website update

data-raw/microorganisms.md5

@@ -1 +1 @@
-b3734ad222d485de6923fc9957d8f2f5
+7846247d4113c4e8f550cfd2cb87467f

data-raw/microorganisms.txt

@@ -45279,7 +45279,7 @@
 "B_STNTR_INDC"	"Stenotrophomonas indicatrix"	"accepted"	"Bacteria"	"Pseudomonadota"	"Gammaproteobacteria"	"Lysobacterales"	"Lysobacteraceae"	"Stenotrophomonas"	"indicatrix"	""	"species"	"Weber et al., 2018"	"LPSN"	"797782"	"516670"		"10701219"			1.5	""
 "B_STNTR_KRNS"	"Stenotrophomonas koreensis"	"accepted"	"Bacteria"	"Pseudomonadota"	"Gammaproteobacteria"	"Lysobacterales"	"Lysobacteraceae"	"Stenotrophomonas"	"koreensis"	""	"species"	"Yang et al., 2006"	"LPSN"	"781248"	"516670"		"3222376"			1.5	""
 "B_STNTR_LCTT"	"Stenotrophomonas lactitubi"	"accepted"	"Bacteria"	"Pseudomonadota"	"Gammaproteobacteria"	"Lysobacterales"	"Lysobacteraceae"	"Stenotrophomonas"	"lactitubi"	""	"species"	"Weber et al., 2018"	"LPSN"	"797783"	"516670"		"10788780"			1.5	""
-"B_STNTR_MLTP"	"Stenotrophomonas maltophilia"	"synonym"	"Bacteria"	"Pseudomonadota"	"Gammaproteobacteria"	"Lysobacterales"	"Lysobacteraceae"	"Stenotrophomonas"	"maltophilia"	""	"species"	"Palleroni et al., 1993"	"LPSN"	"781249"	"516670"	"783141"	"10912104"			1	"113697002"
+"B_STNTR_MLTP"	"Stenotrophomonas maltophilia"	"accepted"	"Bacteria"	"Pseudomonadota"	"Gammaproteobacteria"	"Lysobacterales"	"Lysobacteraceae"	"Stenotrophomonas"	"maltophilia"	""	"species"	"Palleroni et al., 1993"	"LPSN"	"781249"	"516670"		"10912104"			1	"113697002"
 "B_STNTR_NTRT"	"Stenotrophomonas nitritireducens"	"accepted"	"Bacteria"	"Pseudomonadota"	"Gammaproteobacteria"	"Lysobacterales"	"Lysobacteraceae"	"Stenotrophomonas"	"nitritireducens"	""	"species"	"Finkmann et al., 2000"	"LPSN"	"781250"	"516670"		"3222370"			1.5	"416746005"
 "B_STNTR_PNCH"	"Stenotrophomonas panacihumi"	"accepted"	"Bacteria"	"Pseudomonadota"	"Gammaproteobacteria"	"Lysobacterales"	"Lysobacteraceae"	"Stenotrophomonas"	"panacihumi"	""	"species"	"Yi et al., 2010"	"GBIF"				"11141735"			1.5	""
 "B_STNTR_PAVN"	"Stenotrophomonas pavanii"	"accepted"	"Bacteria"	"Pseudomonadota"	"Gammaproteobacteria"	"Lysobacterales"	"Lysobacteraceae"	"Stenotrophomonas"	"pavanii"	""	"species"	"Ramos et al., 2011"	"LPSN"	"789171"	"516670"		"8102737"			1.5	"704977000"

data-raw/reproduction_of_microorganisms.R

@@ -1357,19 +1357,27 @@ taxonomy <- taxonomy %>%
 
 # set class <mo>
 class(taxonomy$mo) <- c("mo", "character")
+microorganisms <- taxonomy
 
-### this was previously needed?? Since 2022 M. catarrhalis seems to be "accepted" again
-# # Moraxella catarrhalis was named Branhamella catarrhalis (Catlin, 1970), but this is unaccepted in clinical microbiology
-# # we keep them both
-# taxonomy$status[which(taxonomy$fullname == "Moraxella catarrhalis")]
-# taxonomy$lpsn_renamed_to[which(taxonomy$fullname == "Moraxella catarrhalis")]
-# taxonomy$status[which(taxonomy$fullname == "Moraxella catarrhalis")] <- "accepted"
-# taxonomy$lpsn_renamed_to[which(taxonomy$fullname == "Moraxella catarrhalis")] <- NA_character_
+
+# Restore 'synonym' microorganisms to 'accepted' --------------------------
+
+# according to LPSN: Stenotrophomonas maltophilia is the correct name if this species is regarded as a separate species (i.e., if its nomenclatural type is not assigned to another species whose name is validly published, legitimate and not rejected and has priority) within a separate genus Stenotrophomonas.
+# https://lpsn.dsmz.de/species/stenotrophomonas-maltophilia
+
+# all MO's to keep as 'accepted', not as 'synonym':
+to_restore <- c("Stenotrophomonas maltophilia",
+                "Moraxella catarrhalis")
+all(to_restore %in% microorganisms$fullname)
+for (nm in to_restore) {
+  microorganisms$lpsn_renamed_to[which(microorganisms$fullname == nm)] <- NA
+  microorganisms$gbif_renamed_to[which(microorganisms$fullname == nm)] <- NA
+  microorganisms$status[which(microorganisms$fullname == nm)] <- "accepted"
+}
 
 
 # Save to package ---------------------------------------------------------
 
-microorganisms <- taxonomy
 usethis::use_data(microorganisms, overwrite = TRUE, version = 2, compress = "xz")
 rm(microorganisms)