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Restored Pichia and Meyerozyma

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dr. M.S. (Matthijs) Berends
2022-09-23 13:12:46 +02:00
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4
man/as.mo.Rd
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@ -162,13 +162,13 @@ The grouping into human pathogenic prevalence (\eqn{p}) is based on experience f
\strong{Group 1} (most prevalent microorganisms) consists of all microorganisms where the taxonomic class is Gammaproteobacteria or where the taxonomic genus is \emph{Enterococcus}, \emph{Staphylococcus} or \emph{Streptococcus}. This group consequently contains all common Gram-negative bacteria, such as \emph{Pseudomonas} and \emph{Legionella} and all species within the order Enterobacterales.
\strong{Group 2} consists of all microorganisms where the taxonomic phylum is Proteobacteria, Firmicutes, Actinobacteria or Sarcomastigophora, or where the taxonomic genus is \emph{Absidia}, \emph{Acanthamoeba}, \emph{Acholeplasma}, \emph{Acremonium}, \emph{Actinotignum}, \emph{Aedes}, \emph{Alistipes}, \emph{Alloprevotella}, \emph{Alternaria}, \emph{Amoeba}, \emph{Anaerosalibacter}, \emph{Ancylostoma}, \emph{Angiostrongylus}, \emph{Anisakis}, \emph{Anopheles}, \emph{Apophysomyces}, \emph{Arachnia}, \emph{Aspergillus}, \emph{Aureobasidium}, \emph{Bacteroides}, \emph{Basidiobolus}, \emph{Beauveria}, \emph{Bergeyella}, \emph{Blastocystis}, \emph{Blastomyces}, \emph{Borrelia}, \emph{Brachyspira}, \emph{Branhamella}, \emph{Butyricimonas}, \emph{Candida}, \emph{Capillaria}, \emph{Capnocytophaga}, \emph{Catabacter}, \emph{Cetobacterium}, \emph{Chaetomium}, \emph{Chlamydia}, \emph{Chlamydophila}, \emph{Chryseobacterium}, \emph{Chrysonilia}, \emph{Cladophialophora}, \emph{Cladosporium}, \emph{Conidiobolus}, \emph{Contracaecum}, \emph{Cordylobia}, \emph{Cryptococcus}, \emph{Curvularia}, \emph{Deinococcus}, \emph{Demodex}, \emph{Dermatobia}, \emph{Dientamoeba}, \emph{Diphyllobothrium}, \emph{Dirofilaria}, \emph{Dysgonomonas}, \emph{Echinostoma}, \emph{Elizabethkingia}, \emph{Empedobacter}, \emph{Entamoeba}, \emph{Enterobius}, \emph{Exophiala}, \emph{Exserohilum}, \emph{Fasciola}, \emph{Flavobacterium}, \emph{Fonsecaea}, \emph{Fusarium}, \emph{Fusobacterium}, \emph{Giardia}, \emph{Haloarcula}, \emph{Halobacterium}, \emph{Halococcus}, \emph{Hendersonula}, \emph{Heterophyes}, \emph{Histomonas}, \emph{Histoplasma}, \emph{Hymenolepis}, \emph{Hypomyces}, \emph{Hysterothylacium}, \emph{Leishmania}, \emph{Lelliottia}, \emph{Leptosphaeria}, \emph{Leptotrichia}, \emph{Lucilia}, \emph{Lumbricus}, \emph{Malassezia}, \emph{Malbranchea}, \emph{Metagonimus}, \emph{Microsporidium}, \emph{Microsporum}, \emph{Mortierella}, \emph{Mucor}, \emph{Mycocentrospora}, \emph{Mycoplasma}, \emph{Myroides}, \emph{Necator}, \emph{Nectria}, \emph{Ochroconis}, \emph{Odoribacter}, \emph{Oesophagostomum}, \emph{Oidiodendron}, \emph{Opisthorchis}, \emph{Ornithobacterium}, \emph{Parabacteroides}, \emph{Pediculus}, \emph{Pedobacter}, \emph{Phlebotomus}, \emph{Phocaeicola}, \emph{Phocanema}, \emph{Phoma}, \emph{Piedraia}, \emph{Pithomyces}, \emph{Pityrosporum}, \emph{Pneumocystis}, \emph{Porphyromonas}, \emph{Prevotella}, \emph{Pseudallescheria}, \emph{Pseudoterranova}, \emph{Pulex}, \emph{Rhizomucor}, \emph{Rhizopus}, \emph{Rhodotorula}, \emph{Riemerella}, \emph{Saccharomyces}, \emph{Sarcoptes}, \emph{Scolecobasidium}, \emph{Scopulariopsis}, \emph{Scytalidium}, \emph{Sphingobacterium}, \emph{Spirometra}, \emph{Spiroplasma}, \emph{Sporobolomyces}, \emph{Stachybotrys}, \emph{Streptobacillus}, \emph{Strongyloides}, \emph{Syngamus}, \emph{Taenia}, \emph{Tannerella}, \emph{Tenacibaculum}, \emph{Terrimonas}, \emph{Toxocara}, \emph{Treponema}, \emph{Trichinella}, \emph{Trichobilharzia}, \emph{Trichoderma}, \emph{Trichomonas}, \emph{Trichophyton}, \emph{Trichosporon}, \emph{Trichostrongylus}, \emph{Trichuris}, \emph{Tritirachium}, \emph{Trombicula}, \emph{Trypanosoma}, \emph{Tunga}, \emph{Ureaplasma}, \emph{Victivallis}, \emph{Wautersiella}, \emph{Weeksella} or \emph{Wuchereria}.
