taxid-changelog
NCBI taxonomic identifier (taxIDs) changelog, tracking taxIDs deletion, new adding, merge, reuse, and rank/name changes.
Please cite: https://doi.org/10.1016/j.jgg.2021.03.006
Table of contents
Download
Format
File format (CSV format with 8 fields):
# fields comments
taxid # taxid
version # version / time of archive, e.g, 2019-07-01
change # change, values:
# NEW newly added
# REUSE_DEL deleted taxids being reused
# REUSE_MER merged taxids being reused
# DELETE deleted
# MERGE merged into another taxid
# ABSORB other taxids merged into this one
# CHANGE_NAME scientific name changed
# CHANGE_RANK rank changed
# CHANGE_LIN_LIN lineage taxids remain but lineage changed
# CHANGE_LIN_TAX lineage taxids changed
# CHANGE_LIN_LEN lineage length changed
change-value # variable values for changes:
# 1) new taxid for MERGE
# 2) merged taxids for ABSORB
# 3) empty for others
name # scientific name
rank # rank
lineage # full lineage of the taxid
lineage-taxids # taxids of the lineage
Example 1:
$ gzip -dc taxid-changelog.csv.gz | head -n 11
taxid,version,change,change-value,name,rank,lineage,lineage-taxids
1,2014-08-01,NEW,,root,no rank,root,1
2,2014-08-01,NEW,,Bacteria,superkingdom,cellular organisms;Bacteria,131567;2
3,2014-08-01,DELETE,,,,,
4,2014-08-01,DELETE,,,,,
5,2014-08-01,DELETE,,,,,
6,2014-08-01,NEW,,Azorhizobium,genus,cellular organisms;Bacteria;Proteobacteria;Alphaproteobacteria;Rhizobiales;Xanthobacteraceae;Azorhizobium,131567;2;1224;28211;356;335928;6
7,2014-08-01,NEW,,Azorhizobium caulinodans,species,cellular organisms;Bacteria;Proteobacteria;Alphaproteobacteria;Rhizobiales;Xanthobacteraceae;Azorhizobium;Azorhizobium caulinodans,131567;2;1224;28211;356;335928;6;7
7,2014-08-01,ABSORB,395,Azorhizobium caulinodans,species,cellular organisms;Bacteria;Proteobacteria;Alphaproteobacteria;Rhizobiales;Xanthobacteraceae;Azorhizobium;Azorhizobium caulinodans,131567;2;1224;28211;356;335928;6;7
8,2014-08-01,DELETE,,,,,
9,2014-08-01,NEW,,Buchnera aphidicola,species,cellular organisms;Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae;Buchnera;Buchnera aphidicola,131567;2;1224;1236;91347;543;32199;9
Example 2 (SARS-CoV-2)
$ pigz -cd taxid-changelog.csv.gz \
| csvtk grep -f taxid -p 2697049 \
| csvtk pretty
taxid version change change-value name rank lineage lineage-taxids
2697049 2020-02-01 NEW Wuhan seafood market pneumonia virus species Viruses;Riboviria;Nidovirales;Cornidovirineae;Coronaviridae;Orthocoronavirinae;Betacoronavirus;unclassified Betacoronavirus;Wuhan seafood market pneumonia virus 10239;2559587;76804;2499399;11118;2501931;694002;696098;2697049
2697049 2020-03-01 CHANGE_NAME Severe acute respiratory syndrome coronavirus 2 no rank Viruses;Riboviria;Nidovirales;Cornidovirineae;Coronaviridae;Orthocoronavirinae;Betacoronavirus;Sarbecovirus;Severe acute respiratory syndrome-related coronavirus;Severe acute respiratory syndrome coronavirus 2 10239;2559587;76804;2499399;11118;2501931;694002;2509511;694009;2697049
2697049 2020-03-01 CHANGE_RANK Severe acute respiratory syndrome coronavirus 2 no rank Viruses;Riboviria;Nidovirales;Cornidovirineae;Coronaviridae;Orthocoronavirinae;Betacoronavirus;Sarbecovirus;Severe acute respiratory syndrome-related coronavirus;Severe acute respiratory syndrome coronavirus 2 10239;2559587;76804;2499399;11118;2501931;694002;2509511;694009;2697049
