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MO group fixes

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dr. M.S. (Matthijs) Berends
2023-07-12 15:04:48 +01:00
parent 9cf054903b
commit 0c46f61260
28 changed files with 1822 additions and 861 deletions
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63
data-raw/microorganisms.groups.txt
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@@ -58,6 +58,13 @@
"B_BRKHL_CEPC-C" "B_BRKHL_VTNM" "Burkholderia cepacia complex" "Burkholderia vietnamiensis"
"F_CANDD_ALBC-C" "F_CANDD_AFRC" "Candida albicans complex" "Candida africana"
"F_CANDD_ALBC-C" "F_CANDD_ALBC" "Candida albicans complex" "Candida albicans"
"F_CANDD_ALBC-C" "F_CANDD_ALBC_ALBC" "Candida albicans complex" "Candida albicans albicans"
"F_CANDD_ALBC-C" "F_CANDD_ALBC_CLSS" "Candida albicans complex" "Candida albicans claussenii"
"F_CANDD_ALBC-C" "F_CANDD_ALBC_MTLN" "Candida albicans complex" "Candida albicans metalondinensis"
"F_CANDD_ALBC-C" "F_CANDD_ALBC_NNLQ" "Candida albicans complex" "Candida albicans non-liquefaciens"
"F_CANDD_ALBC-C" "F_CANDD_ALBC_STLL" "Candida albicans complex" "Candida albicans stellatoidea"
"F_CANDD_ALBC-C" "F_CANDD_ALBC_TRPC" "Candida albicans complex" "Candida albicans tropicalis"
"F_CANDD_ALBC-C" "F_CANDD_ALBC_VLLM" "Candida albicans complex" "Candida albicans vuilleminii"
"F_CANDD_ALBC-C" "F_CANDD_DBLN" "Candida albicans complex" "Candida dubliniensis"
"F_CANDD_GLBR-C" "F_CANDD_BRCR" "Candida glabrata complex" "Candida bracarensis"
"F_CANDD_GLBR-C" "F_CANDD_GLBR" "Candida glabrata complex" "Candida glabrata"
@@ -65,6 +72,11 @@
"F_CANDD_PRPS-C" "F_CANDD_MTPS" "Candida parapsilosis complex" "Candida metapsilosis"
"F_CANDD_PRPS-C" "F_CANDD_ORTH" "Candida parapsilosis complex" "Candida orthopsilosis"
"F_CANDD_PRPS-C" "F_CANDD_PRPS" "Candida parapsilosis complex" "Candida parapsilosis"
"F_CANDD_PRPS-C" "F_CANDD_PRPS_HOKK" "Candida parapsilosis complex" "Candida parapsilosis hokkaii"
"F_CANDD_PRPS-C" "F_CANDD_PRPS_INTR" "Candida parapsilosis complex" "Candida parapsilosis intermedia"
"F_CANDD_PRPS-C" "F_CANDD_PRPS_PRPS" "Candida parapsilosis complex" "Candida parapsilosis parapsilosis"
"F_CANDD_PRPS-C" "F_CANDD_PRPS_QURC" "Candida parapsilosis complex" "Candida parapsilosis querci"
"F_CANDD_PRPS-C" "F_CANDD_PRPS_QRCS" "Candida parapsilosis complex" "Candida parapsilosis quercus"
"P_CHLMS" "F_CANDD_DBSH" "Chilomastix" "Candida duobushaemulonii"
"P_CHLMS" "F_CANDD_HMLN" "Chilomastix" "Candida haemulonii"
"P_CHLMS" "B_CANDD_HMLN-C" "Chilomastix" "Candida haemulonii complex"
@@ -137,6 +149,7 @@
"B_STPHY_CONS" "B_STPHY_SPRP_BOVS" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus saprophyticus bovis"
