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fix reference_df endless loop

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dr. M.S. (Matthijs) Berends
2023-06-26 13:52:02 +02:00
parent 1d9ee39cc7
commit 2d97cca6d9
29 changed files with 215 additions and 200 deletions
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data-raw/microorganisms.txt
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@ -547,6 +547,7 @@
"B_ACNTB_AVST" "Acinetobacter avistercoris" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Pseudomonadales" "Moraxellaceae" "Acinetobacter" "avistercoris" "" "species" "likely facultative anaerobe" "GBIF" "11605583" "3223263" 1.5 ""
"B_ACNTB_BART" "Acinetobacter baretiae" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Pseudomonadales" "Moraxellaceae" "Acinetobacter" "baretiae" "" "species" "Alvarez-Perez et al., 2021" "likely facultative anaerobe" "LPSN" "19553" "515021" "11852261" "3223263" 1.5 ""
"B_ACNTB_BMNN" "Acinetobacter baumannii" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Pseudomonadales" "Moraxellaceae" "Acinetobacter" "baumannii" "" "species" "Bouvet et al., 1986" "aerobe" "LPSN" "772610" "515021" "3223274" "3223263" 1 "91288006,715174007,737526007,447891000124105,715353004"
"B_ACNTB_BMNN-C" "Acinetobacter baumannii complex" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Pseudomonadales" "Moraxellaceae" "Acinetobacter" "baumannii complex" "" "species group" "aerobe" "manually added" "515021" "3223263" 1 ""
"B_ACNTB_BYLY" "Acinetobacter baylyi" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Pseudomonadales" "Moraxellaceae" "Acinetobacter" "baylyi" "" "species" "Carr et al., 2003" "aerobe" "LPSN" "772611" "515021" "3223268" "3223263" 1 "423974000"
"B_ACNTB_BJRN" "Acinetobacter beijerinckii" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Pseudomonadales" "Moraxellaceae" "Acinetobacter" "beijerinckii" "" "species" "Nemec et al., 2009" "aerobe" "LPSN" "787668" "515021" "8317472" "3223263" 1 "771547006"
"B_ACNTB_BERZN" "Acinetobacter berezinae" "synonym" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Pseudomonadales" "Moraxellaceae" "Acinetobacter" "berezinae" "" "species" "Alexandr et al., 2009" "aerobe" "GBIF" "9467748" "3223263" "7798724" 1 ""
@ -8476,6 +8477,7 @@
"B_BRKHL_CATD" "Burkholderia catudaia" "synonym" "Bacteria" "Pseudomonadota" "Betaproteobacteria" "Burkholderiales" "Burkholderiaceae" "Burkholderia" "catudaia" "" "species" "Peeters et al., 2016" "aerobe" "LPSN" "794437" "515281" "796021" "9576146" "3219916" 1.5 ""
"B_BRKHL_CNCP" "Burkholderia cenocepacia" "accepted" "Bacteria" "Pseudomonadota" "Betaproteobacteria" "Burkholderiales" "Burkholderiaceae" "Burkholderia" "cenocepacia" "" "species" "Vandamme et al., 2003" "aerobe" "LPSN" "774276" "515281" "10898083" "3219916" 1 "416941006"
"B_BRKHL_CEPC" "Burkholderia cepacia" "accepted" "Bacteria" "Pseudomonadota" "Betaproteobacteria" "Burkholderiales" "Burkholderiaceae" "Burkholderia" "cepacia" "" "species" "Yabuuchi et al., 1993" "aerobe" "LPSN" "774277" "515281" "10900882" "3219916" 1 "113669008"