2697049 2020-03-01 CHANGE_LIN_LEN Severe acute respiratory syndrome coronavirus 2 no rank Viruses;Riboviria;Nidovirales;Cornidovirineae;Coronaviridae;Orthocoronavirinae;Betacoronavirus;Sarbecovirus;Severe acute respiratory syndrome-related coronavirus;Severe acute respiratory syndrome coronavirus 2 10239;2559587;76804;2499399;11118;2501931;694002;2509511;694009;2697049
2697049 2020-06-01 CHANGE_LIN_LEN Severe acute respiratory syndrome coronavirus 2 no rank Viruses;Riboviria;Orthornavirae;Pisuviricota;Pisoniviricetes;Nidovirales;Cornidovirineae;Coronaviridae;Orthocoronavirinae;Betacoronavirus;Sarbecovirus;Severe acute respiratory syndrome-related coronavirus;Severe acute respiratory syndrome coronavirus 2 10239;2559587;2732396;2732408;2732506;76804;2499399;11118;2501931;694002;2509511;694009;2697049
2697049 2020-07-01 CHANGE_RANK Severe acute respiratory syndrome coronavirus 2 isolate Viruses;Riboviria;Orthornavirae;Pisuviricota;Pisoniviricetes;Nidovirales;Cornidovirineae;Coronaviridae;Orthocoronavirinae;Betacoronavirus;Sarbecovirus;Severe acute respiratory syndrome-related coronavirus;Severe acute respiratory syndrome coronavirus 2 10239;2559587;2732396;2732408;2732506;76804;2499399;11118;2501931;694002;2509511;694009;2697049
2697049 2020-08-01 CHANGE_RANK Severe acute respiratory syndrome coronavirus 2 no rank Viruses;Riboviria;Orthornavirae;Pisuviricota;Pisoniviricetes;Nidovirales;Cornidovirineae;Coronaviridae;Orthocoronavirinae;Betacoronavirus;Sarbecovirus;Severe acute respiratory syndrome-related coronavirus;Severe acute respiratory syndrome coronavirus 2 10239;2559587;2732396;2732408;2732506;76804;2499399;11118;2501931;694002;2509511;694009;2697049
Example 3 (E.coli with taxid 562)
$ pigz -cd taxid-changelog.csv.gz \
| csvtk grep -f taxid -p 562 \
| csvtk pretty
taxid version change change-value name rank lineage lineage-taxids
562 2014-08-01 NEW Escherichia coli species cellular organisms;Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae;Escherichia;Escherichia coli 131567;2;1224;1236;91347;543;561;562
562 2014-08-01 ABSORB 662101;662104 Escherichia coli species cellular organisms;Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae;Escherichia;Escherichia coli 131567;2;1224;1236;91347;543;561;562
562 2015-11-01 ABSORB 1637691 Escherichia coli species cellular organisms;Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae;Escherichia;Escherichia coli 131567;2;1224;1236;91347;543;561;562
562 2016-10-01 CHANGE_LIN_LIN Escherichia coli species cellular organisms;Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia;Escherichia coli 131567;2;1224;1236;91347;543;561;562
562 2018-06-01 ABSORB 469598 Escherichia coli species cellular organisms;Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia;Escherichia coli 131567;2;1224;1236;91347;543;561;562
# merged taxids
$ pigz -cd taxid-changelog.csv.gz \
| csvtk grep -f taxid -p 662101,662104,1637691,469598 \
| csvtk pretty
taxid version change change-value name rank lineage lineage-taxids
469598 2014-08-01 NEW Escherichia sp. 3_2_53FAA species cellular organisms;Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae;Escherichia;Escherichia sp. 3_2_53FAA 131567;2;1224;1236;91347;543;561;469598
469598 2016-10-01 CHANGE_LIN_LIN Escherichia sp. 3_2_53FAA species cellular organisms;Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia;Escherichia sp. 3_2_53FAA 131567;2;1224;1236;91347;543;561;469598
