parent`
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GBIF identifier of the parent taxon
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@@ -116,62 +132,11 @@ A [tibble](https://tibble.tidyverse.org/reference/tibble.html) with 78
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- `snomed`
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Systematized Nomenclature of Medicine (SNOMED) code of the
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microorganism, version of July 16th, 2024 (see *Source*). Use
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microorganism, version of 16th of July, 2024 (see *Source*). Use
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[`mo_snomed()`](https://amr-for-r.org/reference/mo_property.md) to
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retrieve it quickly, see
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[`mo_property()`](https://amr-for-r.org/reference/mo_property.md).
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## Source
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Taxonomic entries were imported in this order of importance:
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1. List of Prokaryotic names with Standing in Nomenclature (LPSN):
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Parte, AC *et al.* (2020). **List of Prokaryotic names with Standing
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in Nomenclature (LPSN) moves to the DSMZ.** International Journal of
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Systematic and Evolutionary Microbiology, 70, 5607-5612;
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[doi:10.1099/ijsem.0.004332](https://doi.org/10.1099/ijsem.0.004332)
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. Accessed from <https://lpsn.dsmz.de> on June 24th, 2024.
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2. MycoBank:
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Vincent, R *et al* (2013). **MycoBank gearing up for new horizons.**
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IMA Fungus, 4(2), 371-9;
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[doi:10.5598/imafungus.2013.04.02.16](https://doi.org/10.5598/imafungus.2013.04.02.16)
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. Accessed from <https://www.mycobank.org> on June 24th, 2024.
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3. Global Biodiversity Information Facility (GBIF):
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GBIF Secretariat (2023). GBIF Backbone Taxonomy. Checklist dataset
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[doi:10.15468/39omei](https://doi.org/10.15468/39omei) . Accessed
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from <https://www.gbif.org> on June 24th, 2024.
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Furthermore, these sources were used for additional details:
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- BacDive:
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Reimer, LC *et al.* (2022). ***BacDive* in 2022: the knowledge base
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for standardized bacterial and archaeal data.** Nucleic Acids Res.,
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50(D1):D741-D74;
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[doi:10.1093/nar/gkab961](https://doi.org/10.1093/nar/gkab961) .
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Accessed from <https://bacdive.dsmz.de> on July 16th, 2024.
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- Systematized Nomenclature of Medicine - Clinical Terms (SNOMED-CT):
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Public Health Information Network Vocabulary Access and Distribution
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System (PHIN VADS). US Edition of SNOMED CT from 1 September 2020.
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Value Set Name 'Microorganism', OID 2.16.840.1.114222.4.11.1009 (v12).
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Accessed from <https://www.cdc.gov/phin/php/phinvads/> on July 16th,
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2024.
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- Grimont *et al.* (2007). Antigenic Formulae of the Salmonella
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Serovars, 9th Edition. WHO Collaborating Centre for Reference and
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Research on *Salmonella* (WHOCC-SALM).
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- Bartlett *et al.* (2022). **A comprehensive list of bacterial
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pathogens infecting humans** *Microbiology* 168:001269;
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[doi:10.1099/mic.0.001269](https://doi.org/10.1099/mic.0.001269)
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## Details
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Please note that entries are only based on LPSN, MycoBank, and GBIF (see
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@@ -194,9 +159,9 @@ Included taxonomic data from [LPSN](https://lpsn.dsmz.de),
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[MycoBank](https://www.mycobank.org), and [GBIF](https://www.gbif.org)
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are:
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- All ~39 000 (sub)species from the kingdoms of Archaea and Bacteria
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- All 2 (sub)species from the kingdoms of Archaea and Bacteria
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- ~28 000 species from the kingdom of Fungi. The kingdom of Fungi is a
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- ~36 000 species from the kingdom of Fungi. The kingdom of Fungi is a
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very large taxon with almost 300,000 different (sub)species, of which
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most are not microbial (but rather macroscopic, like mushrooms).
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Because of this, not all fungi fit the scope of this package. Only
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@@ -204,12 +169,12 @@ are:
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*Candida*, *Cryptococcus*, *Histoplasma*, *Pneumocystis*,
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*Saccharomyces* and *Trichophyton*).