"B_STPHY_CONS" "B_STPHY_SPRP_SPRP" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus saprophyticus saprophyticus"
"B_STPHY_CONS" "B_STPHY_SCHL" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus schleiferi"
"B_STPHY_CONS" "B_STPHY_SCHL_CGLN" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus schleiferi coagulans"
"B_STPHY_CONS" "B_STPHY_SCHL_SCHL" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus schleiferi schleiferi"
"B_STPHY_CONS" "B_STPHY_SCIR" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus sciuri"
"B_STPHY_CONS" "B_STPHY_SCIR_CRNT" "Coagulase-negative Staphylococcus (CoNS)" "Staphylococcus sciuri carnaticus"
@@ -184,6 +197,8 @@
"B_CORYNF" "B_CRYNB" "Coryneform bacterium" "Corynebacterium"
"B_CORYNF" "B_CRYNB_ACCL" "Coryneform bacterium" "Corynebacterium accolens"
"B_CORYNF" "B_CRYNB_AFRM" "Coryneform bacterium" "Corynebacterium afermentans"
"B_CORYNF" "B_CRYNB_AFRM_AFRM" "Coryneform bacterium" "Corynebacterium afermentans afermentans"
"B_CORYNF" "B_CRYNB_AFRM_LPPH" "Coryneform bacterium" "Corynebacterium afermentans lipophilum"
"B_CORYNF" "B_CRYNB_AMYC" "Coryneform bacterium" "Corynebacterium amycolatum"
"B_CORYNF" "B_CRYNB_ARGN" "Coryneform bacterium" "Corynebacterium argentoratense"
"B_CORYNF" "B_CRYNB_ARMC" "Coryneform bacterium" "Corynebacterium aurimucosum"
@@ -192,6 +207,8 @@
"B_CORYNF" "B_CRYNB_COYL" "Coryneform bacterium" "Corynebacterium coyleae"
"B_CORYNF" "B_CRYNB_CYST" "Coryneform bacterium" "Corynebacterium cystitidis"
"B_CORYNF" "B_CRYNB_DPHT" "Coryneform bacterium" "Corynebacterium diphtheriae"
"B_CORYNF" "B_CRYNB_DPHT_DPHT" "Coryneform bacterium" "Corynebacterium diphtheriae diphtheriae"
"B_CORYNF" "B_CRYNB_DPHT_LSNN" "Coryneform bacterium" "Corynebacterium diphtheriae lausannense"
"B_CORYNF" "B_CRYNB_GLCR" "Coryneform bacterium" "Corynebacterium glucuronolyticum"
"B_CORYNF" "B_CRYNB_GLTM" "Coryneform bacterium" "Corynebacterium glutamicum"
"B_CORYNF" "B_CRYNB_JEKM" "Coryneform bacterium" "Corynebacterium jeikeium"
@@ -231,8 +248,14 @@
"B_CORYNF" "B_TRCLL_OTTD" "Coryneform bacterium" "Turicella otitidis"
"B_ENTRBC_CLOC-C" "B_ENTRBC_ASBR" "Enterobacter cloacae complex" "Enterobacter asburiae"
"B_ENTRBC_CLOC-C" "B_ENTRBC_CLOC" "Enterobacter cloacae complex" "Enterobacter cloacae"
"B_ENTRBC_CLOC-C" "B_ENTRBC_CLOC_CLOC" "Enterobacter cloacae complex" "Enterobacter cloacae cloacae"
"B_ENTRBC_CLOC-C" "B_ENTRBC_CLOC_DSSL" "Enterobacter cloacae complex" "Enterobacter cloacae dissolvens"
"B_ENTRBC_CLOC-C" "B_ENTRBC_HRMC" "Enterobacter cloacae complex" "Enterobacter hormaechei"
"B_ENTRBC_CLOC-C" "B_ENTRBC_HRMC_HFFM" "Enterobacter cloacae complex" "Enterobacter hormaechei hoffmannii"