469598 2018-06-01 MERGE 562 Escherichia sp. 3_2_53FAA species cellular organisms;Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia;Escherichia sp. 3_2_53FAA 131567;2;1224;1236;91347;543;561;469598
662101 2014-08-01 MERGE 562
662104 2014-08-01 MERGE 562
1637691 2015-04-01 DELETE
1637691 2015-05-01 REUSE_DEL Escherichia sp. MAR species cellular organisms;Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae;Escherichia;Escherichia sp. MAR 131567;2;1224;1236;91347;543;561;1637691
1637691 2015-11-01 MERGE 562 Escherichia sp. MAR species cellular organisms;Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae;Escherichia;Escherichia sp. MAR 131567;2;1224;1236;91347;543;561;1637691
Example 4 (All subspecies and strain in Akkermansia muciniphila 239935)
# species in Akkermansia
$ taxonkit list --show-rank --show-name --ids 239935
239935 [species] Akkermansia muciniphila
349741 [strain] Akkermansia muciniphila ATCC BAA-835
# check them all
$ pigz -cd taxid-changelog.csv.gz \
| csvtk grep -f taxid -P <(taxonkit list --indent "" --ids 239935) \
| csvtk pretty
taxid version change change-value name rank lineage lineage-taxids
239935 2014-08-01 NEW Akkermansia muciniphila species cellular organisms;Bacteria;Chlamydiae/Verrucomicrobia group;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Verrucomicrobiaceae;Akkermansia;Akkermansia muciniphila 131567;2;51290;74201;203494;48461;203557;239934;239935
239935 2015-05-01 CHANGE_LIN_TAX Akkermansia muciniphila species cellular organisms;Bacteria;Chlamydiae/Verrucomicrobia group;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansia muciniphila 131567;2;51290;74201;203494;48461;1647988;239934;239935
239935 2016-03-01 CHANGE_LIN_TAX Akkermansia muciniphila species cellular organisms;Bacteria;PVC group;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansia muciniphila 131567;2;1783257;74201;203494;48461;1647988;239934;239935
239935 2016-05-01 ABSORB 1834199 Akkermansia muciniphila species cellular organisms;Bacteria;PVC group;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansia muciniphila 131567;2;1783257;74201;203494;48461;1647988;239934;239935
349741 2014-08-01 NEW Akkermansia muciniphila ATCC BAA-835 no rank cellular organisms;Bacteria;Chlamydiae/Verrucomicrobia group;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Verrucomicrobiaceae;Akkermansia;Akkermansia muciniphila;Akkermansia muciniphila ATCC BAA-835 131567;2;51290;74201;203494;48461;203557;239934;239935;349741
349741 2015-05-01 CHANGE_LIN_TAX Akkermansia muciniphila ATCC BAA-835 no rank cellular organisms;Bacteria;Chlamydiae/Verrucomicrobia group;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansia muciniphila;Akkermansia muciniphila ATCC BAA-835 131567;2;51290;74201;203494;48461;1647988;239934;239935;349741
349741 2016-03-01 CHANGE_LIN_TAX Akkermansia muciniphila ATCC BAA-835 no rank cellular organisms;Bacteria;PVC group;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansia muciniphila;Akkermansia muciniphila ATCC BAA-835 131567;2;1783257;74201;203494;48461;1647988;239934;239935;349741
349741 2020-07-01 CHANGE_RANK Akkermansia muciniphila ATCC BAA-835 strain cellular organisms;Bacteria;PVC group;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansia muciniphila;Akkermansia muciniphila ATCC BAA-835 131567;2;1783257;74201;203494;48461;1647988;239934;239935;349741
Results
Tools used:
Taxids were deleted, newly added and re-used
Stats:
$ csvtk join -k -f version \
<(pigz -cd taxid-changelog.csv.gz \