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- ~8 100 (sub)species from the kingdom of Protozoa
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- ~11 000 (sub)species from the kingdom of Protozoa
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- ~1 600 (sub)species from 39 other relevant genera from the kingdom of
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- ~2 000 (sub)species from ~60 other relevant genera from the kingdom of
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Animalia (such as *Strongyloides* and *Taenia*)
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- All ~26 000 previously accepted names of all included (sub)species
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- All ~31 000 previously accepted names of all included (sub)species
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(these were taxonomically renamed)
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- The complete taxonomic tree of all included (sub)species: from kingdom
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@@ -264,6 +229,60 @@ links](https://amr-for-r.org/articles/datasets.html), or explore the
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actual files in [our GitHub
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repository](https://github.com/msberends/AMR/tree/main/data-raw/datasets).
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## References
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Taxonomic entries were imported in this order of importance:
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1. List of Prokaryotic names with Standing in Nomenclature (LPSN):
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Freese, HM *et al.* (2026). **TYGS and LPSN in 2025: a Global Core
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Biodata Resource for genome-based classification and nomenclature of
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prokaryotes within DSMZ Digital Diversity.** Nucleic Acids Research,
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54, D884–D891;
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[doi:10.1093/nar/gkaf1110](https://doi.org/10.1093/nar/gkaf1110) .
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Accessed from <https://lpsn.dsmz.de> on 7th of May, 2026.
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2. MycoBank:
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Vincent, R *et al* (2013). **MycoBank gearing up for new horizons.**
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IMA Fungus, 4(2), 371-9;
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[doi:10.5598/imafungus.2013.04.02.16](https://doi.org/10.5598/imafungus.2013.04.02.16)
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. Accessed from <https://www.mycobank.org> on 7th of May, 2026.
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3. Global Biodiversity Information Facility (GBIF), via Catalogue of
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Life (COL):
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Banki, O. *et al.* (2026). Catalogue of Life (2026-04-18 XR).
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Catalogue of Life Foundation, Amsterdam, Netherlands.
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[doi:10.48580/dgxjw](https://doi.org/10.48580/dgxjw) . Accessed from
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<https://www.gbif.org> on 7th of May, 2026.
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Furthermore, these sources were used for additional details:
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- BacDive:
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Reimer, LC *et al.* (2022). ***BacDive* in 2022: the knowledge base
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for standardized bacterial and archaeal data.** Nucleic Acids Res.,
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50(D1):D741-D74;
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[doi:10.1093/nar/gkab961](https://doi.org/10.1093/nar/gkab961) .
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Accessed from <https://bacdive.dsmz.de> on 7th of May, 2026.
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- Systematized Nomenclature of Medicine - Clinical Terms (SNOMED-CT):
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Public Health Information Network Vocabulary Access and Distribution
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System (PHIN VADS). US Edition of SNOMED CT from 1 September 2020.
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Value Set Name 'Microorganism', OID 2.16.840.1.114222.4.11.1009 (v12).
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Accessed from <https://www.cdc.gov/phin/php/phinvads/> on 16th of
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July, 2024.
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- Grimont *et al.* (2007). Antigenic Formulae of the Salmonella
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Serovars, 9th Edition. WHO Collaborating Centre for Reference and
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Research on *Salmonella* (WHOCC-SALM).
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- Bartlett *et al.* (2022). **A comprehensive list of bacterial
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pathogens infecting humans** *Microbiology* 168:001269;
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[doi:10.1099/mic.0.001269](https://doi.org/10.1099/mic.0.001269)
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## See also
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[`as.mo()`](https://amr-for-r.org/reference/as.mo.md),
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@@ -276,23 +295,24 @@ repository](https://github.com/msberends/AMR/tree/main/data-raw/datasets).