"B_BRKHL_CEPC-C" "Burkholderia cepacia complex" "accepted" "Bacteria" "Pseudomonadota" "Betaproteobacteria" "Burkholderiales" "Burkholderiaceae" "Burkholderia" "cepacia complex" "" "species group" "aerobe" "manually added" "515281" "3219916" 1 ""
"B_BRKHL_CHOC" "Burkholderia choica" "synonym" "Bacteria" "Pseudomonadota" "Betaproteobacteria" "Burkholderiales" "Burkholderiaceae" "Burkholderia" "choica" "" "species" "Vandamme et al., 2013" "aerobe" "LPSN" "791329" "515281" "794372" 1.5 ""
"B_BRKHL_CCVN" "Burkholderia cocovenenans" "synonym" "Bacteria" "Pseudomonadota" "Betaproteobacteria" "Burkholderiales" "Burkholderiaceae" "Burkholderia" "cocovenenans" "" "species" "Gillis et al., 1995" "aerobe" "LPSN" "7156" "515281" "774282" "3219917" "3219916" "3219971" 1 ""
"B_BRKHL_CNCT" "Burkholderia concitans" "synonym" "Bacteria" "Pseudomonadota" "Betaproteobacteria" "Burkholderiales" "Burkholderiaceae" "Burkholderia" "concitans" "" "species" "Peeters et al., 2016" "aerobe" "LPSN" "794438" "515281" "796022" "9429304" "3219916" 1.5 ""
@ -9058,6 +9060,7 @@
"F_CANDD_ALBC" "Candida albicans" "accepted" "Fungi" "Ascomycota" "Saccharomycetes" "Saccharomycetales" "Debaryomycetaceae" "Candida" "albicans" "" "species" "Berkhout" "GBIF" "2599597" "2518121" 1.5 "53326005,243448008,714313009"
"F_CANDD_ALBC_ALBC" "Candida albicans albicans" "synonym" "Fungi" "Ascomycota" "Saccharomycetes" "Saccharomycetales" "Debaryomycetaceae" "Candida" "albicans" "albicans" "subspecies" "GBIF" "11228679" "2599597" "2599597" 1.5 ""
"F_CANDD_ALBC_CLSS" "Candida albicans claussenii" "synonym" "Fungi" "Ascomycota" "Saccharomycetes" "Saccharomycetales" "Debaryomycetaceae" "Candida" "albicans" "claussenii" "subspecies" "Lodder et al." "GBIF" "11281986" "2599597" "2599597" 1.5 ""
"F_CANDD_ALBC-C" "Candida albicans complex" "accepted" "Fungi" "Ascomycota" "Saccharomycetes" "Saccharomycetales" "Debaryomycetaceae" "Candida" "albicans complex" "" "species group" "manually added" "2518121" 1.5 ""
"F_CANDD_ALBC_MTLN" "Candida albicans metalondinensis" "synonym" "Fungi" "Ascomycota" "Saccharomycetes" "Saccharomycetales" "Debaryomycetaceae" "Candida" "albicans" "metalondinensis" "subspecies" "Castell et al." "GBIF" "11270252" "2599597" "2599597" 1.5 ""
"F_CANDD_ALBC_NNLQ" "Candida albicans non-liquefaciens" "synonym" "Fungi" "Ascomycota" "Saccharomycetes" "Saccharomycetales" "Debaryomycetaceae" "Candida" "albicans" "non-liquefaciens" "subspecies" "Sasak" "GBIF" "11323433" "2599597" "2599597" 1.5 ""
"F_CANDD_ALBC_STLL" "Candida albicans stellatoidea" "synonym" "Fungi" "Ascomycota" "Saccharomycetes" "Saccharomycetales" "Debaryomycetaceae" "Candida" "albicans" "stellatoidea" "subspecies" "Jones et al." "GBIF" "11340449" "2599597" "2599597" 1.5 ""
@ -9216,6 +9219,7 @@
"F_CANDD_FNSS" "Candida gifuensis" "synonym" "Fungi" "Ascomycota" "Saccharomycetes" "Saccharomycetales" "Debaryomycetaceae" "Candida" "gifuensis" "" "species" "Tanig" "GBIF" "5495793" "2518121" "2599597" 1.5 ""