\strong{Group 2} consists of all microorganisms where the taxonomic phylum is Proteobacteria, Firmicutes, Actinobacteria or Sarcomastigophora, or where the taxonomic genus is \emph{Absidia}, \emph{Acanthamoeba}, \emph{Acholeplasma}, \emph{Acremonium}, \emph{Actinotignum}, \emph{Aedes}, \emph{Alistipes}, \emph{Alloprevotella}, \emph{Alternaria}, \emph{Amoeba}, \emph{Anaerosalibacter}, \emph{Ancylostoma}, \emph{Angiostrongylus}, \emph{Anisakis}, \emph{Anopheles}, \emph{Apophysomyces}, \emph{Arachnia}, \emph{Aspergillus}, \emph{Aureobasidium}, \emph{Bacteroides}, \emph{Basidiobolus}, \emph{Beauveria}, \emph{Bergeyella}, \emph{Blastocystis}, \emph{Blastomyces}, \emph{Borrelia}, \emph{Brachyspira}, \emph{Branhamella}, \emph{Butyricimonas}, \emph{Candida}, \emph{Capillaria}, \emph{Capnocytophaga}, \emph{Catabacter}, \emph{Cetobacterium}, \emph{Chaetomium}, \emph{Chlamydia}, \emph{Chlamydophila}, \emph{Chryseobacterium}, \emph{Chrysonilia}, \emph{Cladophialophora}, \emph{Cladosporium}, \emph{Conidiobolus}, \emph{Contracaecum}, \emph{Cordylobia}, \emph{Cryptococcus}, \emph{Curvularia}, \emph{Deinococcus}, \emph{Demodex}, \emph{Dermatobia}, \emph{Dientamoeba}, \emph{Diphyllobothrium}, \emph{Dirofilaria}, \emph{Dysgonomonas}, \emph{Echinostoma}, \emph{Elizabethkingia}, \emph{Empedobacter}, \emph{Entamoeba}, \emph{Enterobius}, \emph{Exophiala}, \emph{Exserohilum}, \emph{Fasciola}, \emph{Flavobacterium}, \emph{Fonsecaea}, \emph{Fusarium}, \emph{Fusobacterium}, \emph{Giardia}, \emph{Haloarcula}, \emph{Halobacterium}, \emph{Halococcus}, \emph{Hendersonula}, \emph{Heterophyes}, \emph{Histomonas}, \emph{Histoplasma}, \emph{Hymenolepis}, \emph{Hypomyces}, \emph{Hysterothylacium}, \emph{Leishmania}, \emph{Lelliottia}, \emph{Leptosphaeria}, \emph{Leptotrichia}, \emph{Lucilia}, \emph{Lumbricus}, \emph{Malassezia}, \emph{Malbranchea}, \emph{Metagonimus}, \emph{Meyerozyma}, \emph{Microsporidium}, \emph{Microsporum}, \emph{Mortierella}, \emph{Mucor}, \emph{Mycocentrospora}, \emph{Mycoplasma}, \emph{Myroides}, \emph{Necator}, \emph{Nectria}, \emph{Ochroconis}, \emph{Odoribacter}, \emph{Oesophagostomum}, \emph{Oidiodendron}, \emph{Opisthorchis}, \emph{Ornithobacterium}, \emph{Parabacteroides}, \emph{Pediculus}, \emph{Pedobacter}, \emph{Phlebotomus}, \emph{Phocaeicola}, \emph{Phocanema}, \emph{Phoma}, \emph{Pichia}, \emph{Piedraia}, \emph{Pithomyces}, \emph{Pityrosporum}, \emph{Pneumocystis}, \emph{Porphyromonas}, \emph{Prevotella}, \emph{Pseudallescheria}, \emph{Pseudoterranova}, \emph{Pulex}, \emph{Rhizomucor}, \emph{Rhizopus}, \emph{Rhodotorula}, \emph{Riemerella}, \emph{Saccharomyces}, \emph{Sarcoptes}, \emph{Scolecobasidium}, \emph{Scopulariopsis}, \emph{Scytalidium}, \emph{Sphingobacterium}, \emph{Spirometra}, \emph{Spiroplasma}, \emph{Sporobolomyces}, \emph{Stachybotrys}, \emph{Streptobacillus}, \emph{Strongyloides}, \emph{Syngamus}, \emph{Taenia}, \emph{Tannerella}, \emph{Tenacibaculum}, \emph{Terrimonas}, \emph{Toxocara}, \emph{Treponema}, \emph{Trichinella}, \emph{Trichobilharzia}, \emph{Trichoderma}, \emph{Trichomonas}, \emph{Trichophyton}, \emph{Trichosporon}, \emph{Trichostrongylus}, \emph{Trichuris}, \emph{Tritirachium}, \emph{Trombicula}, \emph{Trypanosoma}, \emph{Tunga}, \emph{Ureaplasma}, \emph{Victivallis}, \emph{Wautersiella}, \emph{Weeksella} or \emph{Wuchereria}.