| csvtk grep -f change -p DELETE \
| csvtk freq -f version) \
<(pigz -cd taxid-changelog.csv.gz \
| csvtk grep -f change -p NEW \
| csvtk freq -f version) \
<(pigz -cd taxid-changelog.csv.gz \
| csvtk grep -f change -p MERGE \
| csvtk freq -f version) \
<(pigz -cd taxid-changelog.csv.gz \
| csvtk grep -f change -p REUSE_DEL \
| csvtk freq -f version) \
<(pigz -cd taxid-changelog.csv.gz \
| csvtk grep -f change -p REUSE_MER \
| csvtk freq -f version) \
| csvtk rename -f -1 -n deleted,newly_added,merged,deleted_reused,merged_reused \
| csvtk pretty
version deleted newly_added merged deleted_reused merged_reused
2014-08-01 310603 1184830 33153
2014-09-01 7957 3362 211 7694
2014-10-01 6535 3856 381 5590
2014-11-01 9568 5849 463 6037
2014-12-01 7147 3699 255 6378
2015-01-01 7650 5104 295 4762
2015-02-01 14911 2699 240 9900
2015-03-01 9123 4117 273 6025
2015-04-01 13748 3398 316 9951
2015-05-01 8381 2639 554 6279
2015-06-01 8629 3320 447 4385
2015-07-01 12746 4140 438 14992
2015-08-01 14680 4300 232 8300
2015-09-01 6646 4083 404 8330
2015-10-01 16933 6052 342 12273
2015-11-01 12169 4727 620 15613
2015-12-01 9782 6298 436 13206
2016-01-01 7834 4133 446 9175
2016-03-01 18825 13532 1230 12250
2016-04-01 10135 6106 469 6461
2016-05-01 13835 4704 449 14778 1
2016-06-01 6303 6110 434 14237 1
2016-08-01 14866 13730 633 10324 2
2016-09-01 8033 4683 273 8450
2016-10-01 6420 2084 219 6213
2016-11-01 5097 3548 1419 3765 2
2016-12-01 5881 3517 219 7113 1
2017-01-01 4208 3102 298 5800
2017-02-01 6762 3108 310 4588
2017-03-01 8929 13341 371 5509
2017-04-01 6721 4026 347 6778
2017-05-01 4904 4306 217 7364
2017-06-01 12789 9715 287 4746
2017-07-01 6974 4622 329 3735 3
2017-08-01 3669 2483 285 14135
2017-09-01 6716 2853 253 3892
2017-10-01 5766 2451 369 4865
2017-12-01 8194 7087 564 8602
2018-01-01 7732 2711 382 4123 1
2018-02-01 9020 4106 325 6676
2018-03-01 17113 9415 326 3743
2018-04-01 14688 16683 422 16358
2018-05-01 31551 4950 292 9794
2018-06-01 31336 6040 430 22034
2018-07-01 35696 10657 260 17726
2018-08-01 21046 11585 246 20586
2018-09-01 4992 10658 404 15697
2018-10-01 78319 34128 384 12118
2018-11-01 34245 31692 509 68228
2018-12-01 5699 1856 210 33487
2019-01-01 3722 2562 330 4653
2019-02-01 5488 5990 404 4411
2019-03-01 12567 6473 219 3598
2019-04-01 12807 19580 271 11672 1
2019-05-01 10502 2453 345 4103
2019-06-01 8008 1458 509 13797
2019-07-01 5050 2192 371 6695
2019-08-01 6041 1611 256 6501
2019-09-01 4975 2541 191 5328
2019-10-01 10854 32970 278 3497
2019-11-01 10648 2025 223 3530
2019-12-01 11905 5727 351 7961
2020-01-01 8928 4337 262 15423
2020-02-01 8566 2024 292 8309
2020-03-01 5752 3051 390 3998
2020-04-01 6982 2149 522 4085
2020-05-01 6380 2277 434 7099
2020-06-01 5648 3182 429 5504
2020-07-01 6715 1982 366 4379
2020-08-01 8667 2053 632 4155
2020-09-01 7135 1457 325 5425
2020-10-01 6091 2567 346 6654
2020-11-01 5126 1479 365 4754
2020-12-01 5726 3696 358 4986
2021-01-01 5506 1661 472 3561
2021-02-01 4320 2260 559 6528
2021-03-01 7015 1395 400 5145
2021-04-01 5230 2101 650 4633 1
2021-05-01 7419 1687 549 4324 2
2021-06-01 6654 2052 321 4623
The paper of NCBI Taxonomy database:
Taxids are stable and persistent—they may be deleted (when taxa are removed from the database), and they may be merged (when taxa are synonymized), but they will never be reused to identify a different taxon.
Deleted taxid can be re-used, e.g., 1157319 was reused to identify the same taxon.
