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Fix some WHONET codes

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dr. M.S. (Matthijs) Berends
2023-04-14 11:12:26 +02:00
parent 549790c2a6
commit 147f9112e9
21 changed files with 109 additions and 60 deletions
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"mo" "fullname" "status" "kingdom" "phylum" "class" "order" "family" "genus" "species" "subspecies" "rank" "ref" "source" "lpsn" "lpsn_parent" "lpsn_renamed_to" "gbif" "gbif_parent" "gbif_renamed_to" "prevalence" "snomed"
"B_GRAMN" "(unknown Gram-negatives)" "accepted" "Bacteria" "(unknown phylum)" "(unknown class)" "(unknown order)" "(unknown family)" "(unknown Gram-negatives)" "(unknown species)" "(unknown subspecies)" "subspecies" "manually added" 2 ""
"B_GRAMP" "(unknown Gram-positives)" "accepted" "Bacteria" "(unknown phylum)" "(unknown class)" "(unknown order)" "(unknown family)" "(unknown Gram-positives)" "(unknown species)" "(unknown subspecies)" "subspecies" "manually added" 2 ""
"B_ANAER" "(unknown anaerobic bacteria)" "accepted" "Bacteria" "(unknown phylum)" "(unknown class)" "(unknown order)" "(unknown family)" "(unknown Gram-negatives)" "(unknown species)" "(unknown subspecies)" "subspecies" "manually added" 2 ""
"F_FUNGUS" "(unknown fungus)" "accepted" "Fungi" "(unknown phylum)" "(unknown class)" "(unknown order)" "(unknown family)" "(unknown genus)" "(unknown species)" "(unknown subspecies)" "subspecies" "manually added" 2 ""
"B_GRAMN" "(unknown Gram-negatives)" "accepted" "Bacteria" "(unknown phylum)" "(unknown class)" "(unknown order)" "(unknown family)" "(unknown Gram-negatives)" "(unknown species)" "(unknown subspecies)" "subspecies" "manually added" 2 ""
"B_GRAMP" "(unknown Gram-positives)" "accepted" "Bacteria" "(unknown phylum)" "(unknown class)" "(unknown order)" "(unknown family)" "(unknown Gram-positives)" "(unknown species)" "(unknown subspecies)" "subspecies" "manually added" 2 ""
"UNKNOWN" "(unknown name)" "accepted" "(unknown kingdom)" "(unknown phylum)" "(unknown class)" "(unknown order)" "(unknown family)" "(unknown genus)" "(unknown species)" "(unknown subspecies)" "subspecies" "manually added" 2 ""
"F_YEAST" "(unknown yeast)" "accepted" "Fungi" "(unknown phylum)" "(unknown class)" "(unknown order)" "(unknown family)" "(unknown genus)" "(unknown species)" "(unknown subspecies)" "subspecies" "manually added" 2 ""
"B_[FAM]_ABDTBCTR" "Abditibacteriaceae" "accepted" "Bacteria" "Abditibacteriota" "Abditibacteriia" "Abditibacteriales" "Abditibacteriaceae" "" "" "" "family" "Tahon et al., 2018" "LPSN" "4812" "4982" "10678443" "10853930" 2 ""
@ -6477,7 +6477,6 @@
"B_AZYRT" "Azyrtalia" "accepted" "Bacteria" "Cyanobacteria" "Cyanobacteriia" "Cyanobacteriales" "Rivulariaceae" "Azyrtalia" "" "" "genus" "Vologdin et al., 1969" "GBIF" "3237706" "4306626" 2 ""
"B_AZYRT_ZNLT" "Azyrtalia zonulata" "accepted" "Bacteria" "Cyanobacteria" "Cyanobacteriia" "Cyanobacteriales" "Rivulariaceae" "Azyrtalia" "zonulata" "" "species" "Vologdin et al., 1969" "GBIF" "11176322" "3237706" 2 ""
"A_B-DKE" "B-DKE" "accepted" "Archaea" "Euryarchaeota" "Thermoplasmata" "Thermoplasmatales" "Thermoplasmataceae" "B-DKE" "" "" "genus" "GBIF" "11214677" "3810" 2 ""
"A_BE-D" "BE-D" "accepted" "Archaea" "Thermoproteota" "Thermoproteia" "Marsarchaeales" "Marsarchaeaceae" "BE-D" "" "" "genus" "GBIF" "11119914" "10885120" 2 ""
"B_BABEL" "Babela" "accepted" "Bacteria" "Dependentiae" "Babeliae" "Babeliales" "Babeliaceae" "Babela" "" "" "genus" "GBIF" "10699249" "10857700" 2 ""
"B_BABEL_MSSL" "Babela massiliensis" "accepted" "Bacteria" "Dependentiae" "Babeliae" "Babeliales" "Babeliaceae" "Babela" "massiliensis" "" "species" "GBIF" "10816215" "10699249" 2 ""
"B_[FAM]_BABELIAC" "Babeliaceae" "accepted" "Bacteria" "Dependentiae" "Babeliae" "Babeliales" "Babeliaceae" "" "" "" "family" "GBIF" "10857700" "10791973" 2 ""
@ -7289,6 +7288,7 @@
"B_BDLLV_STLP" "Bdellovibrio stolpii" "synonym" "Bacteria" "Pseudomonadota" "Oligoflexia" "Bdellovibrionales" "Bdellovibrionaceae" "Bdellovibrio" "stolpii" "" "species" "Seidler et al., 1972" "LPSN" "773991" "516977" "773917" 2 "9752009"
"B_[FAM]_BDLLVBRN" "Bdellovibrionaceae" "accepted" "Bacteria" "Pseudomonadota" "Oligoflexia" "Bdellovibrionales" "Bdellovibrionaceae" "" "" "" "family" "Garrity et al., 2006" "LPSN" "203" "5078" "8932" "652" 2 "427516001"
"B_[ORD]_BDLLVBRN" "Bdellovibrionales" "accepted" "Bacteria" "Pseudomonadota" "Oligoflexia" "Bdellovibrionales" "" "" "" "" "order" "Garrity et al., 2006" "LPSN" "5078" "111" "652" "10808561" 2 "426331002"
"A_BE-D" "BE-D" "accepted" "Archaea" "Thermoproteota" "Thermoproteia" "Marsarchaeales" "Marsarchaeaceae" "BE-D" "" "" "genus" "GBIF" "11119914" "10885120" 2 ""
"F_BEAVR" "Beauveria" "accepted" "Fungi" "Ascomycota" "Sordariomycetes" "Hypocreales" "Cordycipitaceae" "Beauveria" "" "" "genus" "Vuill, 1912" "GBIF" "2560584" "8418" 1.5 "66193005"
"F_BEAVR_ACRD" "Beauveria acridophila" "accepted" "Fungi" "Ascomycota" "Sordariomycetes" "Hypocreales" "Cordycipitaceae" "Beauveria" "acridophila" "" "species" "Sanjuan et al." "GBIF" "10753468" "2560584" 1.5 ""
"F_BEAVR_AMRP" "Beauveria amorpha" "accepted" "Fungi" "Ascomycota" "Sordariomycetes" "Hypocreales" "Cordycipitaceae" "Beauveria" "amorpha" "" "species" "Minnis et al." "GBIF" "7417312" "2560584" 1.5 ""
@ -19169,7 +19169,6 @@
"B_FSBCTR_VARM" "Fusobacterium varium" "accepted" "Bacteria" "Fusobacteriota" "Fusobacteriia" "Fusobacteriales" "Fusobacteriaceae" "Fusobacterium" "varium" "" "species" "Moore et al., 1969" "LPSN" "783893" "515666" "3225872" "4903731" 1 "1972005"