\strong{Group 3} consists of all other microorganisms.
All characters in \eqn{x} and \eqn{n} are ignored that are other than A-Z, a-z, 0-9, spaces and parentheses.
All matches are sorted descending on their matching score and for all user input values, the top match will be returned. This will lead to the effect that e.g., \code{"E. coli"} will return the microbial ID of \emph{Escherichia coli} (\eqn{m = 0.688}, a highly prevalent microorganism found in humans) and not \emph{Entamoeba coli} (\eqn{m = 0.079}, a less prevalent microorganism in humans), although the latter would alphabetically come first.
All matches are sorted descending on their matching score and for all user input values, the top match will be returned. This will lead to the effect that e.g., \code{"E. coli"} will return the microbial ID of \emph{Escherichia coli} (\eqn{m = 0.688}, a highly prevalent microorganism found in humans) and not \emph{Entamoeba coli} (\eqn{m = 0.119}, a less prevalent microorganism in humans), although the latter would alphabetically come first.
}
\section{Reference Data Publicly Available}{

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man/microorganisms.Rd
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@ -3,9 +3,9 @@
\docType{data}
\name{microorganisms}
\alias{microorganisms}
\title{Data Set with 48,651 Microorganisms}
\title{Data Set with 48,787 Microorganisms}
\format{
A \link[tibble:tibble]{tibble} with 48,651 observations and 22 variables:
A \link[tibble:tibble]{tibble} with 48,787 observations and 22 variables:
\itemize{
\item \code{mo}\cr ID of microorganism as used by this package
\item \code{fullname}\cr Full name, like \code{"Escherichia coli"}. For the taxonomic ranks genus, species and subspecies, this is the 'pasted' text of genus, species, and subspecies. For all taxonomic ranks higher than genus, this is the name of the taxon.
@ -47,7 +47,7 @@ For example, \emph{Staphylococcus pettenkoferi} was described for the first time
Included taxonomic data are:
\itemize{
\item All ~34,000 (sub)species from the kingdoms of Archaea and Bacteria
\item ~7,200 (sub)species from the kingdom of Fungi. The kingdom of Fungi is a very large taxon with almost 300,000 different (sub)species, of which most are not microbial (but rather macroscopic, like mushrooms). Because of this, not all fungi fit the scope of this package. Only relevant fungi are covered (such as all species of \emph{Aspergillus}, \emph{Candida}, \emph{Cryptococcus}, \emph{Histoplasma}, \emph{Pneumocystis}, \emph{Saccharomyces} and \emph{Trichophyton}).
\item ~7,400 (sub)species from the kingdom of Fungi. The kingdom of Fungi is a very large taxon with almost 300,000 different (sub)species, of which most are not microbial (but rather macroscopic, like mushrooms). Because of this, not all fungi fit the scope of this package. Only relevant fungi are covered (such as all species of \emph{Aspergillus}, \emph{Candida}, \emph{Cryptococcus}, \emph{Histoplasma}, \emph{Pneumocystis}, \emph{Saccharomyces} and \emph{Trichophyton}).