$ pigz -cd taxid-changelog.csv.gz \
| csvtk grep -f taxid -p 7343,1157319 \
| csvtk pretty
taxid version change change-value name rank lineage lineage-taxids
7343 2014-08-01 DELETE
7343 2015-04-01 REUSE_DEL Paraliodrosophila genus cellular organisms;Eukaryota;Opisthokonta;Metazoa;Eumetazoa;Bilateria;Protostomia;Ecdysozoa;Panarthropoda;Arthropoda;Mandibulata;Pancrustacea;Hexapoda;Insecta;Dicondylia;Pterygota;Neoptera;Endopterygota;Diptera;Brachycera;Muscomorpha;Eremoneura;Cyclorrhapha;Schizophora;Acalyptratae;Ephydroidea;Drosophilidae;Drosophilinae;Drosophilini;Drosophilina;Drosophiliti;Paraliodrosophila 131567;2759;33154;33208;6072;33213;33317;1206794;88770;6656;197563;197562;6960;50557;85512;7496;33340;33392;7147;7203;43733;480118;480117;43738;43741;43746;7214;43845;46877;46879;186285;7343
7343 2015-06-01 DELETE Paraliodrosophila genus cellular organisms;Eukaryota;Opisthokonta;Metazoa;Eumetazoa;Bilateria;Protostomia;Ecdysozoa;Panarthropoda;Arthropoda;Mandibulata;Pancrustacea;Hexapoda;Insecta;Dicondylia;Pterygota;Neoptera;Endopterygota;Diptera;Brachycera;Muscomorpha;Eremoneura;Cyclorrhapha;Schizophora;Acalyptratae;Ephydroidea;Drosophilidae;Drosophilinae;Drosophilini;Drosophilina;Drosophiliti;Paraliodrosophila 131567;2759;33154;33208;6072;33213;33317;1206794;88770;6656;197563;197562;6960;50557;85512;7496;33340;33392;7147;7203;43733;480118;480117;43738;43741;43746;7214;43845;46877;46879;186285;7343
7343 2016-05-01 REUSE_DEL Paraliodrosophila genus cellular organisms;Eukaryota;Opisthokonta;Metazoa;Eumetazoa;Bilateria;Protostomia;Ecdysozoa;Panarthropoda;Arthropoda;Mandibulata;Pancrustacea;Hexapoda;Insecta;Dicondylia;Pterygota;Neoptera;Endopterygota;Diptera;Brachycera;Muscomorpha;Eremoneura;Cyclorrhapha;Schizophora;Acalyptratae;Ephydroidea;Drosophilidae;Drosophilinae;Drosophilini;Drosophilina;Drosophiliti;Paraliodrosophila 131567;2759;33154;33208;6072;33213;33317;1206794;88770;6656;197563;197562;6960;50557;85512;7496;33340;33392;7147;7203;43733;480118;480117;43738;43741;43746;7214;43845;46877;46879;186285;7343
7343 2016-08-01 CHANGE_LIN_LEN Paraliodrosophila genus cellular organisms;Eukaryota;Opisthokonta;Metazoa;Eumetazoa;Bilateria;Protostomia;Ecdysozoa;Panarthropoda;Arthropoda;Mandibulata;Pancrustacea;Hexapoda;Insecta;Dicondylia;Pterygota;Neoptera;Endopterygota;Diptera;Brachycera;Muscomorpha;Eremoneura;Cyclorrhapha;Schizophora;Acalyptratae;Ephydroidea;Drosophilidae;Drosophilinae;Drosophilini;Paraliodrosophila 131567;2759;33154;33208;6072;33213;33317;1206794;88770;6656;197563;197562;6960;50557;85512;7496;33340;33392;7147;7203;43733;480118;480117;43738;43741;43746;7214;43845;46877;7343