"F_CANDD_GGNT" "Candida gigantensis" "accepted" "Fungi" "Ascomycota" "Saccharomycetes" "Saccharomycetales" "Debaryomycetaceae" "Candida" "gigantensis" "" "species" "Suh et al." "GBIF" "3480169" "2518121" 1.5 ""
"F_CANDD_GLBR" "Candida glabrata" "accepted" "Fungi" "Ascomycota" "Saccharomycetes" "Saccharomycetales" "Debaryomycetaceae" "Candida" "glabrata" "" "species" "Mey et al." "GBIF" "2599530" "2518121" 1.5 "444877006,782948004"
"F_CANDD_GLBR-C" "Candida glabrata complex" "accepted" "Fungi" "Ascomycota" "Saccharomycetes" "Saccharomycetales" "Debaryomycetaceae" "Candida" "glabrata complex" "" "species group" "manually added" "2518121" 1.5 ""
"F_CANDD_BRTS" "Candida glabratus" "synonym" "Fungi" "Ascomycota" "Saccharomycetes" "Saccharomycetales" "Debaryomycetaceae" "Candida" "glabratus" "" "species" "Anderson" "GBIF" "7407691" "2518121" "2599530" 1.5 ""
"F_CANDD_GLBS" "Candida glaebosa" "accepted" "Fungi" "Ascomycota" "Saccharomycetes" "Saccharomycetales" "Debaryomycetaceae" "Candida" "glaebosa" "" "species" "Komag et al." "GBIF" "3480310" "2518121" 1.5 ""
"F_CANDD_LBSM" "Candida globosum" "synonym" "Fungi" "Ascomycota" "Saccharomycetes" "Saccharomycetales" "Debaryomycetaceae" "Candida" "globosum" "" "species" "Zach" "GBIF" "3480508" "2518121" "2599539" 1.5 ""
@ -9390,6 +9394,7 @@
"F_CANDD_PRPL" "Candida parapolymorpha" "accepted" "Fungi" "Ascomycota" "Saccharomycetes" "Saccharomycetales" "Debaryomycetaceae" "Candida" "parapolymorpha" "" "species" "Suh et al." "GBIF" "8157046" "2518121" 1.5 ""
"F_CANDD_PRPSL" "Candida parapsilopsis" "synonym" "Fungi" "Ascomycota" "Saccharomycetes" "Saccharomycetales" "Debaryomycetaceae" "Candida" "parapsilopsis" "" "species" "Ashford" "GBIF" "2599545" "2518121" "2599539" 1.5 ""
"F_CANDD_PRPS" "Candida parapsilosis" "accepted" "Fungi" "Ascomycota" "Saccharomycetes" "Saccharomycetales" "Debaryomycetaceae" "Candida" "parapsilosis" "" "species" "Langeron et al." "GBIF" "2599539" "2518121" 1.5 "61302002"
"F_CANDD_PRPS-C" "Candida parapsilosis complex" "accepted" "Fungi" "Ascomycota" "Saccharomycetes" "Saccharomycetales" "Debaryomycetaceae" "Candida" "parapsilosis complex" "" "species group" "manually added" "2518121" 1.5 ""
"F_CANDD_PRPS_HOKK" "Candida parapsilosis hokkaii" "synonym" "Fungi" "Ascomycota" "Saccharomycetes" "Saccharomycetales" "Debaryomycetaceae" "Candida" "parapsilosis" "hokkaii" "subspecies" "Goto et al." "GBIF" "3480002" "2599539" "3479947" 1.5 ""
"F_CANDD_PRPS_INTR" "Candida parapsilosis intermedia" "synonym" "Fungi" "Ascomycota" "Saccharomycetes" "Saccharomycetales" "Debaryomycetaceae" "Candida" "parapsilosis" "intermedia" "subspecies" "Kreger-van Rij et al." "GBIF" "3480258" "2599539" "3479947" 1.5 ""
"F_CANDD_PRPS_PRPS" "Candida parapsilosis parapsilosis" "synonym" "Fungi" "Ascomycota" "Saccharomycetes" "Saccharomycetales" "Debaryomycetaceae" "Candida" "parapsilosis" "parapsilosis" "subspecies" "GBIF" "11331780" "2599539" "2599539" 1.5 ""
@ -11190,6 +11195,7 @@
"B_CTRBC" "Citrobacter" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Citrobacter" "" "" "genus" "Werkman et al., 1932" "facultative anaerobe" "LPSN" "515376" "482" "11150190" "11158430" 1 "1089501000112101,75972000"
