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(v2.1.1.9064) update all microbial taxonomy, add mycobank, big documentation update

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dr. M.S. (Matthijs) Berends
2024-07-16 14:51:57 +02:00
parent 4f9db23684
commit 640888f408
191 changed files with 321091 additions and 89382 deletions
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R/aa_globals.R
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@@ -6,9 +6,9 @@
# https://github.com/msberends/AMR #
# #
# PLEASE CITE THIS SOFTWARE AS: #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# Berends MS, Luz CF, Friedrich AW, et al. (2022). #
# AMR: An R Package for Working with Antimicrobial Resistance Data. #
# Journal of Statistical Software, 104(3), 1-31. #
# https://doi.org/10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen and the University Medical #
@@ -86,26 +86,37 @@ EUCAST_VERSION_EXPERT_RULES <- list(
TAXONOMY_VERSION <- list(
GBIF = list(
accessed_date = as.Date("2024-01-08"),
name = "Global Biodiversity Information Facility (GBIF)",
accessed_date = as.Date("2024-06-24"),
citation = "GBIF Secretariat (2023). GBIF Backbone Taxonomy. Checklist dataset \\doi{10.15468/39omei}.",
url = "https://www.gbif.org"
),
LPSN = list(
accessed_date = as.Date("2022-12-11"),
name = "List of Prokaryotic names with Standing in Nomenclature (LPSN)",
accessed_date = as.Date("2024-06-24"),
citation = "Parte, AC *et al.* (2020). **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}.",
url = "https://lpsn.dsmz.de"
),
MycoBank = list(
name = "MycoBank",
accessed_date = as.Date("2024-06-24"),
citation = "Vincent, R *et al* (2013). **MycoBank gearing up for new horizons.** IMA Fungus, 4(2), 371-9; \\doi{10.5598/imafungus.2013.04.02.16}.",
url = "https://www.mycobank.org"
),
BacDive = list(
accessed_date = as.Date("2023-05-12"),
name = "BacDive",
accessed_date = as.Date("2024-07-16"),
citation = "Reimer, LC *et al.* (2022). ***BacDive* in 2022: the knowledge base for standardized bacterial and archaeal data.** Nucleic Acids Res., 50(D1):D741-D74; \\doi{10.1093/nar/gkab961}.",
url = "https://bacdive.dsmz.de"
),
SNOMED = list(
accessed_date = as.Date("2021-07-01"),
name = "Systematized Nomenclature of Medicine - Clinical Terms (SNOMED-CT)",
accessed_date = as.Date("2024-07-16"),
citation = "Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS). US Edition of SNOMED CT from 1 September 2020. Value Set Name 'Microorganism', OID 2.16.840.1.114222.4.11.1009 (v12).",
url = "https://phinvads.cdc.gov"
),
LOINC = list(
name = "Logical Observation Identifiers Names and Codes (LOINC)",
accessed_date = as.Date("2023-10-19"),
citation = "Logical Observation Identifiers Names and Codes (LOINC), Version 2.76 (18 September, 2023).",
url = "https://loinc.org"