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Catalogue of Life, replaces ITIS

This commit is contained in:
2019-02-18 02:33:37 +01:00
parent 9209787a53
commit 54f8258f8c
88 changed files with 607 additions and 590 deletions

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@ -3,11 +3,11 @@
\docType{data}
\name{microorganisms}
\alias{microorganisms}
\title{Data set with ~20,000 microorganisms}
\format{A \code{\link{data.frame}} with 19,456 observations and 15 variables:
\title{Data set with ~60,000 microorganisms}
\format{A \code{\link{data.frame}} with 56,659 observations and 15 variables:
\describe{
\item{\code{mo}}{ID of microorganism}
\item{\code{tsn}}{Taxonomic Serial Number (TSN), as defined by ITIS}
\item{\code{col_id}}{Catalogue of Life ID}
\item{\code{genus}}{Taxonomic genus of the microorganism as found in ITIS, see Source}
\item{\code{species}}{Taxonomic species of the microorganism as found in ITIS, see Source}
\item{\code{subspecies}}{Taxonomic subspecies of the microorganism as found in ITIS, see Source}
@ -29,20 +29,15 @@ Integrated Taxonomic Information System (ITIS) public online database, \url{http
microorganisms
}
\description{
A data set containing the complete microbial taxonomy of the kingdoms Bacteria, Fungi and Protozoa from ITIS. MO codes can be looked up using \code{\link{as.mo}}.
A data set containing the microbial taxonomy of six kingdoms from the Catalogue of Life. MO codes can be looked up using \code{\link{as.mo}}.
}
\details{
Manually added were:
\itemize{
\item{605 species of Aspergillus (as Aspergillus misses from ITIS, list from https://en.wikipedia.org/wiki/List_of_Aspergillus_species on 2019-02-05)}
\item{23 species of Trichophyton (as Trichophyton misses from ITIS, list from https://en.wikipedia.org/wiki/Trichophyton on 2019-02-05)}
\item{9 species of Streptococcus (beta haemolytic groups A, B, C, D, F, G, H, K and unspecified)}
\item{2 species of Straphylococcus (coagulase-negative [CoNS] and coagulase-positive [CoPS])}
\item{1 species of Candida (C. glabrata)}
\item{9 species of \emph{Streptococcus} (beta haemolytic groups A, B, C, D, F, G, H, K and unspecified)}
\item{2 species of \emph{Staphylococcus} (coagulase-negative [CoNS] and coagulase-positive [CoPS])}
\item{2 other undefined (unknown Gram negatives and unknown Gram positives)}
}
These manual entries have no Taxonomic Serial Number (TSN), so can be looked up with \code{filter(microorganisms, is.na(tsn)}.
}
\section{ITIS}{