"B_FSBCTR_VNCN" "Fusobacterium vincentii" "accepted" "Bacteria" "Fusobacteriota" "Fusobacteriia" "Fusobacteriales" "Fusobacteriaceae" "Fusobacterium" "vincentii" "" "species" "Kook et al., 2022" "LPSN" "28103" "515666" "10808231" "4903731" 1.5 ""
"B_FSBCTR_WTNB" "Fusobacterium watanabei" "accepted" "Bacteria" "Fusobacteriota" "Fusobacteriia" "Fusobacteriales" "Fusobacteriaceae" "Fusobacterium" "watanabei" "" "species" "Tomida et al., 2021" "LPSN" "17647" "515666" 1.5 ""
"B_GBCHB" "GBChlB" "accepted" "Bacteria" "Chlorobiota" "Chlorobiia" "Chlorobiales" "Chloroherpetonaceae" "GBChlB" "" "" "genus" "GBIF" "11171983" "10775177" 2 ""
"B_GBNBC" "Gabonibacter" "accepted" "Bacteria" "Bacteroidota" "Bacteroidia" "Bacteroidales" "Odoribacteraceae" "Gabonibacter" "" "" "genus" "Mourembou et al., 2017" "LPSN" "519111" "2047" "9240178" 2 "785729002"
"B_GBNBC_JSTS" "Gabonibacter justesenii" "synonym" "Bacteria" "Bacteroidota" "Bacteroidia" "Bacteroidales" "Odoribacteraceae" "Gabonibacter" "justesenii" "" "species" "GBIF" "11090238" "9240178" "9415109" 2 ""
"B_GBNBC_MSSL" "Gabonibacter massiliensis" "accepted" "Bacteria" "Bacteroidota" "Bacteroidia" "Bacteroidales" "Odoribacteraceae" "Gabonibacter" "massiliensis" "" "species" "Mourembou et al., 2017" "LPSN" "795002" "519111" "9415109" "9240178" 2 ""
@ -19283,6 +19282,7 @@
"B_GSTRN_PHSC" "Gastranaerophilus phascolarctosicola" "accepted" "Bacteria" "Cyanobacteria" "Vampirovibrionia" "Gastranaerophilales" "Gastranaerophilaceae" "Gastranaerophilus" "phascolarctosicola" "" "species" "GBIF" "10876363" "10700903" 2 ""
"P_GDRYN" "Gaudryina" "accepted" "Protozoa" "Sarcomastigophora" "" "" "Verneulidae" "Gaudryina" "" "" "genus" "GBIF" "10167887" "6123475" 2 ""
"P_GDRYN_KKSN" "Gaudryina kokuseiensis" "accepted" "Protozoa" "Sarcomastigophora" "" "" "Verneulidae" "Gaudryina" "kokuseiensis" "" "species" "Ishizaki" "GBIF" "6123479" "10167887" 2 ""
"B_GBCHB" "GBChlB" "accepted" "Bacteria" "Chlorobiota" "Chlorobiia" "Chlorobiales" "Chloroherpetonaceae" "GBChlB" "" "" "genus" "GBIF" "11171983" "10775177" 2 ""
"P_GMPHR" "Geamphorella" "accepted" "Protozoa" "Amoebozoa" "Lobosa" "Arcellinida" "Nebelidae" "Geamphorella" "" "" "genus" "Bonnet, 1959" "GBIF" "4888795" "2170" 2 ""
"P_GMPHR_LUCD" "Geamphorella lucida" "accepted" "Protozoa" "Amoebozoa" "Lobosa" "Arcellinida" "Nebelidae" "Geamphorella" "lucida" "" "species" "Bonnet, 1959" "GBIF" "10677162" "4888795" 2 ""
"B_GEHNG" "Gehongia" "accepted" "Bacteria" "Bacillota" "Clostridia" "Eubacteriales" "Christensenellaceae" "Gehongia" "" "" "genus" "Liu et al., 2022" "LPSN" "28816" "1935" 2 ""
@ -22583,7 +22583,6 @@
"B_HYNSN_UDNS" "Hyunsoonleella udoensis" "synonym" "Bacteria" "Bacteroidota" "Flavobacteriia" "Flavobacteriales" "Flavobacteriaceae" "Hyunsoonleella" "udoensis" "" "species" "Kim et al., 2016" "LPSN" "793695" "517944" "793694" 2 ""
"B_HYNSN_UDNN" "Hyunsoonleella udonensis" "accepted" "Bacteria" "Bacteroidota" "Flavobacteriia" "Flavobacteriales" "Flavobacteriaceae" "Hyunsoonleella" "udonensis" "" "species" "Kim et al., 2016" "LPSN" "793694" "517944" "8797340" "7660455" 2 ""
"B_HYNSN_ULVA" "Hyunsoonleella ulvae" "accepted" "Bacteria" "Bacteroidota" "Flavobacteriia" "Flavobacteriales" "Flavobacteriaceae" "Hyunsoonleella" "ulvae" "" "species" "Wang et al., 2022" "LPSN" "28379" "517944" 2 ""
"B_ISDG" "ISDg" "accepted" "Bacteria" "Bacillota" "Clostridia" "Eubacteriales" "Lachnospiraceae" "ISDg" "" "" "genus" "GBIF" "11121283" "4713" 2 ""
"A_[FAM]_IAINRCHC" "Iainarchaeaceae" "accepted" "Archaea" "Iainarchaeota" "Iainarchaeia" "Iainarchaeales" "Iainarchaeaceae" "" "" "" "family" "GBIF" "10843220" "10672343" 2 ""
"A_[ORD]_IANRCHLS" "Iainarchaeales" "accepted" "Archaea" "Iainarchaeota" "Iainarchaeia" "Iainarchaeales" "" "" "" "" "order" "GBIF" "10672343" "10847779" 2 ""
"A_[CLS]_IAINARCH" "Iainarchaeia" "accepted" "Archaea" "Iainarchaeota" "Iainarchaeia" "" "" "" "" "" "class" "GBIF" "10847779" "10776132" 2 ""
@ -22793,6 +22792,7 @@
"B_ISCHN_ALKL" "Isachenkonia alkalipeptolytica" "accepted" "Bacteria" "Bacillota" "Clostridia" "Eubacteriales" "Clostridiaceae" "Isachenkonia" "alkalipeptolytica" "" "species" "Zavarzina et al., 2020" "LPSN" "8748" "8742" 2 ""
"B_ISCTS" "Isactis" "accepted" "Bacteria" "Cyanobacteria" "Cyanobacteriia" "Cyanobacteriales" "Rivulariaceae" "Isactis" "" "" "genus" "Thuret et al., 1886" "GBIF" "3219609" "4306626" 2 ""
"B_ISCTS_PLAN" "Isactis plana" "accepted" "Bacteria" "Cyanobacteria" "Cyanobacteriia" "Cyanobacteriales" "Rivulariaceae" "Isactis" "plana" "" "species" "Thur et al." "GBIF" "3219610" "3219609" 2 ""
"B_ISDG" "ISDg" "accepted" "Bacteria" "Bacillota" "Clostridia" "Eubacteriales" "Lachnospiraceae" "ISDg" "" "" "genus" "GBIF" "11121283" "4713" 2 ""
"B_ISHKW" "Ishikawaella" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Ishikawaella" "" "" "genus" "GBIF" "10797324" "11158430" 2 ""
"B_ISHKW_CPSL" "Ishikawaella capsulata" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Ishikawaella" "capsulata" "" "species" "GBIF" "10718144" "10797324" 2 ""
"B_ISBCL" "Isobaculum" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Carnobacteriaceae" "Isobaculum" "" "" "genus" "Collins et al., 2002" "LPSN" "515857" "279" "3227154" 2 "432998006"
@ -23653,7 +23653,6 @@
"B_KYTCC_AERL" "Kytococcus aerolatus" "accepted" "Bacteria" "Actinomycetota" "Actinomycetes" "Micrococcales" "Kytococcaceae" "Kytococcus" "aerolatus" "" "species" "Nouioui et al., 2018" "LPSN" "788155" "515905" "7687887" "3225662" 1.5 ""
"B_KYTCC_SCHR" "Kytococcus schroeteri" "accepted" "Bacteria" "Actinomycetota" "Actinomycetes" "Micrococcales" "Kytococcaceae" "Kytococcus" "schroeteri" "" "species" "Becker et al., 2002" "LPSN" "777226" "515905" "3225663" "3225662" 1 "428721003"
