All functions will, at default, keep old taxonomic properties. Please refer to this example, knowing that Escherichia blattae was renamed to Shimwellia blattae in 2010:
mo_name("Escherichia blattae") will return "Shimwellia blattae" (with a message about the renaming)
mo_ref("Escherichia blattae", keep_synonyms = TRUE) will return "Burgess et al., 1973" (with a warning about the renaming)
mo_ref("Shimwellia blattae", keep_synonyms = FALSE) will return "Priest et al., 2010" (without a message)
All functions will, at default, keep old taxonomic properties. Please refer to this example, knowing that Escherichia blattae was renamed to Shimwellia blattae in 2010:
mo_name("Escherichia blattae") will return "Shimwellia blattae" (with a note about the renaming)
mo_ref("Escherichia blattae", keep_synonyms = TRUE) will return "Burgess et al., 1973" (without a note)
mo_ref("Shimwellia blattae", keep_synonyms = FALSE) will return "Priest et al., 2010" (without a note)
The short name - mo_shortname() - almost always returns the first character of the genus and the full species, like "E. coli". Exceptions are abbreviations of staphylococci (such as "CoNS", Coagulase-Negative Staphylococci) and beta-haemolytic streptococci (such as "GBS", Group B Streptococci). Please bear in mind that e.g. E. coli could mean Escherichia coli (kingdom of Bacteria) as well as Entamoeba coli (kingdom of Protozoa). Returning to the full name will be done using as.mo() internally, giving priority to bacteria and human pathogens, i.e. "E. coli" will be considered Escherichia coli. In other words, mo_fullname(mo_shortname("Entamoeba coli")) returns "Escherichia coli".
Since the top-level of the taxonomy is sometimes referred to as 'kingdom' and sometimes as 'domain', the functions mo_kingdom() and mo_domain() return the exact same results.
-The Gram stain - mo_gramstain() - will be determined based on the taxonomic kingdom and phylum. Originally, Cavalier-Smith defined the so-called subkingdoms Negibacteria and Posibacteria (2002, PMID 11837318), and only considered these phyla as Posibacteria: Actinobacteria, Chloroflexi, Firmicutes, and Tenericutes. All of these phyla were renamed to Actinomycetota, Chloroflexota, Bacillota, and Mycoplasmatota (2021, PMID 34694987). Bacteria in these phyla are considered Gram-positive in this AMR package, except for members of the class Negativicutes (within phylum Bacillota) which are Gram-negative. All other bacteria are considered Gram-negative. Species outside the kingdom of Bacteria will return a value NA. Functions mo_is_gram_negative() and mo_is_gram_positive() always return TRUE or FALSE (or NA when the input is NA or the MO code is UNKNOWN), thus always return FALSE for species outside the taxonomic kingdom of Bacteria.
+Determination of the Gram stain - mo_gramstain() - will be based on the taxonomic kingdom and phylum. Originally, Cavalier-Smith defined the so-called subkingdoms Negibacteria and Posibacteria (2002, PMID 11837318), and only considered these phyla as Posibacteria: Actinobacteria, Chloroflexi, Firmicutes, and Tenericutes. These phyla were renamed to Actinomycetota, Chloroflexota, Bacillota, and Mycoplasmatota (2021, PMID 34694987). Bacteria in these phyla are considered Gram-positive in this AMR package, except for members of the class Negativicutes (within phylum Bacillota) which are Gram-negative. All other bacteria are considered Gram-negative. Species outside the kingdom of Bacteria will return a value NA. Functions mo_is_gram_negative() and mo_is_gram_positive() always return TRUE or FALSE (or NA when the input is NA or the MO code is UNKNOWN), thus always return FALSE for species outside the taxonomic kingdom of Bacteria.
Determination of yeasts - mo_is_yeast() - will be based on the taxonomic kingdom and class. Budding yeasts are fungi of the phylum Ascomycota, class Saccharomycetes (also called Hemiascomycetes). True yeasts are aggregated into the underlying order Saccharomycetales. Thus, for all microorganisms that are member of the taxonomic class Saccharomycetes, the function will return TRUE. It returns FALSE otherwise (or NA when the input is NA or the MO code is UNKNOWN).
