The Catalogue of Life

This package contains the complete taxonomic tree of almost all microorganisms from the authoritative and comprehensive Catalogue of Life.

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.

Examples

# NOT RUN {
# Get version info of included data set
catalogue_of_life_version()


# Get a note when a species was renamed
mo_shortname("Chlamydia psittaci")
# Note: 'Chlamydia psittaci' (Page, 1968) was renamed
#       'Chlamydophila psittaci' (Everett et al., 1999)
# [1] "C. psittaci"

# Get any property from the entire taxonomic tree for all included species
mo_class("E. coli")
# [1] "Gammaproteobacteria"

mo_family("E. coli")
# [1] "Enterobacteriaceae"

mo_gramstain("E. coli") # based on kingdom and phylum, see ?mo_gramstain
# [1] "Gram negative"

mo_ref("E. coli")
# [1] "Castellani et al., 1919"

# Do not get mistaken - the package only includes microorganisms
mo_phylum("C. elegans")
# [1] "Cyanobacteria"                   # Bacteria?!
mo_fullname("C. elegans")
# [1] "Chroococcus limneticus elegans"  # Because a microorganism was found
# }