"B_KYTCC_SDNT" "Kytococcus sedentarius" "accepted" "Bacteria" "Actinomycetota" "Actinomycetes" "Micrococcales" "Kytococcaceae" "Kytococcus" "sedentarius" "" "species" "Nouioui et al., 2018" "LPSN" "777227" "515905" "3225664" "3225662" 1 "113775009"
"B_LS-NO" "LS-NOB" "accepted" "Bacteria" "Nitrospinota" "Nitrospinia" "Nitrospinales" "Nitrospinaceae" "LS-NOB" "" "" "genus" "GBIF" "11159629" "5444" 2 ""
"B_LABED" "Labedaea" "accepted" "Bacteria" "Actinomycetota" "Actinomycetes" "Pseudonocardiales" "Pseudonocardiaceae" "Labedaea" "" "" "genus" "2012" "LPSN" "518231" "1137" "7668340" "3841" 2 ""
"B_LABED_RHZS" "Labedaea rhizosphaerae" "accepted" "Bacteria" "Actinomycetota" "Actinomycetes" "Pseudonocardiales" "Pseudonocardiaceae" "Labedaea" "rhizosphaerae" "" "species" "2012" "LPSN" "790047" "518231" "7830525" "7668340" 2 ""
"B_LBDLL" "Labedella" "accepted" "Bacteria" "Actinomycetota" "Actinomycetes" "Micrococcales" "Microbacteriaceae" "Labedella" "" "" "genus" "Li et al., 2019" "LPSN" "517689" "875" "4899919" 2 ""
@ -25498,6 +25497,7 @@
"B_LTTDB" "Lottiidibacillus" "accepted" "Bacteria" "Bacillota" "Bacilli" "Caryophanales" "Bacillaceae" "Lottiidibacillus" "" "" "genus" "Liu et al., 2020" "LPSN" "9035" "191" 2 ""
"B_LTTDB_PTLL" "Lottiidibacillus patelloidae" "accepted" "Bacteria" "Bacillota" "Bacilli" "Caryophanales" "Bacillaceae" "Lottiidibacillus" "patelloidae" "" "species" "Liu et al., 2020" "LPSN" "15262" "9035" 2 ""
"P_[PHL]_LOUKOZOA" "Loukozoa" "accepted" "Protozoa" "Loukozoa" "" "" "" "" "" "" "phylum" "GBIF" "7872314" "7" 2 ""
"B_LS-NO" "LS-NOB" "accepted" "Bacteria" "Nitrospinota" "Nitrospinia" "Nitrospinales" "Nitrospinaceae" "LS-NOB" "" "" "genus" "GBIF" "11159629" "5444" 2 ""
"B_LUCBCTRM" "Lucibacterium" "synonym" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Vibrionales" "Vibrionaceae" "Lucibacterium" "" "" "genus" "Hendrie et al., 1970" "LPSN" "515980" "1543" "517157" 1 ""
"B_LUCBCTRM_HRVY" "Lucibacterium harveyi" "synonym" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Vibrionales" "Vibrionaceae" "Lucibacterium" "harveyi" "" "species" "Hendrie et al., 1970" "LPSN" "777606" "515980" "783009" 1 ""
"B_LUCFR" "Lucifera" "accepted" "Bacteria" "Bacillota" "Negativicutes" "Selenomonadales" "Sporomusaceae" "Lucifera" "" "" "genus" "Sanchez-Andrea et al., 2019" "LPSN" "521634" "2041" 2 ""
@ -25850,9 +25850,6 @@
"B_LYTCM" "Lyticum" "accepted" "Bacteria" "Pseudomonadota" "Alphaproteobacteria" "Rickettsiales" "Ehrlichiaceae" "Lyticum" "" "" "genus" "Preer et al., 1982" "LPSN" "517271" "473" "3221463" "4901684" 2 "433004006"
"B_LYTCM_FLGL" "Lyticum flagellatum" "accepted" "Bacteria" "Pseudomonadota" "Alphaproteobacteria" "Rickettsiales" "Ehrlichiaceae" "Lyticum" "flagellatum" "" "species" "Preer et al., 1982" "LPSN" "784168" "517271" "3221464" "3221463" 2 "433754005"
"B_LYTCM_SNSM" "Lyticum sinuosum" "accepted" "Bacteria" "Pseudomonadota" "Alphaproteobacteria" "Rickettsiales" "Ehrlichiaceae" "Lyticum" "sinuosum" "" "species" "Preer et al., 1982" "LPSN" "784169" "517271" "3221465" "3221463" 2 "434353007"
"A_MGII-" "MGIIa-I" "accepted" "Archaea" "Thermoplasmatota" "Poseidoniia" "Poseidoniales" "Poseidoniaceae" "MGIIa-I" "" "" "genus" "GBIF" "11196009" "10685831" 2 ""
"A_GII-P" "MGIIb-P" "accepted" "Archaea" "Thermoplasmatota" "Poseidoniia" "Poseidoniales" "Thalassarchaeaceae" "MGIIb-P" "" "" "genus" "GBIF" "11123790" "10752789" 2 ""
"B_MZ-XQ" "MZ-XQ" "accepted" "Bacteria" "Mycoplasmatota" "Mollicutes" "Acholeplasmatales" "Acholeplasmataceae" "MZ-XQ" "" "" "genus" "GBIF" "11137212" 2 ""
"B_MBKBC" "Mabikibacter" "synonym" "Bacteria" "Pseudomonadota" "Alphaproteobacteria" "Hyphomicrobiales" "Notoacmeibacteraceae" "Mabikibacter" "" "" "genus" "Choi et al., 2017" "LPSN" "519257" "2084" "519233" 2 ""
"B_MBKBC_RUBR" "Mabikibacter ruber" "synonym" "Bacteria" "Pseudomonadota" "Alphaproteobacteria" "Hyphomicrobiales" "Notoacmeibacteraceae" "Mabikibacter" "ruber" "" "species" "Choi et al., 2017" "LPSN" "795890" "519257" "795709" "9791970" 2 ""
"B_MCLLB" "Macellibacteroides" "accepted" "Bacteria" "Bacteroidota" "Bacteroidia" "Bacteroidales" "Porphyromonadaceae" "Macellibacteroides" "" "" "genus" "Jabari et al., 2012" "LPSN" "518264" "1100" "8021701" 2 ""
@ -27859,6 +27856,8 @@
"F_MYRZY_PRPS_TXTL" "Meyerozyma parapsilosis tuxtlensis" "synonym" "Fungi" "Ascomycota" "Saccharomycetes" "Saccharomycetales" "Debaryomycetaceae" "Meyerozyma" "parapsilosis" "tuxtlensis" "subspecies" "Herrera et al." "GBIF" "3479713" "5893383" 1.5 ""
"F_MYRZY_PSDG" "Meyerozyma pseudoguilliermondii" "synonym" "Fungi" "Ascomycota" "Saccharomycetes" "Saccharomycetales" "Debaryomycetaceae" "Meyerozyma" "pseudoguilliermondii" "" "species" "GBIF" "3556778" "5893380" "5893383" 1.5 ""
"F_MYRZY_SMTH" "Meyerozyma smithsonii" "accepted" "Fungi" "Ascomycota" "Saccharomycetes" "Saccharomycetales" "Debaryomycetaceae" "Meyerozyma" "smithsonii" "" "species" "Yurkov et al." "GBIF" "10712206" "5893380" 1.5 ""
"A_MGII-" "MGIIa-I" "accepted" "Archaea" "Thermoplasmatota" "Poseidoniia" "Poseidoniales" "Poseidoniaceae" "MGIIa-I" "" "" "genus" "GBIF" "11196009" "10685831" 2 ""
"A_GII-P" "MGIIb-P" "accepted" "Archaea" "Thermoplasmatota" "Poseidoniia" "Poseidoniales" "Thalassarchaeaceae" "MGIIb-P" "" "" "genus" "GBIF" "11123790" "10752789" 2 ""
"B_MCVBR" "Micavibrio" "accepted" "Bacteria" "Pseudomonadota" "Oligoflexia" "Bdellovibrionales" "Bdellovibrionaceae" "Micavibrio" "" "" "genus" "Lambina et al., 1989" "LPSN" "517285" "203" "11199699" "8932" 2 "429897008"
"B_MCVBR_ADMR" "Micavibrio admirandus" "accepted" "Bacteria" "Pseudomonadota" "Oligoflexia" "Bdellovibrionales" "Bdellovibrionaceae" "Micavibrio" "admirandus" "" "species" "Lambina et al., 1989" "LPSN" "784260" "517285" 2 "433368001"
