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New mo algorithm, prepare for 2.0
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Dr. Matthijs Berends
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GitHub
parent
63fe160322
commit
cd2acc4a29
@@ -15,6 +15,7 @@
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\alias{mo_kingdom}
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\alias{mo_domain}
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\alias{mo_type}
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\alias{mo_status}
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\alias{mo_gramstain}
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\alias{mo_is_gram_negative}
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\alias{mo_is_gram_positive}
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@@ -25,6 +26,7 @@
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\alias{mo_authors}
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\alias{mo_year}
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\alias{mo_lpsn}
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\alias{mo_gbif}
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\alias{mo_rank}
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\alias{mo_taxonomy}
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\alias{mo_synonyms}
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@@ -32,76 +34,240 @@
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\alias{mo_url}
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\title{Get Properties of a Microorganism}
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\usage{
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mo_name(x, language = get_AMR_locale(), ...)
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mo_name(
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x,
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language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
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...
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)
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mo_fullname(x, language = get_AMR_locale(), ...)
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mo_fullname(
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x,
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language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
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...
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)
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mo_shortname(x, language = get_AMR_locale(), ...)
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mo_shortname(
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x,
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language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
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...
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)
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mo_subspecies(x, language = get_AMR_locale(), ...)
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mo_subspecies(
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x,
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language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
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...
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)
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mo_species(x, language = get_AMR_locale(), ...)
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mo_species(
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x,
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language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
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...
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)
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mo_genus(x, language = get_AMR_locale(), ...)
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mo_genus(
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x,
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language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
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...
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)
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mo_family(x, language = get_AMR_locale(), ...)
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mo_family(
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x,
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language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
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...
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)
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mo_order(x, language = get_AMR_locale(), ...)
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mo_order(
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x,
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language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
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...
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)
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mo_class(x, language = get_AMR_locale(), ...)
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mo_class(
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x,
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language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
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...
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)
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mo_phylum(x, language = get_AMR_locale(), ...)
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mo_phylum(
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x,
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language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
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...
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)
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mo_kingdom(x, language = get_AMR_locale(), ...)
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mo_kingdom(
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x,
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language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
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...
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)
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mo_domain(x, language = get_AMR_locale(), ...)
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mo_domain(
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x,
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language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
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...
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)
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mo_type(x, language = get_AMR_locale(), ...)
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mo_type(
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x,
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language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
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...
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)
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mo_gramstain(x, language = get_AMR_locale(), ...)
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mo_status(
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x,
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language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
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...
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)
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mo_is_gram_negative(x, language = get_AMR_locale(), ...)
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mo_gramstain(
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x,
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language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
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...
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)
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mo_is_gram_positive(x, language = get_AMR_locale(), ...)
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mo_is_gram_negative(
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x,
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language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
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...
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)
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mo_is_yeast(x, language = get_AMR_locale(), ...)
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mo_is_gram_positive(
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x,
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language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
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...
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)
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mo_is_intrinsic_resistant(x, ab, language = get_AMR_locale(), ...)
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mo_is_yeast(
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x,
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language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
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...
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)
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mo_snomed(x, language = get_AMR_locale(), ...)
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mo_is_intrinsic_resistant(
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x,
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ab,
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language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
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...
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)
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mo_ref(x, language = get_AMR_locale(), ...)
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mo_snomed(
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x,
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language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
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...
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)
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mo_authors(x, language = get_AMR_locale(), ...)
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mo_ref(
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x,
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language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
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...
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)
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mo_year(x, language = get_AMR_locale(), ...)
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mo_authors(
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x,
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language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
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...
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)
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mo_lpsn(x, language = get_AMR_locale(), ...)
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mo_year(
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x,
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language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
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...
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)
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mo_rank(x, language = get_AMR_locale(), ...)
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mo_lpsn(
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x,
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language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
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...
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)
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mo_taxonomy(x, language = get_AMR_locale(), ...)
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mo_gbif(
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x,
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language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
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...
