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Fixes for Salmonella

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dr. M.S. (Matthijs) Berends
2022-12-17 14:31:33 +01:00
parent 5f3a7694aa
commit 23fe427cbc
42 changed files with 375 additions and 445 deletions
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22
data-raw/microorganisms.txt
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@ -41483,7 +41483,6 @@
"B_SLMNL_CHRD" "Salmonella Chiredzi" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Chiredzi" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_CHTT" "Salmonella Chittagong" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Chittagong" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_CHLR" "Salmonella choleraesuis" "synonym" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "choleraesuis" "" "species" "Weldin, 1927" "LPSN" "780746" "516547" "784857" "7515106" "3221815" "9701185" 1 ""
"B_SLMNL_CHLRS" "Salmonella Choleraesuis" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Choleraesuis" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_CHLR_ARZN" "Salmonella choleraesuis arizonae" "synonym" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "choleraesuis" "arizonae" "subspecies" "Le Minor et al., 1985" "LPSN" "780747" "780746" "780755" "5427587" "7515106" "5427586" 1 ""
"B_SLMNL_CHLR_BNGR" "Salmonella choleraesuis bongori" "synonym" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "choleraesuis" "bongori" "subspecies" "Le Minor et al., 1985" "LPSN" "780748" "780746" "780745" "5427597" "7515106" "5427596" 1 ""
"B_SLMNL_CHLR_CHLR" "Salmonella choleraesuis choleraesuis" "synonym" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "choleraesuis" "choleraesuis" "subspecies" "Le Minor et al., 1985" "LPSN" "780749" "780746" "780758" "5427590" "7515106" "5427589" 1 ""
@ -41624,7 +41623,6 @@
"B_SLMNL_ENTR_INDC" "Salmonella enterica indica" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "indica" "subspecies" "Le Minor et al., 1987" "LPSN" "780760" "784857" "5427582" "9701185" 1 ""
"B_SLMNL_ENTR_SALM" "Salmonella enterica salamae" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "salamae" "subspecies" "Le Minor et al., 1987" "LPSN" "780761" "784857" "5427584" "9701185" 1 ""
"B_SLMNL_RTDS" "Salmonella enteritidis" "synonym" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enteritidis" "" "species" "Castellani et al., 1919" "LPSN" "780762" "516547" "784857" "5427592" "3221815" "9701185" 1 ""
"B_SLMNL_ENTRT" "Salmonella Enteritidis" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Enteritidis" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_ENUG" "Salmonella Enugu" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Enugu" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_EPLN" "Salmonella Epalinges" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Epalinges" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_EPCR" "Salmonella Epicrates" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Epicrates" "subspecies" "manually added" "784857" "9701185" 1 ""
@ -42279,7 +42277,6 @@
"B_SLMNL_PLMN" "Salmonella Palamaner" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Palamaner" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_PALM" "Salmonella Palime" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Palime" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_PANM" "Salmonella panama" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "panama" "" "species" "Kauffmann, 1934" "GBIF" "9407232" "3221815" 1 ""
"B_SLMNL_PANAM" "Salmonella Panama" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Panama" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_PAPN" "Salmonella Papuana" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Papuana" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_PARK" "Salmonella Parakou" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Parakou" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_PRTY" "Salmonella paratyphi" "synonym" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "paratyphi" "" "species" "Ezaki et al., 2000" "LPSN" "784858" "516547" "784857" "5427593" "3221815" "9701185" 1 "840687007"
@ -42577,7 +42574,6 @@
"B_SLMNL_TUDU" "Salmonella Tudu" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Tudu" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_TUMD" "Salmonella Tumodi" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Tumodi" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_TYPH" "Salmonella typhi" "synonym" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "typhi" "" "species" "Warren et al., 1930" "LPSN" "784859" "516547" "784857" "5427594" "3221815" "9701185" 1 "712764007"