"A_[FAM]_MICRRCHC" "Micrarchaeaceae" "accepted" "Archaea" "Micrarchaeota" "Micrarchaeia" "Micrarchaeales" "Micrarchaeaceae" "" "" "" "family" "GBIF" "10878041" "10702512" 2 ""
@ -30317,6 +30316,7 @@
"B_MYXSR_BRMN" "Myxosarcina burmensis" "accepted" "Bacteria" "Cyanobacteria" "Cyanobacteriia" "Cyanobacteriales" "Xenococcaceae" "Myxosarcina" "burmensis" "" "species" "Skuja" "GBIF" "3216275" "7729673" 2 ""
"B_MYXSR_CNCN" "Myxosarcina concinna" "accepted" "Bacteria" "Cyanobacteria" "Cyanobacteriia" "Cyanobacteriales" "Xenococcaceae" "Myxosarcina" "concinna" "" "species" "GBIF" "3217367" "7729673" 2 ""
"B_MYXSR_GLCP" "Myxosarcina gloeocapsoides" "accepted" "Bacteria" "Cyanobacteria" "Cyanobacteriia" "Cyanobacteriales" "Xenococcaceae" "Myxosarcina" "gloeocapsoides" "" "species" "Komarek et al." "GBIF" "3217365" "7729673" 2 ""
"B_MZ-XQ" "MZ-XQ" "accepted" "Bacteria" "Mycoplasmatota" "Mollicutes" "Acholeplasmatales" "Acholeplasmataceae" "MZ-XQ" "" "" "genus" "GBIF" "11137212" 2 ""
"B_MZBMY" "Mzabimyces" "synonym" "Bacteria" "Actinomycetota" "Actinomycetes" "Pseudonocardiales" "Pseudonocardiaceae" "Mzabimyces" "" "" "genus" "Saker et al., 2015" "LPSN" "518817" "1137" "518590" 2 ""
"B_MZBMY_ALGR" "Mzabimyces algeriensis" "synonym" "Bacteria" "Actinomycetota" "Actinomycetes" "Pseudonocardiales" "Pseudonocardiaceae" "Mzabimyces" "algeriensis" "" "species" "Saker et al., 2015" "LPSN" "793403" "518817" "795677" 2 ""
"B_NAASI" "Naasia" "accepted" "Bacteria" "Actinomycetota" "Actinomycetes" "Micrococcales" "Microbacteriaceae" "Naasia" "" "" "genus" "Weon et al., 2013" "LPSN" "518394" "875" "8305219" 2 ""
@ -41270,6 +41270,7 @@
"B_SLMNL_ARPH" "Salmonella Arapahoe" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Arapahoe" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_ARCH" "Salmonella Arechavaleta" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Arechavaleta" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_ARGN" "Salmonella Argenteuil" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Argenteuil" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_ARZN" "Salmonella arizonae" "synonym" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "arizonae" "" "species" "Kauffmann, 1964" "LPSN" "780744" "516547" "780755" "5427588" "3221815" 1.5 ""
"B_SLMNL_ARSH" "Salmonella Arusha" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Arusha" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_ASCH" "Salmonella Aschersleben" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Aschersleben" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_ASHN" "Salmonella Ashanti" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Ashanti" "subspecies" "manually added" "784857" "9701185" 1 ""
@ -41378,6 +41379,7 @@
"B_SLMNL_BLTN" "Salmonella Bolton" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Bolton" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_BNMS" "Salmonella Bonames" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Bonames" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_BNRN" "Salmonella Bonariensis" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Bonariensis" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_BNGR" "Salmonella bongori" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "bongori" "" "species" "Reeves et al., 1989" "LPSN" "780745" "516547" "5427596" "3221815" 1 "398393000"
"B_SLMNL_BONN" "Salmonella Bonn" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Bonn" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_BOTL" "Salmonella Bootle" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Bootle" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_BRBC" "Salmonella Borbeck" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Borbeck" "subspecies" "manually added" "784857" "9701185" 1 ""
@ -41480,6 +41482,14 @@
"B_SLMNL_CHNG" "Salmonella Chingola" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Chingola" "subspecies" "manually added" "784857" "9701185" 1 ""
"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_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 ""
"B_SLMNL_CHLR_DRZN" "Salmonella choleraesuis diarizonae" "synonym" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "choleraesuis" "diarizonae" "subspecies" "Le Minor et al., 1985" "LPSN" "780750" "780746" "780757" "5427579" "7515106" "5427578" 1 ""
"B_SLMNL_CHLR_HOTN" "Salmonella choleraesuis houtenae" "synonym" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "choleraesuis" "houtenae" "subspecies" "Le Minor et al., 1985" "LPSN" "780751" "780746" "780759" "5427581" "7515106" "5427580" 1 ""
"B_SLMNL_CHLR_INDC" "Salmonella choleraesuis indica" "synonym" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "choleraesuis" "indica" "subspecies" "Le Minor et al., 1987" "LPSN" "780752" "780746" "780760" "5427583" "7515106" "5427582" 1 ""
"B_SLMNL_CHLR_SALM" "Salmonella choleraesuis salamae" "synonym" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "choleraesuis" "salamae" "subspecies" "Le Minor et al., 1985" "LPSN" "780753" "780746" "780761" "5427585" "7515106" "5427584" 1 ""
"B_SLMNL_CHMD" "Salmonella Chomedey" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Chomedey" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_CHRS" "Salmonella Christiansborg" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Christiansborg" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_CLCK" "Salmonella Clackamas" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Clackamas" "subspecies" "manually added" "784857" "9701185" 1 ""
@ -41542,6 +41552,7 @@