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)
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mo_synonyms(x, language = get_AMR_locale(), ...)
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mo_rank(
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x,
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language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
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...
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)
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mo_info(x, language = get_AMR_locale(), ...)
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mo_taxonomy(
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x,
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language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
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...
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)
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mo_url(x, open = FALSE, language = get_AMR_locale(), ...)
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mo_synonyms(
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x,
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language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
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...
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)
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mo_property(x, property = "fullname", language = get_AMR_locale(), ...)
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mo_info(
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x,
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language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
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...
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)
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mo_url(
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x,
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open = FALSE,
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language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
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...
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)
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mo_property(
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x,
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property = "fullname",
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language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
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...
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)
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}
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\arguments{
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\item{x}{any \link{character} (vector) that can be coerced to a valid microorganism code with \code{\link[=as.mo]{as.mo()}}. Can be left blank for auto-guessing the column containing microorganism codes if used in a data set, see \emph{Examples}.}
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\item{language}{language of the returned text, defaults to system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}) and can be overwritten by setting the option \code{AMR_locale}, e.g. \code{options(AMR_locale = "de")}, see \link{translate}. Also used to translate text like "no growth". Use \code{language = NULL} or \code{language = ""} to prevent translation.}
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\item{language}{language to translate text like "no growth", which defaults to the system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}})}
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\item{...}{other arguments passed on to \code{\link[=as.mo]{as.mo()}}, such as 'allow_uncertain' and 'ignore_pattern'}
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\item{keep_synonyms}{a \link{logical} to indicate if old, previously valid taxonomic names must be preserved and not be corrected to currently accepted names. The default is \code{FALSE}, which will return a note if old taxonomic names were processed. The default can be set with \code{options(AMR_keep_synonyms = TRUE)} or \code{options(AMR_keep_synonyms = FALSE)}.}
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\item{...}{other arguments passed on to \code{\link[=as.mo]{as.mo()}}, such as 'minimum_matching_score', 'ignore_pattern', and 'remove_from_input'}
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\item{ab}{any (vector of) text that can be coerced to a valid antibiotic code with \code{\link[=as.ab]{as.ab()}}}
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\item{open}{browse the URL using \code{\link[utils:browseURL]{browseURL()}}}
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\item{property}{one of the column names of the \link{microorganisms} data set: "mo", "fullname", "kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies", "rank", "ref", "species_id", "source", "prevalence" or "snomed", or must be \code{"shortname"}}
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\item{property}{one of the column names of the \link{microorganisms} data set: "mo", "fullname", "status", "kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies", "rank", "ref", "source", "lpsn", "lpsn_parent", "lpsn_renamed_to", "gbif", "gbif_parent", "gbif_renamed_to", "prevalence" or "snomed", or must be \code{"shortname"}}
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}
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\value{
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\itemize{
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@@ -116,11 +282,11 @@ mo_property(x, property = "fullname", language = get_AMR_locale(), ...)
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Use these functions to return a specific property of a microorganism based on the latest accepted taxonomy. All input values will be evaluated internally with \code{\link[=as.mo]{as.mo()}}, which makes it possible to use microbial abbreviations, codes and names as input. See \emph{Examples}.