"B_ENTRBC_CLOC-C" "B_ENTRBC_HRMC_HRMC" "Enterobacter cloacae complex" "Enterobacter hormaechei hormaechei"
"B_ENTRBC_CLOC-C" "B_ENTRBC_HRMC_OHAR" "Enterobacter cloacae complex" "Enterobacter hormaechei oharae"
"B_ENTRBC_CLOC-C" "B_ENTRBC_HRMC_STGR" "Enterobacter cloacae complex" "Enterobacter hormaechei steigerwaltii"
"B_ENTRBC_CLOC-C" "B_ENTRBC_HRMC_XNGF" "Enterobacter cloacae complex" "Enterobacter hormaechei xiangfangensis"
"B_ENTRBC_CLOC-C" "B_ENTRBC_KOBE" "Enterobacter cloacae complex" "Enterobacter kobei"
"B_ENTRBC_CLOC-C" "B_ENTRBC_LDWG" "Enterobacter cloacae complex" "Enterobacter ludwigii"
"B_ENTRBC_CLOC-C" "B_ENTRBC_NMPR" "Enterobacter cloacae complex" "Enterobacter nimipressuralis"
@@ -284,18 +307,30 @@
"F_MYRZY_GLLR-C" "F_MYRZY_CRBB" "Meyerozyma guilliermondii complex" "Meyerozyma caribbica"
"F_MYRZY_GLLR-C" "F_MYRZY_CRPP" "Meyerozyma guilliermondii complex" "Meyerozyma carpophila"
"F_MYRZY_GLLR-C" "F_MYRZY_GLLR" "Meyerozyma guilliermondii complex" "Meyerozyma guilliermondii"
"F_MYRZY_GLLR-C" "F_MYRZY_GLLR_CRPP" "Meyerozyma guilliermondii complex" "Meyerozyma guilliermondii carpophila"
"F_MYRZY_GLLR-C" "F_MYRZY_GLLR_JPNC" "Meyerozyma guilliermondii complex" "Meyerozyma guilliermondii japonica"
"F_MYRZY_GLLR-C" "F_MYRZY_GLLR_MUHR" "Meyerozyma guilliermondii complex" "Meyerozyma guilliermondii muhira"
"F_MYRZY_GLLR-C" "F_MYRZY_GLLR_PSDG" "Meyerozyma guilliermondii complex" "Meyerozyma guilliermondii pseudoguilliermondii"
"B_MYCBC_AVIM-C" "B_MYCBC_AVIM" "Mycobacterium avium-intracellulare complex" "Mycobacterium avium"
"B_MYCBC_AVIM-C" "B_MYCBC_AVIM_AVIM" "Mycobacterium avium-intracellulare complex" "Mycobacterium avium avium"
"B_MYCBC_AVIM-C" "B_MYCBC_AVIM_PRTB" "Mycobacterium avium-intracellulare complex" "Mycobacterium avium paratuberculosis"
"B_MYCBC_AVIM-C" "B_MYCBC_AVIM_SLVT" "Mycobacterium avium-intracellulare complex" "Mycobacterium avium silvaticum"
"B_MYCBC_AVIM-C" "B_MYCBC_LLRE" "Mycobacterium avium-intracellulare complex" "Mycobacterium intracellulare"
"B_MYCBC_AVIM-C" "B_MYCBC_LLRE_CHMR" "Mycobacterium avium-intracellulare complex" "Mycobacterium intracellulare chimaera"
"B_MYCBC_AVIM-C" "B_MYCBC_LLRE_INTR" "Mycobacterium avium-intracellulare complex" "Mycobacterium intracellulare intracellulare"
"B_MYCBC_AVIM-C" "B_MYCBC_LLRE_YNGN" "Mycobacterium avium-intracellulare complex" "Mycobacterium intracellulare yongonense"
"B_MYCBC_TBRC-C" "B_MYCBC_AFRC" "Mycobacterium tuberculosis complex" "Mycobacterium africanum"
"B_MYCBC_TBRC-C" "B_MYCBC_BOVS" "Mycobacterium tuberculosis complex" "Mycobacterium bovis"
"B_MYCBC_TBRC-C" "B_MYCBC_BOVS_BOVS" "Mycobacterium tuberculosis complex" "Mycobacterium bovis bovis"
"B_MYCBC_TBRC-C" "B_MYCBC_BOVS_CAPR" "Mycobacterium tuberculosis complex" "Mycobacterium bovis caprae"