\item ~4,900 (sub)species from the kingdom of Protozoa
\item ~1,500 (sub)species from ~50 other relevant genera from the kingdom of Animalia (such as \emph{Strongyloides} and \emph{Taenia})
\item All ~9,400 previously accepted names of all included (sub)species (these were taxonomically renamed)

4
man/mo_matching_score.Rd
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@ -34,13 +34,13 @@ The grouping into human pathogenic prevalence (\eqn{p}) is based on experience f
\strong{Group 1} (most prevalent microorganisms) consists of all microorganisms where the taxonomic class is Gammaproteobacteria or where the taxonomic genus is \emph{Enterococcus}, \emph{Staphylococcus} or \emph{Streptococcus}. This group consequently contains all common Gram-negative bacteria, such as \emph{Pseudomonas} and \emph{Legionella} and all species within the order Enterobacterales.
\strong{Group 2} consists of all microorganisms where the taxonomic phylum is Proteobacteria, Firmicutes, Actinobacteria or Sarcomastigophora, or where the taxonomic genus is \emph{Absidia}, \emph{Acanthamoeba}, \emph{Acholeplasma}, \emph{Acremonium}, \emph{Actinotignum}, \emph{Aedes}, \emph{Alistipes}, \emph{Alloprevotella}, \emph{Alternaria}, \emph{Amoeba}, \emph{Anaerosalibacter}, \emph{Ancylostoma}, \emph{Angiostrongylus}, \emph{Anisakis}, \emph{Anopheles}, \emph{Apophysomyces}, \emph{Arachnia}, \emph{Aspergillus}, \emph{Aureobasidium}, \emph{Bacteroides}, \emph{Basidiobolus}, \emph{Beauveria}, \emph{Bergeyella}, \emph{Blastocystis}, \emph{Blastomyces}, \emph{Borrelia}, \emph{Brachyspira}, \emph{Branhamella}, \emph{Butyricimonas}, \emph{Candida}, \emph{Capillaria}, \emph{Capnocytophaga}, \emph{Catabacter}, \emph{Cetobacterium}, \emph{Chaetomium}, \emph{Chlamydia}, \emph{Chlamydophila}, \emph{Chryseobacterium}, \emph{Chrysonilia}, \emph{Cladophialophora}, \emph{Cladosporium}, \emph{Conidiobolus}, \emph{Contracaecum}, \emph{Cordylobia}, \emph{Cryptococcus}, \emph{Curvularia}, \emph{Deinococcus}, \emph{Demodex}, \emph{Dermatobia}, \emph{Dientamoeba}, \emph{Diphyllobothrium}, \emph{Dirofilaria}, \emph{Dysgonomonas}, \emph{Echinostoma}, \emph{Elizabethkingia}, \emph{Empedobacter}, \emph{Entamoeba}, \emph{Enterobius}, \emph{Exophiala}, \emph{Exserohilum}, \emph{Fasciola}, \emph{Flavobacterium}, \emph{Fonsecaea}, \emph{Fusarium}, \emph{Fusobacterium}, \emph{Giardia}, \emph{Haloarcula}, \emph{Halobacterium}, \emph{Halococcus}, \emph{Hendersonula}, \emph{Heterophyes}, \emph{Histomonas}, \emph{Histoplasma}, \emph{Hymenolepis}, \emph{Hypomyces}, \emph{Hysterothylacium}, \emph{Leishmania}, \emph{Lelliottia}, \emph{Leptosphaeria}, \emph{Leptotrichia}, \emph{Lucilia}, \emph{Lumbricus}, \emph{Malassezia}, \emph{Malbranchea}, \emph{Metagonimus}, \emph{Microsporidium}, \emph{Microsporum}, \emph{Mortierella}, \emph{Mucor}, \emph{Mycocentrospora}, \emph{Mycoplasma}, \emph{Myroides}, \emph{Necator}, \emph{Nectria}, \emph{Ochroconis}, \emph{Odoribacter}, \emph{Oesophagostomum}, \emph{Oidiodendron}, \emph{Opisthorchis}, \emph{Ornithobacterium}, \emph{Parabacteroides}, \emph{Pediculus}, \emph{Pedobacter}, \emph{Phlebotomus}, \emph{Phocaeicola}, \emph{Phocanema}, \emph{Phoma}, \emph{Piedraia}, \emph{Pithomyces}, \emph{Pityrosporum}, \emph{Pneumocystis}, \emph{Porphyromonas}, \emph{Prevotella}, \emph{Pseudallescheria}, \emph{Pseudoterranova}, \emph{Pulex}, \emph{Rhizomucor}, \emph{Rhizopus}, \emph{Rhodotorula}, \emph{Riemerella}, \emph{Saccharomyces}, \emph{Sarcoptes}, \emph{Scolecobasidium}, \emph{Scopulariopsis}, \emph{Scytalidium}, \emph{Sphingobacterium}, \emph{Spirometra}, \emph{Spiroplasma}, \emph{Sporobolomyces}, \emph{Stachybotrys}, \emph{Streptobacillus}, \emph{Strongyloides}, \emph{Syngamus}, \emph{Taenia}, \emph{Tannerella}, \emph{Tenacibaculum}, \emph{Terrimonas}, \emph{Toxocara}, \emph{Treponema}, \emph{Trichinella}, \emph{Trichobilharzia}, \emph{Trichoderma}, \emph{Trichomonas}, \emph{Trichophyton}, \emph{Trichosporon}, \emph{Trichostrongylus}, \emph{Trichuris}, \emph{Tritirachium}, \emph{Trombicula}, \emph{Trypanosoma}, \emph{Tunga}, \emph{Ureaplasma}, \emph{Victivallis}, \emph{Wautersiella}, \emph{Weeksella} or \emph{Wuchereria}.