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}
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\details{
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All functions will return the most recently known taxonomic property according to the Catalogue of Life, except for \code{\link[=mo_ref]{mo_ref()}}, \code{\link[=mo_authors]{mo_authors()}} and \code{\link[=mo_year]{mo_year()}}. Please refer to this example, knowing that \emph{Escherichia blattae} was renamed to \emph{Shimwellia blattae} in 2010:
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All functions will, at default, keep old taxonomic properties. Please refer to this example, knowing that \emph{Escherichia blattae} was renamed to \emph{Shimwellia blattae} in 2010:
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\itemize{
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\item \code{mo_name("Escherichia blattae")} will return \code{"Shimwellia blattae"} (with a message about the renaming)
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\item \code{mo_ref("Escherichia blattae")} will return \code{"Burgess et al., 1973"} (with a message about the renaming)
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\item \code{mo_ref("Shimwellia blattae")} will return \code{"Priest et al., 2010"} (without a message)
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\item \code{mo_ref("Escherichia blattae", keep_synonyms = TRUE)} will return \code{"Burgess et al., 1973"} (with a warning about the renaming)
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\item \code{mo_ref("Shimwellia blattae", keep_synonyms = FALSE)} will return \code{"Priest et al., 2010"} (without a message)
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}
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The short name - \code{\link[=mo_shortname]{mo_shortname()}} - almost always returns the first character of the genus and the full species, like \code{"E. coli"}. Exceptions are abbreviations of staphylococci (such as \emph{"CoNS"}, Coagulase-Negative Staphylococci) and beta-haemolytic streptococci (such as \emph{"GBS"}, Group B Streptococci). Please bear in mind that e.g. \emph{E. coli} could mean \emph{Escherichia coli} (kingdom of Bacteria) as well as \emph{Entamoeba coli} (kingdom of Protozoa). Returning to the full name will be done using \code{\link[=as.mo]{as.mo()}} internally, giving priority to bacteria and human pathogens, i.e. \code{"E. coli"} will be considered \emph{Escherichia coli}. In other words, \code{mo_fullname(mo_shortname("Entamoeba coli"))} returns \code{"Escherichia coli"}.
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@@ -137,7 +303,7 @@ All output \link[=translate]{will be translated} where possible.
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The function \code{\link[=mo_url]{mo_url()}} will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species.
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SNOMED codes - \code{\link[=mo_snomed]{mo_snomed()}} - are from the US Edition of SNOMED CT from 1 September 2020. See \emph{Source} and the \link{microorganisms} data set for more info.
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SNOMED codes - \code{\link[=mo_snomed]{mo_snomed()}} - are from the version of 1 July, 2021. See \emph{Source} and the \link{microorganisms} data set for more info.
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}
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\section{Matching Score for Microorganisms}{
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@@ -150,38 +316,36 @@ where:
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\item \ifelse{html}{\out{<i>x</i> is the user input;}}{\eqn{x} is the user input;}
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\item \ifelse{html}{\out{<i>n</i> is a taxonomic name (genus, species, and subspecies);}}{\eqn{n} is a taxonomic name (genus, species, and subspecies);}
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\item \ifelse{html}{\out{<i>l<sub>n</sub></i> is the length of <i>n</i>;}}{l_n is the length of \eqn{n};}
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\item \ifelse{html}{\out{<i>lev</i> is the <a href="https://en.wikipedia.org/wiki/Levenshtein_distance">Levenshtein distance function</a>, which counts any insertion, deletion and substitution as 1 that is needed to change <i>x</i> into <i>n</i>;}}{lev is the Levenshtein distance function, which counts any insertion, deletion and substitution as 1 that is needed to change \eqn{x} into \eqn{n};}