7343 2017-03-01 CHANGE_LIN_LIN Paraliodrosophila genus cellular organisms;Eukaryota;Opisthokonta;Metazoa;Eumetazoa;Bilateria;Protostomia;Ecdysozoa;Panarthropoda;Arthropoda;Mandibulata;Pancrustacea;Hexapoda;Insecta;Dicondylia;Pterygota;Neoptera;Holometabola;Diptera;Brachycera;Muscomorpha;Eremoneura;Cyclorrhapha;Schizophora;Acalyptratae;Ephydroidea;Drosophilidae;Drosophilinae;Drosophilini;Paraliodrosophila 131567;2759;33154;33208;6072;33213;33317;1206794;88770;6656;197563;197562;6960;50557;85512;7496;33340;33392;7147;7203;43733;480118;480117;43738;43741;43746;7214;43845;46877;7343
1157319 2014-08-01 NEW Lactococcus phage ASCC no rank Viruses;dsDNA viruses, no RNA stage;Caudovirales;Siphoviridae;unclassified Siphoviridae;Lactococcus phage 936 sensu lato;Lactococcus phage ASCC 10239;35237;28883;10699;196894;354259;1157319
1157319 2018-06-01 CHANGE_LIN_LEN Lactococcus phage ASCC no rank Viruses;dsDNA viruses, no RNA stage;Caudovirales;Siphoviridae;Sk1virus;unclassified Sk1virus;Lactococcus phage 936 sensu lato;Lactococcus phage ASCC 10239;35237;28883;10699;1623305;2050979;354259;1157319
1157319 2019-04-01 CHANGE_LIN_LEN Lactococcus phage ASCC no rank Viruses;Caudovirales;Siphoviridae;Skunavirus;unclassified Sk1virus;Lactococcus phage 936 sensu lato;Lactococcus phage ASCC 10239;28883;10699;1623305;2050979;354259;1157319
1157319 2019-05-01 CHANGE_LIN_LIN Lactococcus phage ASCC no rank Viruses;Caudovirales;Siphoviridae;Skunavirus;unclassified Skunavirus;Lactococcus phage 936 sensu lato;Lactococcus phage ASCC 10239;28883;10699;1623305;2050979;354259;1157319
1157319 2019-06-01 DELETE Lactococcus phage ASCC no rank Viruses;Caudovirales;Siphoviridae;Skunavirus;unclassified Skunavirus;Lactococcus phage 936 sensu lato;Lactococcus phage ASCC 10239;28883;10699;1623305;2050979;354259;1157319
1157319 2019-07-01 REUSE_DEL Lactococcus phage ASCC species Viruses;Caudovirales;Siphoviridae;Skunavirus;unclassified Skunavirus;Lactococcus phage ASCC 10239;28883;10699;1623305;2050979;1157319
1157319 2020-06-01 CHANGE_LIN_LEN Lactococcus phage ASCC species Viruses;Duplodnaviria;Heunggongvirae;Uroviricota;Caudoviricetes;Caudovirales;Siphoviridae;Skunavirus;unclassified Skunavirus;Lactococcus phage ASCC 10239;2731341;2731360;2731618;2731619;28883;10699;1623305;2050979;1157319
The full list:
$ pigz -cd taxid-changelog.csv.gz \
| grep REUSE_DEL \
| csvtk cut -f 1 \
> reuse_del.txt
$ pigz -cd taxid-changelog.csv.gz \
| csvtk grep -f taxid -P reuse_del.txt \
| csvtk fold -f taxid -v change \
| csvtk grep -f change -r -p ^DELETE -v \
| csvtk cut -f taxid \
> reuse_del.afterAug2014.txt
$ pigz -cd taxid-changelog.csv.gz \
| csvtk grep -f taxid -P reuse_del.afterAug2014.txt \
> reuse_del.afterAug2014.txt.detail
Don't worry, reused taxIDs are assigned to the same taxon.