\strong{Group 2} consists of all microorganisms where the taxonomic phylum is Proteobacteria, Firmicutes, Actinobacteria or Sarcomastigophora, or where the taxonomic genus is \emph{Absidia}, \emph{Acanthamoeba}, \emph{Acholeplasma}, \emph{Acremonium}, \emph{Actinotignum}, \emph{Aedes}, \emph{Alistipes}, \emph{Alloprevotella}, \emph{Alternaria}, \emph{Amoeba}, \emph{Anaerosalibacter}, \emph{Ancylostoma}, \emph{Angiostrongylus}, \emph{Anisakis}, \emph{Anopheles}, \emph{Apophysomyces}, \emph{Arachnia}, \emph{Aspergillus}, \emph{Aureobasidium}, \emph{Bacteroides}, \emph{Basidiobolus}, \emph{Beauveria}, \emph{Bergeyella}, \emph{Blastocystis}, \emph{Blastomyces}, \emph{Borrelia}, \emph{Brachyspira}, \emph{Branhamella}, \emph{Butyricimonas}, \emph{Candida}, \emph{Capillaria}, \emph{Capnocytophaga}, \emph{Catabacter}, \emph{Cetobacterium}, \emph{Chaetomium}, \emph{Chlamydia}, \emph{Chlamydophila}, \emph{Chryseobacterium}, \emph{Chrysonilia}, \emph{Cladophialophora}, \emph{Cladosporium}, \emph{Conidiobolus}, \emph{Contracaecum}, \emph{Cordylobia}, \emph{Cryptococcus}, \emph{Curvularia}, \emph{Deinococcus}, \emph{Demodex}, \emph{Dermatobia}, \emph{Dientamoeba}, \emph{Diphyllobothrium}, \emph{Dirofilaria}, \emph{Dysgonomonas}, \emph{Echinostoma}, \emph{Elizabethkingia}, \emph{Empedobacter}, \emph{Entamoeba}, \emph{Enterobius}, \emph{Exophiala}, \emph{Exserohilum}, \emph{Fasciola}, \emph{Flavobacterium}, \emph{Fonsecaea}, \emph{Fusarium}, \emph{Fusobacterium}, \emph{Giardia}, \emph{Haloarcula}, \emph{Halobacterium}, \emph{Halococcus}, \emph{Hendersonula}, \emph{Heterophyes}, \emph{Histomonas}, \emph{Histoplasma}, \emph{Hymenolepis}, \emph{Hypomyces}, \emph{Hysterothylacium}, \emph{Leishmania}, \emph{Lelliottia}, \emph{Leptosphaeria}, \emph{Leptotrichia}, \emph{Lucilia}, \emph{Lumbricus}, \emph{Malassezia}, \emph{Malbranchea}, \emph{Metagonimus}, \emph{Meyerozyma}, \emph{Microsporidium}, \emph{Microsporum}, \emph{Mortierella}, \emph{Mucor}, \emph{Mycocentrospora}, \emph{Mycoplasma}, \emph{Myroides}, \emph{Necator}, \emph{Nectria}, \emph{Ochroconis}, \emph{Odoribacter}, \emph{Oesophagostomum}, \emph{Oidiodendron}, \emph{Opisthorchis}, \emph{Ornithobacterium}, \emph{Parabacteroides}, \emph{Pediculus}, \emph{Pedobacter}, \emph{Phlebotomus}, \emph{Phocaeicola}, \emph{Phocanema}, \emph{Phoma}, \emph{Pichia}, \emph{Piedraia}, \emph{Pithomyces}, \emph{Pityrosporum}, \emph{Pneumocystis}, \emph{Porphyromonas}, \emph{Prevotella}, \emph{Pseudallescheria}, \emph{Pseudoterranova}, \emph{Pulex}, \emph{Rhizomucor}, \emph{Rhizopus}, \emph{Rhodotorula}, \emph{Riemerella}, \emph{Saccharomyces}, \emph{Sarcoptes}, \emph{Scolecobasidium}, \emph{Scopulariopsis}, \emph{Scytalidium}, \emph{Sphingobacterium}, \emph{Spirometra}, \emph{Spiroplasma}, \emph{Sporobolomyces}, \emph{Stachybotrys}, \emph{Streptobacillus}, \emph{Strongyloides}, \emph{Syngamus}, \emph{Taenia}, \emph{Tannerella}, \emph{Tenacibaculum}, \emph{Terrimonas}, \emph{Toxocara}, \emph{Treponema}, \emph{Trichinella}, \emph{Trichobilharzia}, \emph{Trichoderma}, \emph{Trichomonas}, \emph{Trichophyton}, \emph{Trichosporon}, \emph{Trichostrongylus}, \emph{Trichuris}, \emph{Tritirachium}, \emph{Trombicula}, \emph{Trypanosoma}, \emph{Tunga}, \emph{Ureaplasma}, \emph{Victivallis}, \emph{Wautersiella}, \emph{Weeksella} or \emph{Wuchereria}.