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\item \ifelse{html}{\out{<i>lev</i> is the <a href="https://en.wikipedia.org/wiki/Levenshtein_distance">Levenshtein distance function</a> (counting any insertion as 1, and any deletion or substitution as 2) that is needed to change <i>x</i> into <i>n</i>;}}{lev is the Levenshtein distance function (counting any insertion as 1, and any deletion or substitution as 2) that is needed to change \eqn{x} into \eqn{n};}
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\item \ifelse{html}{\out{<i>p<sub>n</sub></i> is the human pathogenic prevalence group of <i>n</i>, as described below;}}{p_n is the human pathogenic prevalence group of \eqn{n}, as described below;}
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\item \ifelse{html}{\out{<i>k<sub>n</sub></i> is the taxonomic kingdom of <i>n</i>, set as Bacteria = 1, Fungi = 2, Protozoa = 3, Archaea = 4, others = 5.}}{l_n is the taxonomic kingdom of \eqn{n}, set as Bacteria = 1, Fungi = 2, Protozoa = 3, Archaea = 4, others = 5.}
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}
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The grouping into human pathogenic prevalence (\eqn{p}) is based on experience from several microbiological laboratories in the Netherlands in conjunction with international reports on pathogen prevalence. \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{Acremonium}, \emph{Actinotignum}, \emph{Alternaria}, \emph{Anaerosalibacter}, \emph{Apophysomyces}, \emph{Arachnia}, \emph{Aspergillus}, \emph{Aureobacterium}, \emph{Aureobasidium}, \emph{Bacteroides}, \emph{Basidiobolus}, \emph{Beauveria}, \emph{Blastocystis}, \emph{Branhamella}, \emph{Calymmatobacterium}, \emph{Candida}, \emph{Capnocytophaga}, \emph{Catabacter}, \emph{Chaetomium}, \emph{Chryseobacterium}, \emph{Chryseomonas}, \emph{Chrysonilia}, \emph{Cladophialophora}, \emph{Cladosporium}, \emph{Conidiobolus}, \emph{Cryptococcus}, \emph{Curvularia}, \emph{Exophiala}, \emph{Exserohilum}, \emph{Flavobacterium}, \emph{Fonsecaea}, \emph{Fusarium}, \emph{Fusobacterium}, \emph{Hendersonula}, \emph{Hypomyces}, \emph{Koserella}, \emph{Lelliottia}, \emph{Leptosphaeria}, \emph{Leptotrichia}, \emph{Malassezia}, \emph{Malbranchea}, \emph{Mortierella}, \emph{Mucor}, \emph{Mycocentrospora}, \emph{Mycoplasma}, \emph{Nectria}, \emph{Ochroconis}, \emph{Oidiodendron}, \emph{Phoma}, \emph{Piedraia}, \emph{Pithomyces}, \emph{Pityrosporum}, \emph{Prevotella}, \emph{Pseudallescheria}, \emph{Rhizomucor}, \emph{Rhizopus}, \emph{Rhodotorula}, \emph{Scolecobasidium}, \emph{Scopulariopsis}, \emph{Scytalidium}, \emph{Sporobolomyces}, \emph{Stachybotrys}, \emph{Stomatococcus}, \emph{Treponema}, \emph{Trichoderma}, \emph{Trichophyton}, \emph{Trichosporon}, \emph{Tritirachium} or \emph{Ureaplasma}. \strong{Group 3} consists of all other microorganisms.
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The grouping into human pathogenic prevalence (\eqn{p}) is based on experience from several microbiological laboratories in the Netherlands in conjunction with international reports on pathogen prevalence:
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\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.
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|
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\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.
|
||||
|
||||
Since \code{AMR} version 1.8.1, common microorganism abbreviations are ignored in determining the matching score. These abbreviations are currently: AIEC, ATEC, BORSA, CRSM, DAEC, EAEC, EHEC, EIEC, EPEC, ETEC, GISA, MRPA, MRSA, MRSE, MSSA, MSSE, NMEC, PISP, PRSP, STEC, UPEC, VISA, VISP, VRE, VRSA and VRSP.
|
||||
}
|
||||
|
||||
\section{Catalogue of Life}{
|
||||
|
||||
\if{html}{\figure{logo_col.png}{options: height="40" style=margin-bottom:"5"} \cr}
|
||||
This package contains the complete taxonomic tree of almost all microorganisms (~71,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, \url{http://www.catalogueoflife.org}). The CoL is the most comprehensive and authoritative global index of species currently available. Nonetheless, we supplemented the CoL data with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, \href{https://lpsn.dsmz.de}{lpsn.dsmz.de}). This supplementation is needed until the \href{https://github.com/CatalogueOfLife/general}{CoL+ project} is finished, which we await.
|
||||
|
||||
\link[=catalogue_of_life]{Click here} for more information about the included taxa. Check which versions of the CoL and LPSN were included in this package with \code{\link[=catalogue_of_life_version]{catalogue_of_life_version()}}.