"B_MYCBC_TBRC-C" "B_MYCBC_CAPR" "Mycobacterium tuberculosis complex" "Mycobacterium caprae"
"B_MYCBC_TBRC-C" "B_MYCBC_MCRT" "Mycobacterium tuberculosis complex" "Mycobacterium microti"
"B_MYCBC_TBRC-C" "B_MYCBC_MUNG" "Mycobacterium tuberculosis complex" "Mycobacterium mungi"
"B_MYCBC_TBRC-C" "B_MYCBC_ORYG" "Mycobacterium tuberculosis complex" "Mycobacterium orygis"
"B_MYCBC_TBRC-C" "B_MYCBC_PNNP" "Mycobacterium tuberculosis complex" "Mycobacterium pinnipedii"
"B_MYCBC_TBRC-C" "B_MYCBC_TBRC" "Mycobacterium tuberculosis complex" "Mycobacterium tuberculosis"
"B_MYCBC_TBRC-C" "B_MYCBC_TBRC_CAPR" "Mycobacterium tuberculosis complex" "Mycobacterium tuberculosis caprae"
"B_MYCBC_TBRC-C" "B_MYCBC_TBRC_TBRC" "Mycobacterium tuberculosis complex" "Mycobacterium tuberculosis tuberculosis"
"B_PSDMN_FLRS-C" "B_PSDMN_FLRS" "Pseudomonas fluorescens complex" "Pseudomonas fluorescens"
"B_MYCBC_RGM" "B_MYCBC_ABSC_ABSC" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium abscessus abscessus"
"B_MYCBC_RGM" "B_MYCBC_ABSC_BLLT" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium abscessus bolletii"
@@ -318,6 +353,10 @@
"B_MYCBC_RGM" "B_MYCBC_CNRS" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium canariasense"
"B_MYCBC_RGM" "B_MYCBC_CLRF" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium celeriflavum"
"B_MYCBC_RGM" "B_MYCBC_CHLN" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium chelonae"
"B_MYCBC_RGM" "B_MYCBC_CHLN_ABSC" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium chelonae abscessus"
"B_MYCBC_RGM" "B_MYCBC_CHLN_BOVS" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium chelonae bovis"
"B_MYCBC_RGM" "B_MYCBC_CHLN_CHLN" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium chelonae chelonae"
"B_MYCBC_RGM" "B_MYCBC_CHLN_GWNK" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium chelonae gwanakae"
"B_MYCBC_RGM" "B_MYCBC_CHIT" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium chitae"
"B_MYCBC_RGM" "B_MYCBC_CHLR" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium chlorophenolicum"
"B_MYCBC_RGM" "B_MYCBC_CHBN" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium chubuense"
@@ -331,6 +370,8 @@
"B_MYCBC_RGM" "B_MYCBC_FLVS" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium flavescens"
"B_MYCBC_RGM" "B_MYCBC_VRNS" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium fluoranthenivorans"
"B_MYCBC_RGM" "B_MYCBC_FRTT" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium fortuitum"
"B_MYCBC_RGM" "B_MYCBC_FRTT_ACTM" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium fortuitum acetamidolyticum"
"B_MYCBC_RGM" "B_MYCBC_FRTT_FRTT" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium fortuitum fortuitum"