\strong{Group 3} consists of all other microorganisms.
All characters in \eqn{x} and \eqn{n} are ignored that are other than A-Z, a-z, 0-9, spaces and parentheses.
All matches are sorted descending on their matching score and for all user input values, the top match will be returned. This will lead to the effect that e.g., \code{"E. coli"} will return the microbial ID of \emph{Escherichia coli} (\eqn{m = 0.688}, a highly prevalent microorganism found in humans) and not \emph{Entamoeba coli} (\eqn{m = 0.079}, a less prevalent microorganism in humans), although the latter would alphabetically come first.
All matches are sorted descending on their matching score and for all user input values, the top match will be returned. This will lead to the effect that e.g., \code{"E. coli"} will return the microbial ID of \emph{Escherichia coli} (\eqn{m = 0.688}, a highly prevalent microorganism found in humans) and not \emph{Entamoeba coli} (\eqn{m = 0.119}, a less prevalent microorganism in humans), although the latter would alphabetically come first.
}
\section{Reference Data Publicly Available}{

4
man/mo_property.Rd
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@ -317,13 +317,13 @@ The grouping into human pathogenic prevalence (\eqn{p}) is based on experience f
\strong{Group 1} (most prevalent microorganisms) consists of all microorganisms where the taxonomic class is Gammaproteobacteria or where the taxonomic genus is \emph{Enterococcus}, \emph{Staphylococcus} or \emph{Streptococcus}. This group consequently contains all common Gram-negative bacteria, such as \emph{Pseudomonas} and \emph{Legionella} and all species within the order Enterobacterales.
\strong{Group 2} consists of all microorganisms where the taxonomic phylum is Proteobacteria, Firmicutes, Actinobacteria or Sarcomastigophora, or where the taxonomic genus is \emph{Absidia}, \emph{Acanthamoeba}, \emph{Acholeplasma}, \emph{Acremonium}, \emph{Actinotignum}, \emph{Aedes}, \emph{Alistipes}, \emph{Alloprevotella}, \emph{Alternaria}, \emph{Amoeba}, \emph{Anaerosalibacter}, \emph{Ancylostoma}, \emph{Angiostrongylus}, \emph{Anisakis}, \emph{Anopheles}, \emph{Apophysomyces}, \emph{Arachnia}, \emph{Aspergillus}, \emph{Aureobasidium}, \emph{Bacteroides}, \emph{Basidiobolus}, \emph{Beauveria}, \emph{Bergeyella}, \emph{Blastocystis}, \emph{Blastomyces}, \emph{Borrelia}, \emph{Brachyspira}, \emph{Branhamella}, \emph{Butyricimonas}, \emph{Candida}, \emph{Capillaria}, \emph{Capnocytophaga}, \