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updated microorganism codes

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dr. M.S. (Matthijs) Berends
2023-05-26 16:10:01 +02:00
parent 0bcf55d3b6
commit c6135d2082
14 changed files with 59 additions and 42 deletions
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man/mo_property.Rd
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@@ -333,7 +333,7 @@ Determination of bacterial oxygen tolerance (\code{\link[=mo_oxygen_tolerance]{m
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.
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.
SNOMED codes (\code{\link[=mo_snomed]{mo_snomed()}}) are from the version of July 1st, 2021. See \emph{Source} and the \link{microorganisms} data set for more info.
Old taxonomic names (so-called 'synonyms') can be retrieved with \code{\link[=mo_synonyms]{mo_synonyms()}} (which will have the scientific reference as \link[base:names]{name}), the current taxonomic name can be retrieved with \code{\link[=mo_current]{mo_current()}}. Both functions return full names.
@@ -353,11 +353,11 @@ This function uses \code{\link[=as.mo]{as.mo()}} internally, which uses an advan
\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{Micro.rganisms} 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 11 December, 2022.
\item GBIF Secretariat (2022). GBIF Backbone Taxonomy. Checklist dataset \doi{10.15468/39omei}. Accessed from \url{https://www.gbif.org} on 11 December, 2022.
\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 December 11th, 2022.
\item GBIF Secretariat (2022). GBIF Backbone Taxonomy. Checklist dataset \doi{10.15468/39omei}. Accessed from \url{https://www.gbif.org} on December 11th, 2022.
\item Reimer, LC \emph{et al.} (2022). \strong{\emph{BacDive} in 2022: the knowledge base for standardized bacterial and archaeal data.} Nucleic Acids Res., 50(D1):D741-D74; \doi{10.1093/nar/gkab961}. Accessed from \url{https://bacdive.dsmz.de} on May 12th, 2023.
\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}
\item Bartlett A \emph{et al.} (2022). \strong{A comprehensive list of bacterial pathogens infecting humans} \emph{Microbiology} 168:001269; \doi{10.1099/mic.0.001269}
\item Reimer \emph{et al.} (2022). \strong{\emph{BacDive} in 2022: the knowledge base for standardized bacterial and archaeal data.} \emph{Nucleic Acids Res.} 2022 Jan 7;50(D1):D741-D746; \doi{10.1093/nar/gkab961}
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