"B_SLMNL_DESS" "Salmonella Dessau" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Dessau" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_DTML" "Salmonella Detmold" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Detmold" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_DVRS" "Salmonella Deversoir" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Deversoir" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_DRZN" "Salmonella diarizonae" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "diarizonae" "" "species" "GBIF" "516547" "10672082" "3221815" 1.5 ""
"B_SLMNL_DIBR" "Salmonella Dibra" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Dibra" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_DTRC" "Salmonella Dietrichsdorf" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Dietrichsdorf" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_DPPL" "Salmonella Dieuppeul" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Dieuppeul" "subspecies" "manually added" "784857" "9701185" 1 ""
@ -41603,6 +41614,15 @@
"B_SLMNL_ENCN" "Salmonella Encino" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Encino" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_ENSC" "Salmonella Enschede" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Enschede" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_ENTB" "Salmonella Entebbe" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Entebbe" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_ENTR" "Salmonella enterica" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "" "species" "Le Minor et al., 1987" "LPSN" "784857" "516547" "9701185" "3221815" 1 "110378009,397502001,398428002,398508004,398371005,398620001,398488004"
"B_SLMNL_ENTR_ARZN" "Salmonella enterica arizonae" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "arizonae" "subspecies" "Le Minor et al., 1987" "LPSN" "780755" "784857" "5427586" "9701185" 1 ""
"B_SLMNL_ENTR_BNGR" "Salmonella enterica bongori" "synonym" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "bongori" "subspecies" "Le Minor et al., 1987" "LPSN" "780756" "784857" "780745" "5427598" "9701185" "5427596" 1 ""
"B_SLMNL_ENTR_DRZN" "Salmonella enterica diarizonae" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "diarizonae" "subspecies" "Le Minor et al., 1987" "LPSN" "780757" "784857" "5427578" "9701185" 1 ""
"B_SLMNL_ENTR_ENTR" "Salmonella enterica enterica" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "enterica" "subspecies" "Le Minor et al., 1987" "LPSN" "780758" "784857" "5427589" "9701185" 1 ""
"B_SLMNL_ENTR_HOTN" "Salmonella enterica houtenae" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "houtenae" "subspecies" "Le Minor et al., 1987" "LPSN" "780759" "784857" "5427580" "9701185" 1 ""
"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_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 ""
@ -41725,6 +41745,10 @@
"B_SLMNL_GRPB" "Salmonella Group B" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "Group B" "" "species" "manually added" "516547" "3221815" 1.5 ""
"B_SLMNL_GRPC" "Salmonella Group C" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "Group C" "" "species" "manually added" "516547" "3221815" 1.5 ""
"B_SLMNL_GRPD" "Salmonella Group D" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "Group D" "" "species" "manually added" "516547" "3221815" 1.5 ""
"B_SLMNL_GRPE" "Salmonella Group E" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "Group E" "" "species" "manually added" "516547" "3221815" 1.5 ""
"B_SLMNL_GRPF" "Salmonella Group F" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "Group F" "" "species" "manually added" "516547" "3221815" 1.5 ""
"B_SLMNL_GRPG" "Salmonella Group G" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "Group G" "" "species" "manually added" "516547" "3221815" 1.5 ""
"B_SLMNL_GRPH" "Salmonella Group H" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "Group H" "" "species" "manually added" "516547" "3221815" 1.5 ""
"B_SLMNL_GNSS" "Salmonella Grumpensis" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Grumpensis" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_GRPR" "Salmonella Guarapiranga" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Guarapiranga" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_GURN" "Salmonella Guerin" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Guerin" "subspecies" "manually added" "784857" "9701185" 1 ""
@ -41788,6 +41812,7 @@
"B_SLMNL_HNGK" "Salmonella Hongkong" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Hongkong" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_HRSH" "Salmonella Horsham" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Horsham" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_HSTN" "Salmonella Houston" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Houston" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_HOTN" "Salmonella houtenae" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "houtenae" "" "species" "GBIF" "516547" "7617321" "3221815" 1.5 ""
"B_SLMNL_HDDN" "Salmonella Huddinge" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Huddinge" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_HTTW" "Salmonella Huettwilen" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Huettwilen" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_HULL" "Salmonella Hull" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Hull" "subspecies" "manually added" "784857" "9701185" 1 ""
@ -42257,6 +42282,7 @@
"B_SLMNL_PKST" "Salmonella Pakistan" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Pakistan" "subspecies" "manually added" "784857" "9701185" 1 ""
"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" "516547" "9407232" "3221815" 1.5 ""