emph{Catabacter}, \emph{Cetobacterium}, \emph{Chaetomium}, \emph{Chlamydia}, \emph{Chlamydophila}, \emph{Chryseobacterium}, \emph{Chrysonilia}, \emph{Cladophialophora}, \emph{Cladosporium}, \emph{Conidiobolus}, \emph{Contracaecum}, \emph{Cordylobia}, \emph{Cryptococcus}, \emph{Curvularia}, \emph{Deinococcus}, \emph{Demodex}, \emph{Dermatobia}, \emph{Dientamoeba}, \emph{Diphyllobothrium}, \emph{Dirofilaria}, \emph{Dysgonomonas}, \emph{Echinostoma}, \emph{Elizabethkingia}, \emph{Empedobacter}, \emph{Entamoeba}, \emph{Enterobius}, \emph{Exophiala}, \emph{Exserohilum}, \emph{Fasciola}, \emph{Flavobacterium}, \emph{Fonsecaea}, \emph{Fusarium}, \emph{Fusobacterium}, \emph{Giardia}, \emph{Haloarcula}, \emph{Halobacterium}, \emph{Halococcus}, \emph{Hendersonula}, \emph{Heterophyes}, \emph{Histomonas}, \emph{Histoplasma}, \emph{Hymenolepis}, \emph{Hypomyces}, \emph{Hysterothylacium}, \emph{Leishmania}, \emph{Lelliottia}, \emph{Leptosphaeria}, \emph{Leptotrichia}, \emph{Lucilia}, \emph{Lumbricus}, \emph{Malassezia}, \emph{Malbranchea}, \emph{Metagonimus}, \emph{Microsporidium}, \emph{Microsporum}, \emph{Mortierella}, \emph{Mucor}, \emph{Mycocentrospora}, \emph{Mycoplasma}, \emph{Myroides}, \emph{Necator}, \emph{Nectria}, \emph{Ochroconis}, \emph{Odoribacter}, \emph{Oesophagostomum}, \emph{Oidiodendron}, \emph{Opisthorchis}, \emph{Ornithobacterium}, \emph{Parabacteroides}, \emph{Pediculus}, \emph{Pedobacter}, \emph{Phlebotomus}, \emph{Phocaeicola}, \emph{Phocanema}, \emph{Phoma}, \emph{Piedraia}, \emph{Pithomyces}, \emph{Pityrosporum}, \emph{Pneumocystis}, \emph{Porphyromonas}, \emph{Prevotella}, \emph{Pseudallescheria}, \emph{Pseudoterranova}, \emph{Pulex}, \emph{Rhizomucor}, \emph{Rhizopus}, \emph{Rhodotorula}, \emph{Riemerella}, \emph{Saccharomyces}, \emph{Sarcoptes}, \emph{Scolecobasidium}, \emph{Scopulariopsis}, \emph{Scytalidium}, \emph{Sphingobacterium}, \emph{Spirometra}, \emph{Spiroplasma}, \emph{Sporobolomyces}, \emph{Stachybotrys}, \emph{Streptobacillus}, \emph{Strongyloides}, \emph{Syngamus}, \emph{Taenia}, \emph{Tannerella}, \emph{Tenacibaculum}, \emph{Terrimonas}, \emph{Toxocara}, \emph{Treponema}, \emph{Trichinella}, \emph{Trichobilharzia}, \emph{Trichoderma}, \emph{Trichomonas}, \emph{Trichophyton}, \emph{Trichosporon}, \emph{Trichostrongylus}, \emph{Trichuris}, \emph{Tritirachium}, \emph{Trombicula}, \emph{Trypanosoma}, \emph{Tunga}, \emph{Ureaplasma}, \emph{Victivallis}, \emph{Wautersiella}, \emph{Weeksella} or \emph{Wuchereria}.
