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as.mo improvement

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dr. M.S. (Matthijs) Berends
2019-02-25 10:42:57 +01:00
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@ -63,7 +63,7 @@ Use the \code{\link{mo_property}} functions to get properties based on the retur
This function uses Artificial Intelligence (AI) to help getting fast and logical results. It tries to find matches in this order:
\itemize{
\item{Taxonomic kingdom: it first searches in Bacteria, then Fungi, then Protozoa}
\item{Human pathogenic prevalence: it first searches in more prevalent microorganisms, then less prevalent ones}
\item{Human pathogenic prevalence: it first searches in more prevalent microorganisms, then less prevalent ones (see section \emph{Microbial prevalence of pathogens in humans})}
\item{Valid MO codes and full names: it first searches in already valid MO code and known genus/species combinations}
\item{Breakdown of input values: from here it starts to breakdown input values to find possible matches}
}
@ -100,6 +100,20 @@ Use \code{mo_uncertainties()} to get a vector with all values that were coerced
Use \code{mo_renamed()} to get a vector with all values that could be coerced based on an old, previously accepted taxonomic name.
}
\section{Microbial prevalence of pathogens in humans}{
The artificial intelligence takes into account microbial prevalence of pathogens in humans. It uses three groups and every (sub)species is in the group it matches first. These groups are:
\itemize{
\item{1 (most prevalent): class is Gammaproteobacteria \strong{or} genus is one of: \emph{Enterococcus}, \emph{Staphylococcus}, \emph{Streptococcus}.}
\item{2: phylum is one of: Proteobacteria, Firmicutes, Actinobacteria, Sarcomastigophora \strong{or} genus is one of: \emph{Aspergillus}, \emph{Bacteroides}, \emph{Candida}, \emph{Capnocytophaga}, \emph{Chryseobacterium}, \emph{Cryptococcus}, \emph{Elisabethkingia}, \emph{Flavobacterium}, \emph{Fusobacterium}, \emph{Giardia}, \emph{Leptotrichia}, \emph{Mycoplasma}, \emph{Prevotella}, \emph{Rhodotorula}, \emph{Treponema}, \emph{Trichophyton}.}
\item{3 (least prevalent): all others.}
}
Group 1 contains all common Gram negatives, like all Enterobacteriaceae and e.g. \emph{Pseudomonas} and \emph{Legionella}.
Group 2 probably contains all microbial pathogens ever found in humans.
}
\section{Source}{
[1] Becker K \emph{et al.} \strong{Coagulase-Negative Staphylococci}. 2014. Clin Microbiol Rev. 27(4): 870–926. \url{https://dx.doi.org/10.1128/CMR.00109-13}