Merged taxid can also be re-used (become independent again?), e.g.,
$ pigz -cd taxid-changelog.csv.gz \
| csvtk grep -f taxid -p 101480,36032 \
| csvtk pretty
taxid version change change-value name rank lineage lineage-taxids
36032 2014-08-01 MERGE 1249076
36032 2016-06-01 REUSE_MER Barnettozyma wickerhamii species cellular organisms;Eukaryota;Opisthokonta;Fungi;Dikarya;Ascomycota;saccharomyceta;Saccharomycotina;Saccharomycetes;Saccharomycetales;Phaffomycetaceae;Barnettozyma;Barnettozyma wickerhamii 131567;2759;33154;4751;451864;4890;716545;147537;4891;4892;115784;599802;36032
101480 2014-08-01 MERGE 63407
101480 2016-05-01 REUSE_MER Trichophyton interdigitale species cellular organisms;Eukaryota;Opisthokonta;Fungi;Dikarya;Ascomycota;saccharomyceta;Pezizomycotina;leotiomyceta;Eurotiomycetes;Eurotiomycetidae;Onygenales;Arthrodermataceae;Trichophyton;Trichophyton interdigitale 131567;2759;33154;4751;451864;4890;716545;147538;716546;147545;451871;33183;34384;5550;101480
Scientific names and ranks changed
Scientific changed, e.g.,
$ pigz -cd taxid-changelog.csv.gz \
| csvtk grep -f taxid -p 11,152 \
| csvtk cut -f -lineage,-lineage-taxids \
| csvtk pretty
taxid version change change-value name rank
11 2014-08-01 NEW [Cellvibrio] gilvus species
11 2015-05-01 CHANGE_LIN_LEN [Cellvibrio] gilvus species
11 2015-11-01 CHANGE_NAME Cellulomonas gilvus species
11 2015-11-01 CHANGE_LIN_LIN Cellulomonas gilvus species
11 2016-03-01 CHANGE_LIN_LEN Cellulomonas gilvus species
152 2014-08-01 NEW Treponema stenostrepta species
152 2015-06-01 CHANGE_NAME Treponema stenostreptum species
152 2015-06-01 CHANGE_LIN_LIN Treponema stenostreptum species
Rank changed, e.g.,
$ pigz -cd taxid-changelog.csv.gz \
| csvtk grep -f taxid -p 1189,2763 \
| csvtk cut -f -lineage,-lineage-taxids \
| csvtk pretty
taxid version change change-value name rank
1189 2014-08-01 NEW Stigonematales order
1189 2016-03-01 CHANGE_LIN_LEN Stigonematales order
1189 2016-09-01 CHANGE_NAME Stigonemataceae family
1189 2016-09-01 CHANGE_RANK Stigonemataceae family
1189 2016-09-01 CHANGE_LIN_LEN Stigonemataceae family
2763 2014-08-01 NEW Rhodophyta no rank
2763 2019-02-01 CHANGE_RANK Rhodophyta phylum
Stats:
$ csvtk join -k -f version \
<(pigz -cd taxid-changelog.csv.gz \
| csvtk grep -f change -p CHANGE_NAME \
| csvtk freq -f version) \
<(pigz -cd taxid-changelog.csv.gz \
| csvtk grep -f change -p CHANGE_RANK \
| csvtk freq -f version) \
| csvtk rename -f -1 -n name-changed,rank-changed \
| csvtk pretty
version name-changed rank-changed
2014-09-01 386 32
2014-10-01 643 51
2014-11-01 468 71
2014-12-01 460 48
2015-01-01 483 104
2015-02-01 407 82
2015-03-01 553 86
2015-04-01 595 64
2015-05-01 415 44
2015-06-01 1278 31
2015-07-01 673 141
2015-08-01 280 31
2015-09-01 418 36
2015-10-01 529 34
2015-11-01 1087 58
2015-12-01 1063 104
2016-01-01 929 107
2016-03-01 2032 173
2016-04-01 1190 123
2016-05-01 706 31
2016-06-01 573 153
2016-08-01 1073 338
2016-09-01 884 109
2016-10-01 994 50
2016-11-01 898 174
2016-12-01 853 174
2017-01-01 732 43
2017-02-01 948 91
2017-03-01 2022 408
2017-04-01 784 102
2017-06-01 574 361
2017-05-01 606 276
2017-07-01 523 88
2017-08-01 568 22
2017-09-01 660 97
2017-10-01 894 96
2017-12-01 1829 109
2018-01-01 733 28
2018-02-01 701 29
2018-03-01 706 97
2018-04-01 1562 75
2018-05-01 640 70
2018-06-01 721 54
2018-07-01 1028 220
2018-08-01 718 122
2018-09-01 599 147
2018-10-01 536 61
2018-11-01 371 69
2018-12-01 244 34
2019-01-01 532 77
2019-02-01 372 572
2019-03-01 395 59
2019-04-01 537 297
2019-05-01 415 580
2019-06-01 326 293
2019-07-01 293 37
2019-08-01 423 70
2019-09-01 287 14
2019-10-01 465 11
2019-11-01 378 78
2020-01-01 497 40
2020-02-01 361 24
2020-03-01 805 33
2020-04-01 572 15
2020-05-01 848 36
2020-06-01 495 775
2020-07-01 611 215932
2020-08-01 631 167799
2020-09-01 748 34
2020-10-01 1206 42
2020-11-01 610 126
2020-12-01 566 84
2021-01-01 983 48
2021-02-01 1931 51
2021-03-01 1327 50
What happend on 2020-07-01?