\strong{Group 2} consists of all microorganisms where the taxonomic phylum is Proteobacteria, Firmicutes, Actinobacteria or Sarcomastigophora, or where the taxonomic genus is \emph{Absidia}, \emph{Acanthamoeba}, \emph{Acholeplasma}, \emph{Acremonium}, \emph{Actinotignum}, \emph{Aedes}, \emph{Alistipes}, \emph{Alloprevotella}, \emph{Alternaria}, \emph{Amoeba}, \emph{Anaerosalibacter}, \emph{Ancylostoma}, \emph{Angiostrongylus}, \emph{Anisakis}, \emph{Anopheles}, \emph{Apophysomyces}, \emph{Arachnia}, \emph{Aspergillus}, \emph{Aureobasidium}, \emph{Bacteroides}, \emph{Basidiobolus}, \emph{Beauveria}, \emph{Bergeyella}, \emph{Blastocystis}, \emph{Blastomyces}, \emph{Borrelia}, \emph{Brachyspira}, \emph{Branhamella}, \emph{Butyricimonas}, \emph{Candida}, \emph{Capillaria}, \emph{Capnocytophaga}, \emph{Catabacter}, \emph{Cetobacterium}, \emph{Chaetomium}, \emph{Chlamydia}, \emph{Chlamydophila}, \emph{Chryseobacterium}, \emph{Chrysonilia}, \emph{Cladophialophora}, \emph{Cladosporium}, \emph{Conidiobolus}, \emph{Contracaecum}, \emph{Cordylobia}, \emph{Cryptococcus}, \emph{Curvularia}, \emph{Deinococcus}, \emph{Demodex}, \emph{Dermatobia}, \emph{Dientamoeba}, \emph{Diphyllobothrium}, \emph{Dirofilaria}, \emph{Dysgonomonas}, \emph{Echinostoma}, \emph{Elizabethkingia}, \emph{Empedobacter}, \emph{Entamoeba}, \emph{Enterobius}, \emph{Exophiala}, \emph{Exserohilum}, \emph{Fasciola}, \emph{Flavobacterium}, \emph{Fonsecaea}, \emph{Fusarium}, \emph{Fusobacterium}, \emph{Giardia}, \emph{Haloarcula}, \emph{Halobacterium}, \emph{Halococcus}, \emph{Hendersonula}, \emph{Heterophyes}, \emph{Histomonas}, \emph{Histoplasma}, \emph{Hymenolepis}, \emph{Hypomyces}, \emph{Hysterothylacium}, \emph{Leishmania}, \emph{Lelliottia}, \emph{Leptosphaeria}, \emph{Leptotrichia}, \emph{Lucilia}, \emph{Lumbricus}, \emph{Malassezia}, \emph{Malbranchea}, \emph{Metagonimus}, \emph{Meyerozyma}, \emph{Microsporidium}, \emph{Microsporum}, \emph{Mortierella}, \emph{Mucor}, \emph{Mycocentrospora}, \emph{Mycoplasma}, \emph{Myroides}, \emph{Necator}, \emph{Nectria}, \emph{Ochroconis}, \emph{Odoribacter}, \emph{Oesophagostomum}, \emph{Oidiodendron}, \emph{Opisthorchis}, \emph{Ornithobacterium}, \emph{Parabacteroides}, \emph{Pediculus}, \emph{Pedobacter}, \emph{Phlebotomus}, \emph{Phocaeicola}, \emph{Phocanema}, \emph{Phoma}, \emph{Pichia}, \emph{Piedraia}, \emph{Pithomyces}, \emph{Pityrosporum}, \emph{Pneumocystis}, \emph{Porphyromonas}, \emph{Prevotella}, \emph{Pseudallescheria}, \emph{Pseudoterranova}, \emph{Pulex}, \emph{Rhizomucor}, \emph{Rhizopus}, \emph{Rhodotorula}, \emph{Riemerella}, \emph{Saccharomyces}, \emph{Sarcoptes}, \emph{Scolecobasidium}, \emph{Scopulariopsis}, \emph{Scytalidium}, \emph{Sphingobacterium}, \emph{Spirometra}, \emph{Spiroplasma}, \emph{Sporobolomyces}, \emph{Stachybotrys}, \emph{Streptobacillus}, \emph{Strongyloides}, \emph{Syngamus}, \emph{Taenia}, \emph{Tannerella}, \emph{Tenacibaculum}, \emph{Terrimonas}, \emph{Toxocara}, \emph{Treponema}, \emph{Trichinella}, \emph{Trichobilharzia}, \emph{Trichoderma}, \emph{Trichomonas}, \emph{Trichophyton}, \emph{Trichosporon}, \emph{Trichostrongylus}, \emph{Trichuris}, \emph{Tritirachium}, \emph{Trombicula}, \emph{Trypanosoma}, \emph{Tunga}, \emph{Ureaplasma}, \emph{Victivallis}, \emph{Wautersiella}, \emph{Weeksella} or \emph{Wuchereria}.
\strong{Group 3} consists of all other microorganisms.
All characters in \eqn{x} and \eqn{n} are ignored that are other than A-Z, a-z, 0-9, spaces and parentheses.
All matches are sorted descending on their matching score and for all user input values, the top match will be returned. This will lead to the effect that e.g., \code{"E. coli"} will return the microbial ID of \emph{Escherichia coli} (\eqn{m = 0.688}, a highly prevalent microorganism found in humans) and not \emph{Entamoeba coli} (\eqn{m = 0.079}, a less prevalent microorganism in humans), although the latter would alphabetically come first.
All matches are sorted descending on their matching score and for all user input values, the top match will be returned. This will lead to the effect that e.g., \code{"E. coli"} will return the microbial ID of \emph{Escherichia coli} (\eqn{m = 0.688}, a highly prevalent microorganism found in humans) and not \emph{Entamoeba coli} (\eqn{m = 0.119}, a less prevalent microorganism in humans), although the latter would alphabetically come first.
}
\section{Source}{