"B_MYCBC_RGM" "B_MYCBC_FRNK" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium franklinii"
"B_MYCBC_RGM" "B_MYCBC_FRDR" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium frederiksbergense"
"B_MYCBC_RGM" "B_MYCBC_GADM" "Rapidly growing Mycobacterium (RGM)" "Mycobacterium gadium"
@@ -391,6 +432,10 @@
"B_MYCBC_SGM" "B_MYCBC_MLMN" "Slowly growing Mycobacterium (SGM)" "Mycobacterium malmoense"
"B_MYCBC_SGM" "B_MYCBC_MRNM" "Slowly growing Mycobacterium (SGM)" "Mycobacterium marinum"
"B_STRPT_GRPA" "B_STRPT_PYGN" "Streptococcus Group A" "Streptococcus pyogenes"
"B_STRPT_ABCG" "B_STRPT_GRPA" "Streptococcus Group A, B, C, G" "Streptococcus Group A"
"B_STRPT_ABCG" "B_STRPT_GRPB" "Streptococcus Group A, B, C, G" "Streptococcus Group B"
"B_STRPT_ABCG" "B_STRPT_GRPC" "Streptococcus Group A, B, C, G" "Streptococcus Group C"
"B_STRPT_ABCG" "B_STRPT_GRPG" "Streptococcus Group A, B, C, G" "Streptococcus Group G"
"B_STRPT_ABCG" "B_STRPT_AGLC" "Streptococcus Group A, B, C, G" "Streptococcus agalactiae"
"B_STRPT_ABCG" "B_STRPT_CANS" "Streptococcus Group A, B, C, G" "Streptococcus canis"
"B_STRPT_ABCG" "B_STRPT_DYSG" "Streptococcus Group A, B, C, G" "Streptococcus dysgalactiae"
@@ -412,6 +457,11 @@
"B_STRPT_GRPF" "B_STRPT_ANGN" "Streptococcus Group F" "Streptococcus anginosus"
"B_STRPT_GRPF" "B_STRPT_ANGN_ANGN" "Streptococcus Group F" "Streptococcus anginosus anginosus"
"B_STRPT_GRPF" "B_STRPT_ANGN_WHLY" "Streptococcus Group F" "Streptococcus anginosus whileyi"
"B_STRPT_GRPF" "B_STRPT_CNST" "Streptococcus Group F" "Streptococcus constellatus"
"B_STRPT_GRPF" "B_STRPT_CNST_CNST" "Streptococcus Group F" "Streptococcus constellatus constellatus"
"B_STRPT_GRPF" "B_STRPT_CNST_PHRY" "Streptococcus Group F" "Streptococcus constellatus pharyngis"
"B_STRPT_GRPF" "B_STRPT_CNST_VBRG" "Streptococcus Group F" "Streptococcus constellatus viborgensis"
"B_STRPT_GRPF" "B_STRPT_INTR" "Streptococcus Group F" "Streptococcus intermedius"
"B_STRPT_GRPG" "B_STRPT_CANS" "Streptococcus Group G" "Streptococcus canis"
"B_STRPT_GRPG" "B_STRPT_DYSG" "Streptococcus Group G" "Streptococcus dysgalactiae"
"B_STRPT_GRPG" "B_STRPT_DYSG_DYSG" "Streptococcus Group G" "Streptococcus dysgalactiae dysgalactiae"
@@ -420,10 +470,18 @@
"B_STRPT_GRPK" "B_STRPT_SLVR" "Streptococcus Group K" "Streptococcus salivarius"
"B_STRPT_GRPK" "B_STRPT_SLVR_SLVR" "Streptococcus Group K" "Streptococcus salivarius salivarius"
"B_STRPT_GRPK" "B_STRPT_SLVR_THRM" "Streptococcus Group K" "Streptococcus salivarius thermophilus"
"B_STRPT_GRPL" "B_STRPT_DYSG" "Streptococcus Group L" "Streptococcus dysgalactiae"
"B_STRPT_GRPL" "B_STRPT_DYSG_DYSG" "Streptococcus Group L" "Streptococcus dysgalactiae dysgalactiae"