-Intrinsic resistance - mo_is_intrinsic_resistant() - will be determined based on the intrinsic_resistant data set, which is based on 'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3 (2021). The mo_is_intrinsic_resistant() functions can be vectorised over arguments x (input for microorganisms) and over ab (input for antibiotics).
+Determination of intrinsic resistance - mo_is_intrinsic_resistant() - will be based on the intrinsic_resistant data set, which is based on 'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3 (2021). The mo_is_intrinsic_resistant() function can be vectorised over both argument x (input for microorganisms) and ab (input for antibiotics).
All output will be translated where possible.
The function mo_url() will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species.
SNOMED codes - mo_snomed() - are from the version of 1 July, 2021. See Source and the microorganisms data set for more info.
@@ -433,7 +433,7 @@
Group 2 consists of all microorganisms where the taxonomic phylum is Proteobacteria, Firmicutes, Actinobacteria or Sarcomastigophora, or where the taxonomic genus is Absidia, Acanthamoeba, Acholeplasma, Acremonium, Actinotignum, Aedes, Alistipes, Alloprevotella, Alternaria, Amoeba, Anaerosalibacter, Ancylostoma, Angiostrongylus, Anisakis, Anopheles, Apophysomyces, Arachnia, Aspergillus, Aureobasidium, Bacteroides, Basidiobolus, Beauveria, Bergeyella, Blastocystis, Blastomyces, Borrelia, Brachyspira, Branhamella, Butyricimonas, Candida, Capillaria, Capnocytophaga, Catabacter, Cetobacterium, Chaetomium, Chlamydia, Chlamydophila, Chryseobacterium, Chrysonilia, Cladophialophora, Cladosporium, Conidiobolus, Contracaecum, Cordylobia, Cryptococcus, Curvularia, Deinococcus, Demodex, Dermatobia, Dientamoeba, Diphyllobothrium, Dirofilaria, Dysgonomonas, Echinostoma, Elizabethkingia, Empedobacter, Entamoeba, Enterobius, Exophiala, Exserohilum, Fasciola, Flavobacterium, Fonsecaea, Fusarium, Fusobacterium, Giardia, Haloarcula, Halobacterium, Halococcus, Hendersonula, Heterophyes, Histomonas, Histoplasma, Hymenolepis, Hypomyces, Hysterothylacium, Leishmania, Lelliottia, Leptosphaeria, Leptotrichia, Lucilia, Lumbricus, Malassezia, Malbranchea, Metagonimus, Meyerozyma, Microsporidium, Microsporum, Mortierella, Mucor, Mycocentrospora, Mycoplasma, Myroides, Necator, Nectria, Ochroconis, Odoribacter, Oesophagostomum, Oidiodendron, Opisthorchis, Ornithobacterium, Parabacteroides, Pediculus, Pedobacter, Phlebotomus, Phocaeicola, Phocanema, Phoma, Pichia, Piedraia, Pithomyces, Pityrosporum, Pneumocystis, Porphyromonas, Prevotella, Pseudallescheria, Pseudoterranova, Pulex, Rhizomucor, Rhizopus, Rhodotorula, Riemerella, Saccharomyces, Sarcoptes, Scolecobasidium, Scopulariopsis, Scytalidium, Sphingobacterium, Spirometra, Spiroplasma, Sporobolomyces, Stachybotrys, Streptobacillus, Strongyloides, Syngamus, Taenia, Tannerella, Tenacibaculum, Terrimonas, Toxocara, Treponema, Trichinella, Trichobilharzia, Trichoderma, Trichomonas, Trichophyton, Trichosporon, Trichostrongylus, Trichuris, Tritirachium, Trombicula, Trypanosoma, Tunga, Ureaplasma, Victivallis, Wautersiella, Weeksella or Wuchereria.
Group 3 consists of all other microorganisms.
All characters in \(x\) and \(n\) 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., "E. coli" will return the microbial ID of Escherichia coli (\(m = 0.688\), a highly prevalent microorganism found in humans) and not Entamoeba coli (\(m = 0.119\), 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., "E. coli" will return the microbial ID of Escherichia coli (\(m = 0.688\), a highly prevalent microorganism found in humans) and not Entamoeba coli (\(m = 0.079\), a less prevalent microorganism in humans), although the latter would alphabetically come first.