Data set with ~65,000 microorganisms

A data set containing the microbial taxonomy of six kingdoms from the Catalogue of Life. MO codes can be looked up using as.mo.

microorganisms

Format

A data.frame with 68,260 observations and 16 variables:

mo

ID of microorganism as used by this package

col_id

Catalogue of Life ID

fullname

Full name, like "Escherichia coli"

kingdom, phylum, class, order, family, genus, species, subspecies

Taxonomic rank of the microorganism

rank

Text of the taxonomic rank of the microorganism, like "species" or "genus"

ref

Author(s) and year of concerning scientific publication

species_id

ID of the species as used by the Catalogue of Life

source

Either "CoL", "DSMZ" (see source) or "manually added"

prevalence

Prevalence of the microorganism, see ?as.mo

Source

Catalogue of Life: Annual Checklist (public online taxonomic database), http://www.catalogueoflife.org (check included annual version with catalogue_of_life_version()).

Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Germany, Prokaryotic Nomenclature Up-to-Date, http://www.dsmz.de/bacterial-diversity/prokaryotic-nomenclature-up-to-date (check included version with catalogue_of_life_version()).

Details

Manually added were:

  • 9 entries of Streptococcus (beta haemolytic groups A, B, C, D, F, G, H, K and unspecified)

  • 2 entries of Staphylococcus (coagulase-negative [CoNS] and coagulase-positive [CoPS])

  • 3 entries of Trichomonas (Trichomonas vaginalis, and its family and genus)

  • 5 other 'undefined' entries (unknown, unknown Gram negatives, unknown Gram positives, unknown yeast and unknown fungus)

  • 8,970 species from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen) that are not in the Catalogue of Life

About the records from DSMZ (see source)

Names of prokaryotes are defined as being validly published by the International Code of Nomenclature of Bacteria. Validly published are all names which are included in the Approved Lists of Bacterial Names and the names subsequently published in the International Journal of Systematic Bacteriology (IJSB) and, from January 2000, in the International Journal of Systematic and Evolutionary Microbiology (IJSEM) as original articles or in the validation lists.

From: https://www.dsmz.de/support/bacterial-nomenclature-up-to-date-downloads/readme.html

Catalogue of Life


This package contains the complete taxonomic tree of almost all microorganisms (~65,000 species) from the authoritative and comprehensive Catalogue of Life (http://www.catalogueoflife.org). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.

Click here for more information about the included taxa. The Catalogue of Life releases updates annually; check which version was included in this package with catalogue_of_life_version().

Read more on our website!

On our website https://msberends.gitlab.io/AMR you can find a tutorial about how to conduct AMR analysis, the complete documentation of all functions (which reads a lot easier than here in R) and an example analysis using WHONET data.

See also

as.mo, mo_property, microorganisms.codes