Data set with ~60,000 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 57,158 observations and 14 variables:

mo

ID of microorganism as used by this package

col_id

Catalogue of Life ID

fullname

Full name, like "Echerichia coli"

kingdom

Taxonomic kingdom of the microorganism

phylum

Taxonomic phylum of the microorganism

class

Taxonomic class of the microorganism

order

Taxonomic order of the microorganism

family

Taxonomic family of the microorganism

genus

Taxonomic genus of the microorganism

species

Taxonomic species of the microorganism

subspecies

Taxonomic subspecies of the microorganism

rank

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

Catalogue of Life: Annual Checklist (public online database), www.catalogueoflife.org.

Details

Manually added were:

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

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

  • 2 other undefined (unknown Gram negatives and unknown Gram positives)

Catalogue of Life


This package contains the complete taxonomic tree of almost all microorganisms from the authoritative and comprehensive Catalogue of Life (http://www.catalogueoflife.org). This data is updated annually - check the included version with catalogue_of_life_version.

Included are:

  • All ~55,000 (sub)species from the kingdoms of Archaea, Bacteria, Protozoa and Viruses

  • All ~3,500 (sub)species from these orders of the kingdom of Fungi: Eurotiales, Onygenales, Pneumocystales, Saccharomycetales, Schizosaccharomycetales and Tremellales. 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 and including everything would tremendously slow down our algorithms too. By only including the aforementioned taxonomic orders, the most relevant fungi are covered (like all species of Aspergillus, Candida, Cryptococcus, Histplasma, Pneumocystis, Saccharomyces and Trichophyton).

  • All ~15,000 previously accepted names of included (sub)species that have been taxonomically renamed

  • The complete taxonomic tree of all included (sub)species: from kingdom to subspecies

  • The responsible author(s) and year of scientific publication

The Catalogue of Life (http://www.catalogueoflife.org) is the most comprehensive and authoritative global index of species currently available. It holds essential information on the names, relationships and distributions of over 1.6 million species. The Catalogue of Life is used to support the major biodiversity and conservation information services such as the Global Biodiversity Information Facility (GBIF), Encyclopedia of Life (EoL) and the International Union for Conservation of Nature Red List. It is recognised by the Convention on Biological Diversity as a significant component of the Global Taxonomy Initiative and a contribution to Target 1 of the Global Strategy for Plant Conservation.

The syntax used to transform the original data to a cleansed R format, can be found here: https://gitlab.com/msberends/AMR/blob/master/reproduction_of_microorganisms.R.

Read more on our website!

On our website https://msberends.gitlab.io/AMR you can find a comprehensive 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