"B_SLMNL_TYPHI" "Salmonella Typhi" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Typhi" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_HMRM" "Salmonella typhimurium" "synonym" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "typhimurium" "" "species" "Castellani et al., 1919" "LPSN" "780770" "516547" "784857" "5427591" "3221815" "9701185" 1 ""
"B_SLMNL_THSS" "Salmonella Typhisuis" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Typhisuis" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_TYRS" "Salmonella Tyresoe" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Tyresoe" "subspecies" "manually added" "784857" "9701185" 1 ""
@ -45499,15 +45495,15 @@
"B_STRPT_GLLL_PSTR" "Streptococcus gallolyticus pasteurianus" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "gallolyticus" "pasteurianus" "subspecies" "Beck et al., 2008" "LPSN" "781340" "781337" "3227070" 1 ""
"B_STRPT_GARV" "Streptococcus garvieae" "synonym" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "garvieae" "" "species" "Collins et al., 1984" "LPSN" "781341" "517118" "777418" 1 ""
"B_STRPT_GRDN" "Streptococcus gordonii" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "gordonii" "" "species" "Kilian et al., 1989" "LPSN" "781342" "517118" 1 "113986004"
"B_STRPT_GRPA" "Streptococcus group A" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "group A" "" "species" "Lancefield, 1933" "manually added" 1 ""
"B_STRPT_GRPB" "Streptococcus group B" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "group B" "" "species" "Lancefield, 1933" "manually added" 1 ""
"B_STRPT_GRPC" "Streptococcus group C" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "group C" "" "species" "Lancefield, 1933" "manually added" 1 ""
"B_STRPT_GRPD" "Streptococcus group D" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "group D" "" "species" "Lancefield, 1933" "manually added" 1 ""
"B_STRPT_GRPF" "Streptococcus group F" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "group F" "" "species" "Lancefield, 1933" "manually added" 1 ""
"B_STRPT_GRPG" "Streptococcus group G" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "group G" "" "species" "Lancefield, 1933" "manually added" 1 ""
"B_STRPT_GRPH" "Streptococcus group H" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "group H" "" "species" "Lancefield, 1933" "manually added" 1 ""
"B_STRPT_GRPK" "Streptococcus group K" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "group K" "" "species" "Lancefield, 1933" "manually added" 1 ""
"B_STRPT_GRPL" "Streptococcus group L" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "group L" "" "species" "Lancefield, 1933" "manually added" 1 ""
"B_STRPT_GRPA" "Streptococcus Group A" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "Group A" "" "species" "Lancefield, 1933" "manually added" 1 ""
"B_STRPT_GRPB" "Streptococcus Group B" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "Group B" "" "species" "Lancefield, 1933" "manually added" 1 ""
"B_STRPT_GRPC" "Streptococcus Group C" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "Group C" "" "species" "Lancefield, 1933" "manually added" 1 ""
"B_STRPT_GRPD" "Streptococcus Group D" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "Group D" "" "species" "Lancefield, 1933" "manually added" 1 ""
"B_STRPT_GRPF" "Streptococcus Group F" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "Group F" "" "species" "Lancefield, 1933" "manually added" 1 ""
"B_STRPT_GRPG" "Streptococcus Group G" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "Group G" "" "species" "Lancefield, 1933" "manually added" 1 ""
"B_STRPT_GRPH" "Streptococcus Group H" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "Group H" "" "species" "Lancefield, 1933" "manually added" 1 ""
"B_STRPT_GRPK" "Streptococcus Group K" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "Group K" "" "species" "Lancefield, 1933" "manually added" 1 ""
"B_STRPT_GRPL" "Streptococcus Group L" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "Group L" "" "species" "Lancefield, 1933" "manually added" 1 ""
"B_STRPT_GWNG" "Streptococcus gwangjuense" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "gwangjuense" "" "species" "GBIF" "11190550" "3223465" 1 ""
"B_STRPT_HLCH" "Streptococcus halichoeri" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "halichoeri" "" "species" "Shewmaker et al., 2016" "LPSN" "781344" "517118" 1 "438161002"
"B_STRPT_HLTS" "Streptococcus halitosis" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "halitosis" "" "species" "GBIF" "10822581" "3223465" 1 ""