"B_CTRBC_AMLNT" "Citrobacter amalonatica" "synonym" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Citrobacter" "amalonatica" "" "species" "Young et al., 1971" "aerobe" "GBIF" "5427576" "11150190" "3221795" 1 ""
"B_CTRBC_AMLN" "Citrobacter amalonaticus" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Citrobacter" "amalonaticus" "" "species" "Brenner et al., 1982" "aerobe" "LPSN" "774743" "515376" "3221795" "11150190" 1 "1089101000112105,55744003"
"B_CTRBC_AMLN-C" "Citrobacter amalonaticus complex" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Citrobacter" "amalonaticus complex" "" "species group" "aerobe" "manually added" "515376" "11150190" 1 ""
"B_CTRBC_BTTR" "Citrobacter bitternis" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Citrobacter" "bitternis" "" "species" "Ko et al., 2015" "likely facultative anaerobe" "GBIF" "11113073" "11150190" 1.5 ""
"B_CTRBC_BRAK" "Citrobacter braakii" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Citrobacter" "braakii" "" "species" "Brenner et al., 1993" "aerobe" "LPSN" "774744" "515376" "3221791" "11150190" 1 "1089301000112107,114262000"
"B_CTRBC_CRON" "Citrobacter cronae" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Citrobacter" "cronae" "" "species" "Oberhettinger et al., 2020" "likely facultative anaerobe" "LPSN" "7473" "515376" "11248376" "11150190" "3221797" 1 ""
@ -16134,6 +16140,7 @@
"B_ENTRBC_CHND" "Enterobacter chuandaensis" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Enterobacter" "chuandaensis" "" "species" "Wu et al., 2019" "facultative anaerobe" "LPSN" "800158" "515587" "10745032" "11204930" 1.5 ""
"B_ENTRBC_CLOC" "Enterobacter cloacae" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Enterobacter" "cloacae" "" "species" "Hormaeche et al., 1960" "aerobe" "LPSN" "775933" "515587" "11234351" "11204930" 1 "714007005,737529000,14385002,721910001,714317005"
"B_ENTRBC_CLOC_CLOC" "Enterobacter cloacae cloacae" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Enterobacter" "cloacae" "cloacae" "subspecies" "Hoffmann et al., 2005" "LPSN" "775934" "775933" "7234533" "11234351" 1 ""
"B_ENTRBC_CLOC-C" "Enterobacter cloacae complex" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Enterobacter" "cloacae complex" "" "species group" "aerobe" "manually added" "515587" "11204930" 1 ""
"B_ENTRBC_CLOC_DSSL" "Enterobacter cloacae dissolvens" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Enterobacter" "cloacae" "dissolvens" "subspecies" "Hoffmann et al., 2005" "aerobe" "LPSN" "775935" "775933" "3221982" "11234351" 1 ""
"B_ENTRBC_COWN" "Enterobacter cowanii" "synonym" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Enterobacter" "cowanii" "" "species" "Inoue et al., 2001" "aerobe" "LPSN" "775936" "515587" "791223" 1 ""
"B_ENTRBC_DSSL" "Enterobacter dissolvens" "synonym" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Enterobacter" "dissolvens" "" "species" "Brenner et al., 1988" "aerobe" "LPSN" "775937" "515587" "775935" "3221983" "11204930" "3221982" 1.5 ""