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``` r
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microorganisms
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#> # A tibble: 78,679 × 26
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#> mo fullname status kingdom phylum class order family genus species
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#> <mo> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
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#> 1 B_GRAMN (unknown … unkno… Bacter… (unkn… (unk… (unk… "(unk… (unk… "(unkn…
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#> 2 B_GRAMP (unknown … unkno… Bacter… (unkn… (unk… (unk… "(unk… (unk… "(unkn…
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#> 3 B_ANAER-NEG (unknown … unkno… Bacter… (unkn… (unk… (unk… "(unk… (unk… "(unkn…
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#> 4 B_ANAER-POS (unknown … unkno… Bacter… (unkn… (unk… (unk… "(unk… (unk… "(unkn…
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#> 5 B_ANAER (unknown … unkno… Bacter… (unkn… (unk… (unk… "(unk… (unk… "(unkn…
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#> 6 F_FUNGUS (unknown … unkno… Fungi (unkn… (unk… (unk… "(unk… (unk… "(unkn…
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#> 7 UNKNOWN (unknown … unkno… (unkno… (unkn… (unk… (unk… "(unk… (unk… "(unkn…
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#> 8 P_PROTOZOAN (unknown … unkno… Protoz… (unkn… (unk… (unk… "(unk… (unk… "(unkn…
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#> 9 F_YEAST (unknown … unkno… Fungi (unkn… (unk… (unk… "(unk… (unk… "(unkn…
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#> 10 F_AABRN Aabaarnia unkno… Fungi Ascom… Leca… Ostr… "" Aaba… ""
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#> # ℹ 78,669 more rows
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#> # ℹ 16 more variables: subspecies <chr>, rank <chr>, ref <chr>,
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#> # oxygen_tolerance <chr>, source <chr>, lpsn <chr>, lpsn_parent <chr>,
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#> # lpsn_renamed_to <chr>, mycobank <chr>, mycobank_parent <chr>,
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#> # mycobank_renamed_to <chr>, gbif <chr>, gbif_parent <chr>,
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#> # gbif_renamed_to <chr>, prevalence <dbl>, snomed <list>
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#> # A tibble: 96,982 × 28
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#> mo fullname status domain kingdom phylum class order family
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#> <mo> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
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#> 1 B_GRAMN (unknown Gr… unkno… Bacte… (unkno… (unkn… (unk… (unk… (unkn…
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#> 2 B_GRAMP (unknown Gr… unkno… Bacte… (unkno… (unkn… (unk… (unk… (unkn…
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#> 3 B_ANAER-NEG (unknown an… unkno… Bacte… (unkno… (unkn… (unk… (unk… (unkn…
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#> 4 B_ANAER-POS (unknown an… unkno… Bacte… (unkno… (unkn… (unk… (unk… (unkn…
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#> 5 B_ANAER (unknown an… unkno… Bacte… (unkno… (unkn… (unk… (unk… (unkn…
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#> 6 F_FUNGUS (unknown fu… unkno… Fungi Fungi (unkn… (unk… (unk… (unkn…
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#> 7 UNKNOWN (unknown na… unkno… (unkn… (unkno… (unkn… (unk… (unk… (unkn…
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#> 8 P_PROTOZOAN (unknown pr… unkno… Proto… Protoz… (unkn… (unk… (unk… (unkn…
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#> 9 F_YEAST (unknown ye… unkno… Fungi Fungi (unkn… (unk… (unk… (unkn…
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#> 10 B_[FAM]_ABDTBCTR Abditibacte… accep… Bacte… Pseudo… Abdit… Abdi… Abdi… Abdit…
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#> # ℹ 96,972 more rows
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#> # ℹ 19 more variables: genus <chr>, species <chr>, subspecies <chr>,
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#> # rank <chr>, ref <chr>, oxygen_tolerance <chr>, morphology <chr>,
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#> # source <chr>, lpsn <chr>, lpsn_parent <chr>, lpsn_renamed_to <chr>,
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#> # mycobank <chr>, mycobank_parent <chr>, mycobank_renamed_to <chr>,
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#> # gbif <chr>, gbif_parent <chr>, gbif_renamed_to <chr>, prevalence <dbl>,
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#> # snomed <list>
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```
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Reference in New Issue
Block a user