"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" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Paratyphi" "subspecies" "manually added" "784857" "9701185" 1 ""
@ -42459,6 +42485,7 @@
"B_SLMNL_STVN" "Salmonella Stuivenberg" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Stuivenberg" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_STTT" "Salmonella Stuttgart" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Stuttgart" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_SUBR" "Salmonella Suberu" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Suberu" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_SBTR" "Salmonella subterranea" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "subterranea" "" "species" "Shelobolina et al., 2005" "LPSN" "780769" "516547" "5427595" "3221815" 1.5 ""
"B_SLMNL_SUDN" "Salmonella Sudan" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Sudan" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_SLLD" "Salmonella Suelldorf" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Suelldorf" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_SNDS" "Salmonella Sundsvall" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Sundsvall" "subspecies" "manually added" "784857" "9701185" 1 ""
@ -42696,29 +42723,6 @@
"B_SLMNL_ZONG" "Salmonella Zongo" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Zongo" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_ZULN" "Salmonella Zuilen" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Zuilen" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_ZWCK" "Salmonella Zwickau" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "Zwickau" "subspecies" "manually added" "784857" "9701185" 1 ""
"B_SLMNL_ARZN" "Salmonella arizonae" "synonym" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "arizonae" "" "species" "Kauffmann, 1964" "LPSN" "780744" "516547" "780755" "5427588" "3221815" 1.5 ""
"B_SLMNL_BNGR" "Salmonella bongori" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "bongori" "" "species" "Reeves et al., 1989" "LPSN" "780745" "516547" "5427596" "3221815" 1 "398393000"
"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_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 ""
"B_SLMNL_CHLR_DRZN" "Salmonella choleraesuis diarizonae" "synonym" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "choleraesuis" "diarizonae" "subspecies" "Le Minor et al., 1985" "LPSN" "780750" "780746" "780757" "5427579" "7515106" "5427578" 1 ""
"B_SLMNL_CHLR_HOTN" "Salmonella choleraesuis houtenae" "synonym" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "choleraesuis" "houtenae" "subspecies" "Le Minor et al., 1985" "LPSN" "780751" "780746" "780759" "5427581" "7515106" "5427580" 1 ""
"B_SLMNL_CHLR_INDC" "Salmonella choleraesuis indica" "synonym" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "choleraesuis" "indica" "subspecies" "Le Minor et al., 1987" "LPSN" "780752" "780746" "780760" "5427583" "7515106" "5427582" 1 ""
"B_SLMNL_CHLR_SALM" "Salmonella choleraesuis salamae" "synonym" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "choleraesuis" "salamae" "subspecies" "Le Minor et al., 1985" "LPSN" "780753" "780746" "780761" "5427585" "7515106" "5427584" 1 ""
"B_SLMNL_DRZN" "Salmonella diarizonae" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "diarizonae" "" "species" "GBIF" "516547" "10672082" "3221815" 1.5 ""
"B_SLMNL_ENTR" "Salmonella enterica" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "" "species" "Le Minor et al., 1987" "LPSN" "784857" "516547" "9701185" "3221815" 1 "110378009,397502001,398428002,398508004,398371005,398620001,398488004"
"B_SLMNL_ENTR_ARZN" "Salmonella enterica arizonae" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "arizonae" "subspecies" "Le Minor et al., 1987" "LPSN" "780755" "784857" "5427586" "9701185" 1 ""
"B_SLMNL_ENTR_BNGR" "Salmonella enterica bongori" "synonym" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "bongori" "subspecies" "Le Minor et al., 1987" "LPSN" "780756" "784857" "780745" "5427598" "9701185" "5427596" 1 ""
"B_SLMNL_ENTR_DRZN" "Salmonella enterica diarizonae" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "diarizonae" "subspecies" "Le Minor et al., 1987" "LPSN" "780757" "784857" "5427578" "9701185" 1 ""
"B_SLMNL_ENTR_ENTR" "Salmonella enterica enterica" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "enterica" "subspecies" "Le Minor et al., 1987" "LPSN" "780758" "784857" "5427589" "9701185" 1 ""
"B_SLMNL_ENTR_HOTN" "Salmonella enterica houtenae" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "enterica" "houtenae" "subspecies" "Le Minor et al., 1987" "LPSN" "780759" "784857" "5427580" "9701185" 1 ""
"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_HOTN" "Salmonella houtenae" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "houtenae" "" "species" "GBIF" "516547" "7617321" "3221815" 1.5 ""
"B_SLMNL_PANM" "Salmonella panama" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "panama" "" "species" "Kauffmann, 1934" "GBIF" "516547" "9407232" "3221815" 1.5 ""
"B_SLMNL_SBTR" "Salmonella subterranea" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Salmonella" "subterranea" "" "species" "Shelobolina et al., 2005" "LPSN" "780769" "516547" "5427595" "3221815" 1.5 ""
"B_SLSPL" "Salsipaludibacter" "accepted" "Bacteria" "Actinomycetota" "Nitriliruptoria" "Salsipaludibacterales" "Salsipaludibacteraceae" "Salsipaludibacter" "" "" "genus" "Almeida et al., 2022" "LPSN" "25963" "25953" 2 ""
"B_SLSPL_ALBS" "Salsipaludibacter albus" "accepted" "Bacteria" "Actinomycetota" "Nitriliruptoria" "Salsipaludibacterales" "Salsipaludibacteraceae" "Salsipaludibacter" "albus" "" "species" "Almeida et al., 2022" "LPSN" "25977" "25963" 2 ""
