Data set with ~65,000 microorganisms
microorganisms.RdA 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 67,903 observations and 16 variables:
moID of microorganism as used by this package
col_idCatalogue of Life ID
fullnameFull name, like
"Escherichia coli"kingdom,phylum,class,order,family,genus,species,subspeciesTaxonomic rank of the microorganism
rankText of the taxonomic rank of the microorganism, like
"species"or"genus"refAuthor(s) and year of concerning scientific publication
species_idID of the species as used by the Catalogue of Life
sourceEither
"CoL","DSMZ"(see source) or "manually added"prevalencePrevalence of the microorganism, see
?as.mo
Source
Catalogue of Life: Annual Checklist (public online taxonomic database), 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 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])
3 other undefined (unknown, unknown Gram negatives and unknown Gram positives)
8,830 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.