microorganisms {AMR}R Documentation

Data Set with 78 679 Taxonomic Records of Microorganisms

Description

A data set containing the full microbial taxonomy (last updated: June 24th, 2024) of six kingdoms. This data set is the backbone of this AMR package. MO codes can be looked up using as.mo() and microorganism properties can be looked up using any of the mo_* functions.

This data set is carefully crafted, yet made 100% reproducible from public and authoritative taxonomic sources (using this script), namely: List of Prokaryotic names with Standing in Nomenclature (LPSN) for bacteria, MycoBank for fungi, and Global Biodiversity Information Facility (GBIF) for all others taxons.

Usage

microorganisms

Format

A tibble with 78 679 observations and 26 variables:

Details

Please note that entries are only based on LPSN, MycoBank, and GBIF (see below). Since these sources incorporate entries based on (recent) publications in the International Journal of Systematic and Evolutionary Microbiology (IJSEM), it can happen that the year of publication is sometimes later than one might expect.

For example, Staphylococcus pettenkoferi was described for the first time in Diagnostic Microbiology and Infectious Disease in 2002 (doi:10.1016/s0732-8893(02)00399-1), but it was not until 2007 that a publication in IJSEM followed (doi:10.1099/ijs.0.64381-0). Consequently, the AMR package returns 2007 for mo_year("S. pettenkoferi").

Included Taxa

Included taxonomic data from LPSN, MycoBank, and GBIF are:

Manual additions

For convenience, some entries were added manually:

The syntax used to transform the original data to a cleansed R format, can be found here.

Download Our Reference Data

All reference data sets in the AMR package - including information on microorganisms, antimicrobials, and clinical breakpoints - are freely available for download in multiple formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata.

For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems.

Visit our website for direct download links, or explore the actual files in our GitHub repository.

Source

Taxonomic entries were imported in this order of importance:

  1. List of Prokaryotic names with Standing in Nomenclature (LPSN):

    Parte, AC et al. (2020). List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. International Journal of Systematic and Evolutionary Microbiology, 70, 5607-5612; doi:10.1099/ijsem.0.004332. Accessed from https://lpsn.dsmz.de on June 24th, 2024.

  2. MycoBank:

    Vincent, R et al (2013). MycoBank gearing up for new horizons. IMA Fungus, 4(2), 371-9; doi:10.5598/imafungus.2013.04.02.16. Accessed from https://www.mycobank.org on June 24th, 2024.

  3. Global Biodiversity Information Facility (GBIF):

    GBIF Secretariat (2023). GBIF Backbone Taxonomy. Checklist dataset doi:10.15468/39omei. Accessed from https://www.gbif.org on June 24th, 2024.

Furthermore, these sources were used for additional details:

See Also

as.mo(), mo_property(), microorganisms.groups, microorganisms.codes, intrinsic_resistant

Examples

microorganisms

[Package AMR version 3.0.0 Index]