"B_[FAM]_SLSPLDBC" "Salsipaludibacteraceae" "accepted" "Bacteria" "Actinomycetota" "Nitriliruptoria" "Salsipaludibacterales" "Salsipaludibacteraceae" "" "" "" "family" "Almeida et al., 2022" "LPSN" "25953" "25966" 2 ""
@ -45428,15 +45432,6 @@
"B_STRPTB_RATT" "Streptobacillus ratti" "accepted" "Bacteria" "Fusobacteriota" "Fusobacteriia" "Fusobacteriales" "Leptotrichiaceae" "Streptobacillus" "ratti" "" "species" "Eisenberg et al., 2016" "LPSN" "794063" "516688" "9144099" "3225903" 1.5 ""
"B_[FAM]_STRPTCCC" "Streptococcaceae" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "" "" "" "family" "Deibel et al., 1974" "LPSN" "1344" "5123" "4899829" "577" "7798" 2 "115107007"
"B_STRPT" "Streptococcus" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "" "" "genus" "Rosenbach, 1884" "LPSN" "517118" "1344" "3223465" "4899829" 1 "58800005,414871004,70160008"
"B_STRPT_GRPA" "Streptococcus Group A" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "Group A" "" "species" "Lancefield, 1933" "manually added" 1.5 ""
"B_STRPT_GRPB" "Streptococcus Group B" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "Group B" "" "species" "Lancefield, 1933" "manually added" 1.5 ""
"B_STRPT_GRPC" "Streptococcus Group C" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "Group C" "" "species" "Lancefield, 1933" "manually added" 1.5 ""
"B_STRPT_GRPD" "Streptococcus Group D" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "Group D" "" "species" "Lancefield, 1933" "manually added" 1.5 ""
"B_STRPT_GRPF" "Streptococcus Group F" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "Group F" "" "species" "Lancefield, 1933" "manually added" 1.5 ""
"B_STRPT_GRPG" "Streptococcus Group G" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "Group G" "" "species" "Lancefield, 1933" "manually added" 1.5 ""
"B_STRPT_GRPH" "Streptococcus Group H" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "Group H" "" "species" "Lancefield, 1933" "manually added" 1.5 ""
"B_STRPT_GRPK" "Streptococcus Group K" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "Group K" "" "species" "Lancefield, 1933" "manually added" 1.5 ""
"B_STRPT_GRPL" "Streptococcus Group L" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "Group L" "" "species" "Lancefield, 1933" "manually added" 1.5 ""
"B_STRPT_ACDM" "Streptococcus acidominimus" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "acidominimus" "" "species" "Ayers et al., 1922" "LPSN" "781295" "517118" 1 "51182006"
"B_STRPT_ADJC" "Streptococcus adjacens" "synonym" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "adjacens" "" "species" "Bouvet et al., 1989" "LPSN" "781296" "517118" "776611" 1.5 ""
"B_STRPT_AGLC" "Streptococcus agalactiae" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "agalactiae" "" "species" "Lehmann et al., 1896" "LPSN" "781297" "517118" 1 "713924007,43492007"
@ -45506,6 +45501,18 @@
"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" 1.25 ""
"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" 1.5 ""
"B_STRPT_GRPB" "Streptococcus Group B" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "Group B" "" "species" "Lancefield, 1933" "manually added" 1.5 ""
"B_STRPT_GRPC" "Streptococcus Group C" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "Group C" "" "species" "Lancefield, 1933" "manually added" 1.5 ""
"B_STRPT_GRPD" "Streptococcus Group D" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "Group D" "" "species" "Lancefield, 1933" "manually added" 1.5 ""
"B_STRPT_GRPE" "Streptococcus Group E" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "Group E" "" "species" "Lancefield, 1933" "manually added" 1.5 ""
"B_STRPT_GRPF" "Streptococcus Group F" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "Group F" "" "species" "Lancefield, 1933" "manually added" 1.5 ""
"B_STRPT_GRPG" "Streptococcus Group G" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "Group G" "" "species" "Lancefield, 1933" "manually added" 1.5 ""
"B_STRPT_GRPH" "Streptococcus Group H" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "Group H" "" "species" "Lancefield, 1933" "manually added" 1.5 ""
"B_STRPT_GRPI" "Streptococcus Group I" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "Group I" "" "species" "Lancefield, 1933" "manually added" 1.5 ""
"B_STRPT_GRPJ" "Streptococcus Group J" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "Group J" "" "species" "Lancefield, 1933" "manually added" 1.5 ""
"B_STRPT_GRPK" "Streptococcus Group K" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "Group K" "" "species" "Lancefield, 1933" "manually added" 1.5 ""
"B_STRPT_GRPL" "Streptococcus Group L" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "Group L" "" "species" "Lancefield, 1933" "manually added" 1.5 ""
"B_STRPT_GWNG" "Streptococcus gwangjuense" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "gwangjuense" "" "species" "GBIF" "11190550" "3223465" 1.5 ""
"B_STRPT_HLCH" "Streptococcus halichoeri" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "halichoeri" "" "species" "Shewmaker et al., 2016" "LPSN" "781344" "517118" 1.25 "438161002"
"B_STRPT_HLTS" "Streptococcus halitosis" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Streptococcaceae" "Streptococcus" "halitosis" "" "species" "GBIF" "10822581" "3223465" 1.5 ""
@ -51722,7 +51729,6 @@
"A_WKNGR_YPNS" "Wukongarchaeum yapensis" "accepted" "Archaea" "Asgardarchaeota" "Wukongarchaeia" "Wukongarchaeales" "Wukongarchaeaceae" "Wukongarchaeum" "yapensis" "" "species" "GBIF" "11649514" "11817462" 2 ""
"B_WKNGB" "Wukongibacter" "accepted" "Bacteria" "Bacillota" "Clostridia" "Eubacteriales" "Peptostreptococcaceae" "Wukongibacter" "" "" "genus" "Li et al., 2016" "LPSN" "519079" "1053" "9506110" "7800" 2 ""
