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