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(v3.0.1.9059) Update taxonomy of microorganisms

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Matthijs Berends
2026-06-23 01:38:13 +02:00
committed by GitHub
parent 0af3f84655
commit 3f9f931777
123 changed files with 121928 additions and 94162 deletions
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20
R/aa_globals.R
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@@ -104,26 +104,27 @@ EUCAST_VERSION_EXPECTED_PHENOTYPES <- list(
TAXONOMY_VERSION <- list(
GBIF = list(
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}.",
name = "Global Biodiversity Information Facility (GBIF), via Catalogue of Life (COL)",
accessed_date = as.Date("2026-05-07"),
# take the citation from https://www.gbif.org/dataset/7ddf754f-d193-4cc9-b351-99906754a03b#citation
citation = "Banki, O. *et al.* (2026). Catalogue of Life (2026-04-18 XR). Catalogue of Life Foundation, Amsterdam, Netherlands. \\doi{10.48580/dgxjw}.",
url = "https://www.gbif.org"
),
LPSN = list(
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}.",
accessed_date = as.Date("2026-05-07"),
citation = "Freese, HM *et al.* (2026). **TYGS and LPSN in 2025: a Global Core Biodata Resource for genome-based classification and nomenclature of prokaryotes within DSMZ Digital Diversity.** Nucleic Acids Research, 54, D884\u2013D891; \\doi{10.1093/nar/gkaf1110}.",
url = "https://lpsn.dsmz.de"
),
MycoBank = list(
name = "MycoBank",
accessed_date = as.Date("2024-06-24"),
accessed_date = as.Date("2026-05-07"),
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(
name = "BacDive",
accessed_date = as.Date("2024-07-16"),
accessed_date = as.Date("2026-05-07"),
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"
),
@@ -148,10 +149,13 @@ TAXONOMY_VERSION <- list(
)
globalVariables(c(
".coverage",
".GenericCallEnv",
".lower",
".mo",
".rowid",
".syndromic_group",
".upper",
"ab",
"ab_txt",
"affect_ab_name",
@@ -187,6 +191,7 @@ globalVariables(c(
"hjust",
"host_index",
"host_match",
"incidence",
"input",
"input_given",
"intrinsic_resistant",
@@ -214,6 +219,7 @@ globalVariables(c(
"old",
"old_name",
"p_susceptible",
"pathogen",
"pattern",
"R",
"rank_index",