"B_STRPT_GRPL" "B_STRPT_DYSG_EQSM" "Streptococcus Group L" "Streptococcus dysgalactiae equisimilis"
"B_STRPT_VIRI" "B_STRPT_MILL" "Viridans Group Streptococcus (VGS)" "Milleri Group Streptococcus (MGS)"
"B_STRPT_VIRI" "B_STRPT_ACDM" "Viridans Group Streptococcus (VGS)" "Streptococcus acidominimus"
"B_STRPT_VIRI" "B_STRPT_ANGN" "Viridans Group Streptococcus (VGS)" "Streptococcus anginosus"
"B_STRPT_VIRI" "B_STRPT_ANGN_ANGN" "Viridans Group Streptococcus (VGS)" "Streptococcus anginosus anginosus"
"B_STRPT_VIRI" "B_STRPT_ANGN_WHLY" "Viridans Group Streptococcus (VGS)" "Streptococcus anginosus whileyi"
"B_STRPT_VIRI" "B_STRPT_CNST" "Viridans Group Streptococcus (VGS)" "Streptococcus constellatus"
"B_STRPT_VIRI" "B_STRPT_CNST_CNST" "Viridans Group Streptococcus (VGS)" "Streptococcus constellatus constellatus"
"B_STRPT_VIRI" "B_STRPT_CNST_PHRY" "Viridans Group Streptococcus (VGS)" "Streptococcus constellatus pharyngis"
"B_STRPT_VIRI" "B_STRPT_CNST_VBRG" "Viridans Group Streptococcus (VGS)" "Streptococcus constellatus viborgensis"
"B_STRPT_VIRI" "B_STRPT_CRCT" "Viridans Group Streptococcus (VGS)" "Streptococcus criceti"
"B_STRPT_VIRI" "B_STRPT_CRST" "Viridans Group Streptococcus (VGS)" "Streptococcus cristatus"
"B_STRPT_VIRI" "B_STRPT_DOWN" "Viridans Group Streptococcus (VGS)" "Streptococcus downei"
@@ -435,9 +493,14 @@
"B_STRPT_VIRI" "B_STRPT_MITS" "Viridans Group Streptococcus (VGS)" "Streptococcus mitis"
"B_STRPT_VIRI" "B_STRPT_MTNS" "Viridans Group Streptococcus (VGS)" "Streptococcus mutans"
"B_STRPT_VIRI" "B_STRPT_ORLS" "Viridans Group Streptococcus (VGS)" "Streptococcus oralis"
"B_STRPT_VIRI" "B_STRPT_ORLS_DNTS" "Viridans Group Streptococcus (VGS)" "Streptococcus oralis dentisani"
"B_STRPT_VIRI" "B_STRPT_ORLS_ORLS" "Viridans Group Streptococcus (VGS)" "Streptococcus oralis oralis"
"B_STRPT_VIRI" "B_STRPT_ORLS_TGRN" "Viridans Group Streptococcus (VGS)" "Streptococcus oralis tigurinus"
"B_STRPT_VIRI" "B_STRPT_PRSN" "Viridans Group Streptococcus (VGS)" "Streptococcus parasanguinis"
"B_STRPT_VIRI" "B_STRPT_RATT" "Viridans Group Streptococcus (VGS)" "Streptococcus ratti"
"B_STRPT_VIRI" "B_STRPT_SLVR" "Viridans Group Streptococcus (VGS)" "Streptococcus salivarius"
"B_STRPT_VIRI" "B_STRPT_SLVR_SLVR" "Viridans Group Streptococcus (VGS)" "Streptococcus salivarius salivarius"
"B_STRPT_VIRI" "B_STRPT_SLVR_THRM" "Viridans Group Streptococcus (VGS)" "Streptococcus salivarius thermophilus"
"B_STRPT_VIRI" "B_STRPT_SNGN" "Viridans Group Streptococcus (VGS)" "Streptococcus sanguinis"
"B_STRPT_VIRI" "B_STRPT_SBRN" "Viridans Group Streptococcus (VGS)" "Streptococcus sobrinus"
"B_STRPT_VIRI" "B_STRPT_SUIS" "Viridans Group Streptococcus (VGS)" "Streptococcus suis"