|
||||
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}{
|
||||
|
||||
\enumerate{
|
||||
\item Becker K \emph{et al.} \strong{Coagulase-Negative Staphylococci}. 2014. Clin Microbiol Rev. 27(4): 870-926; \doi{10.1128/CMR.00109-13}
|
||||
\item Becker K \emph{et al.} \strong{Implications of identifying the recently defined members of the \emph{S. aureus} complex, \emph{S. argenteus} and \emph{S. schweitzeri}: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).} 2019. Clin Microbiol Infect; \doi{10.1016/j.cmi.2019.02.028}
|
||||
\item Becker K \emph{et al.} \strong{Emergence of coagulase-negative staphylococci} 2020. Expert Rev Anti Infect Ther. 18(4):349-366; \doi{10.1080/14787210.2020.1730813}
|
||||
\item Lancefield RC \strong{A serological differentiation of human and other groups of hemolytic streptococci}. 1933. J Exp Med. 57(4): 571-95; \doi{10.1084/jem.57.4.571}
|
||||
\item Catalogue of Life: 2019 Annual Checklist, \url{http://www.catalogueoflife.org}
|
||||
\item List of Prokaryotic names with Standing in Nomenclature (5 October 2021), \doi{10.1099/ijsem.0.004332}
|
||||
\item US Edition of SNOMED CT from 1 September 2020, retrieved from the Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS), OID 2.16.840.1.114222.4.11.1009, version 12; url: \url{https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009}
|
||||
\item Berends MS \emph{et al.} (2022). \strong{AMR: An R Package for Working with Antimicrobial Resistance Data}. \emph{Journal of Statistical Software}, 104(3), 1-31; \doi{10.18637/jss.v104.i03}
|
||||
\item Becker K \emph{et al.} (2014). \strong{Coagulase-Negative Staphylococci.} \emph{Clin Microbiol Rev.} 27(4): 870-926; \doi{10.1128/CMR.00109-13}
|
||||
\item Becker K \emph{et al.} (2019). \strong{Implications of identifying the recently defined members of the \emph{S. aureus} complex, \emph{S. argenteus} and \emph{S. schweitzeri}: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).} \emph{Clin Microbiol Infect}; \doi{10.1016/j.cmi.2019.02.028}
|
||||
\item Becker K \emph{et al.} (2020). \strong{Emergence of coagulase-negative staphylococci} \emph{Expert Rev Anti Infect Ther.} 18(4):349-366; \doi{10.1080/14787210.2020.1730813}
|
||||
\item Lancefield RC (1933). \strong{A serological differentiation of human and other groups of hemolytic streptococci}. \emph{J Exp Med.} 57(4): 571-95; \doi{10.1084/jem.57.4.571}
|
||||
\item Berends MS \emph{et al.} (2022). \strong{Trends in Occurrence and Phenotypic Resistance of Coagulase-Negative Staphylococci (CoNS) Found in Human Blood in the Northern Netherlands between 2013 and 2019} \emph{Microorganisms} 10(9), 1801; \doi{10.3390/microorganisms10091801}
|
||||
\item Parte, AC \emph{et al.} (2020). \strong{List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ.} International Journal of Systematic and Evolutionary Microbiology, 70, 5607-5612; \doi{10.1099/ijsem.0.004332}. Accessed from \url{https://lpsn.dsmz.de} on 12 September, 2022.
|
||||
\item GBIF Secretariat (November 26, 2021). GBIF Backbone Taxonomy. Checklist dataset \doi{10.15468/39omei}. Accessed from \url{https://www.gbif.org} on 12 September, 2022.
|
||||
\item Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS). US Edition of SNOMED CT from 1 September 2020. Value Set Name 'Microoganism', OID 2.16.840.1.114222.4.11.1009 (v12). URL: \url{https://phinvads.cdc.gov}
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
Reference in New Issue
Block a user