"B_WKNGB_BDNS" "Wukongibacter baidiensis" "accepted" "Bacteria" "Bacillota" "Clostridia" "Eubacteriales" "Peptostreptococcaceae" "Wukongibacter" "baidiensis" "" "species" "Li et al., 2016" "LPSN" "794822" "519079" "9479445" "9506110" 2 ""
"B_XYC" "XYC" "accepted" "Bacteria" "Nitrospirota" "Thermodesulfovibrionia" "Thermodesulfovibrionales" "Magnetobacteriaceae" "XYC" "" "" "genus" "GBIF" "11695901" "10718264" 2 ""
"P_XNTHS" "Xanthiosphaera" "accepted" "Protozoa" "Sarcomastigophora" "" "" "" "Xanthiosphaera" "" "" "genus" "GBIF" "9472186" 2 ""
"P_XNTHS_LPPC" "Xanthiosphaera lappacea" "accepted" "Protozoa" "Sarcomastigophora" "" "" "" "Xanthiosphaera" "lappacea" "" "species" "Haeckel" "GBIF" "6123506" "9472186" 2 ""
"B_XNTHB" "Xanthobacter" "accepted" "Bacteria" "Pseudomonadota" "Alphaproteobacteria" "Hyphomicrobiales" "Xanthobacteraceae" "Xanthobacter" "" "" "genus" "Wiegel et al., 1978" "LPSN" "516929" "1568" 2 "439120008"
@ -51892,6 +51898,7 @@
"B_[FAM]_XPHNMTBC" "Xiphinematobacteraceae" "accepted" "Bacteria" "Verrucomicrobiota" "Verrucomicrobiae" "Chthoniobacterales" "Xiphinematobacteraceae" "" "" "" "family" "GBIF" "10770063" "10733345" 2 ""
"B_XUHSH" "Xuhuaishuia" "synonym" "Bacteria" "Pseudomonadota" "Alphaproteobacteria" "Rhodobacterales" "Rhodobacteraceae" "Xuhuaishuia" "" "" "genus" "Wang et al., 2016" "LPSN" "518921" "1175" "518801" 2 ""
"B_XUHSH_MNGN" "Xuhuaishuia manganoxidans" "synonym" "Bacteria" "Pseudomonadota" "Alphaproteobacteria" "Rhodobacterales" "Rhodobacteraceae" "Xuhuaishuia" "manganoxidans" "" "species" "Wang et al., 2016" "LPSN" "793971" "518921" "793304" 2 ""
"B_XYC" "XYC" "accepted" "Bacteria" "Nitrospirota" "Thermodesulfovibrionia" "Thermodesulfovibrionales" "Magnetobacteriaceae" "XYC" "" "" "genus" "GBIF" "11695901" "10718264" 2 ""
"B_XYLNB" "Xylanibacillus" "accepted" "Bacteria" "Bacillota" "Bacilli" "Caryophanales" "Paenibacillaceae" "Xylanibacillus" "" "" "genus" "Kukolya et al., 2018" "LPSN" "520351" "1013" 2 ""
"B_XYLNB_CMPS" "Xylanibacillus composti" "accepted" "Bacteria" "Bacillota" "Bacilli" "Caryophanales" "Paenibacillaceae" "Xylanibacillus" "composti" "" "species" "Kukolya et al., 2018" "LPSN" "797542" "520351" 2 ""
"B_XBCTR" "Xylanibacter" "synonym" "Bacteria" "Bacteroidota" "Bacteroidia" "Bacteroidales" "Prevotellaceae" "Xylanibacter" "" "" "genus" "Hitch et al., 2022" "LPSN" "516940" "1105" "516385" 2 ""

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data-raw/microorganisms.xlsx
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data-raw/reproduction_of_clinical_breakpoints.R
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@ -44,10 +44,18 @@ whonet_organisms <- read_tsv("data-raw/WHONET/Resources/Organisms.txt", na = c("
# remove old taxonomic names
filter(TAXONOMIC_STATUS == "C") %>%
transmute(ORGANISM_CODE = tolower(WHONET_ORG_CODE), ORGANISM) %>%
# what's wrong here? 'sau' is both S. areus and S. aureus sp. aureus
mutate(
# what's wrong here? all these are only in the table on subspecies level (where species == subspecies), not on species level
ORGANISM = if_else(ORGANISM_CODE == "sau", "Staphylococcus aureus", ORGANISM),
ORGANISM = if_else(ORGANISM_CODE == "pam", "Pasteurella multocida", ORGANISM)
ORGANISM = if_else(ORGANISM_CODE == "pam", "Pasteurella multocida", ORGANISM),
ORGANISM = if_else(ORGANISM_CODE == "kpn", "Klebsiella pneumoniae", ORGANISM),
ORGANISM = if_else(ORGANISM_CODE == "caj", "Campylobacter jejuni", ORGANISM),
ORGANISM = if_else(ORGANISM_CODE == "mmo", "Morganella morganii", ORGANISM),
ORGANISM = if_else(ORGANISM_CODE == "sap", "Staphylococcus saprophyticus", ORGANISM),
ORGANISM = if_else(ORGANISM_CODE == "fne", "Fusobacterium necrophorum", ORGANISM),
ORGANISM = if_else(ORGANISM_CODE == "fnu", "Fusobacterium nucleatum", ORGANISM),
ORGANISM = if_else(ORGANISM_CODE == "sdy", "Streptococcus dysgalactiae", ORGANISM),
ORGANISM = if_else(ORGANISM_CODE == "axy", "Achromobacter xylosoxidans", ORGANISM)
)
whonet_breakpoints <- read_tsv("data-raw/WHONET/Resources/Breakpoints.txt", na = c("", "NA", "-"), show_col_types = FALSE) %>%
filter(BREAKPOINT_TYPE == "Human", GUIDELINES %in% c("CLSI", "EUCAST"))
@ -64,6 +72,36 @@ whonet_organisms <- whonet_organisms %>%
ORGANISM = c("Enterobacterales", "Campylobacter")
))
mo_reset_session()
whonet_organisms.bak <- whonet_organisms
whonet_organisms <- whonet_organisms.bak %>%
mutate(mo = as.mo(gsub("(sero[a-z]*| complex| nontypable| non[-][a-zA-Z]+|var[.]| not .*|sp[.],.*|, .*variant.*|, .*toxin.*|, microaer.*| beta-haem[.])", "", ORGANISM),
keep_synonyms = TRUE,
language = "en"),
mo = as.mo(ifelse(ORGANISM %like% "Anaerobic", "B_ANAER", mo)),
mo_name = mo_name(mo,
keep_synonyms = TRUE,
language = "en"))
# update microorganisms.codes with the latest WHONET codes
new_mo_codes <- whonet_organisms %>%
mutate(
first_part = sapply(ORGANISM, function(x) strsplit(gsub("[^a-zA-Z _-]+", "", x), " ")[[1]][1], USE.NAMES = FALSE),
keep = mo_name %like_case% first_part | ORGANISM %like% "Gram " | ORGANISM == "Other")
microorganisms.codes <- microorganisms.codes %>%
# remove all old WHONET codes, whether we (in the end) keep them or not
filter(!toupper(code) %in% toupper(new_mo_codes$ORGANISM_CODE)) %>%
bind_rows(new_mo_codes %>%
filter(keep == TRUE) %>%
transmute(code = toupper(ORGANISM_CODE),
mo = mo)) %>%
arrange(code)
# save to package
usethis::use_data(microorganisms.codes, overwrite = TRUE, compress = "xz", version = 2)
rm(microorganisms.codes)
devtools::load_all()
breakpoints <- whonet_breakpoints %>%
mutate(ORGANISM_CODE = tolower(ORGANISM_CODE)) %>%
left_join(whonet_organisms) %>%