$ pigz -cd taxid-changelog.csv.gz \
| csvtk grep -f version -p 2020-07-01 \
| csvtk grep -f change -p CHANGE_RANK \
| csvtk freq -f rank -nr \
| csvtk pretty
rank frequency
isolate 111108
strain 101971
serotype 1144
clade 822
forma specialis 740
serogroup 71
genotype 20
biotype 17
species 14
morph 11
pathogroup 5
subvariety 5
family 1
genus 1
subgenus 1
tribe 1
# where are they from
$ pigz -cd taxid-changelog.csv.gz \
| csvtk grep -f version -p 2020-07-01 \
| csvtk grep -f change -p CHANGE_RANK \
| csvtk cut -f taxid \
> rank-changed-2020-07.taxid
# ranks before 2020-07-01
pigz -cd taxid-changelog.csv.gz \
| csvtk grep -f taxid -P rank-changed-2020-07.taxid \
| csvtk grep -f version -p 2020-07-01 -p 2020-08-01 -p 2020-09-01 -v \
| csvtk cut -f taxid,version,rank \
| csvtk sort -k taxid:n -k version:r \
| csvtk uniq -f taxid \
> rank-changed-2020-07.taxid.before-2020-07.csv
# ranks on 2020-07-01
$ pigz -cd taxid-changelog.csv.gz \
| csvtk grep -f taxid -P rank-changed-2020-07.taxid \
| csvtk grep -f version -p 2020-07-01 \
| csvtk cut -f taxid,version,rank \
> rank-changed-2020-07.taxid.2020-07.csv
# join
$ csvtk join --outer-join -f taxid rank-changed-2020-07.taxid.before-2020-07.csv rank-changed-2020-07.taxid.2020-07.csv \
| csvtk rename -f 3 -n "<2020.07" \
| csvtk rename -f 5 -n 2020.07 \
| csvtk freq -f "<2020.07,2020.07" -nr \
| csvtk pretty
<2020.07 2020.07 frequency
no rank isolate 110937
no rank strain 102294
no rank serotype 1144
no rank clade 939
no rank forma specialis 759
species isolate 663
no rank serogroup 71
no rank genotype 20
no rank biotype 17
no rank species 14
no rank morph 11
subspecies species 11
no rank pathogroup 5
no rank subvariety 5
species strain 3
subfamily family 3
subfamily tribe 3
varietas species 3
genus subgenus 2
subgenus genus 2
What happend on 2020-08-01?
$ pigz -cd taxid-changelog.csv.gz \
| csvtk grep -f version -p 2020-08-01 \
| csvtk grep -f change -p CHANGE_RANK \
| csvtk freq -f rank -nr \
| csvtk pretty
rank frequency
no rank 167603
serotype 106
clade 59
species 15
subspecies 9
subgenus 3
varietas 3
family 1
Well, lots of "isolate" and "strain" are changed back to "no rank" again.
# taxid with rank changed to "no rank" on 2020-08-01
$ pigz -cd taxid-changelog.csv.gz \
| csvtk grep -f version -p 2020-08-01 \
| csvtk grep -f rank -p "no rank" \
| csvtk cut -f taxid \
> norank-2020-08.taxid
# ranks before 2020-07-01
$ pigz -cd taxid-changelog.csv.gz \
| csvtk grep -f taxid -P norank-2020-08.taxid \
| csvtk grep -f version -p 2020-07-01 -p 2020-08-01 -p 2020-09-01 -v \
| csvtk cut -f taxid,version,rank \
| csvtk sort -k taxid:n -k version:r \
| csvtk uniq -f taxid \
> norank-2020-08.taxid.before-2020-07.csv
# ranks on 2020-07-01
$ pigz -cd taxid-changelog.csv.gz \
| csvtk grep -f taxid -P norank-2020-08.taxid \
| csvtk grep -f version -p 2020-07-01 \
| csvtk cut -f taxid,version,rank \
> norank-2020-08.taxid.2020-07.csv
# join
$ csvtk join --outer-join -f taxid norank-2020-08.taxid.before-2020-07.csv norank-2020-08.taxid.2020-07.csv \
| csvtk rename -f 3 -n "<2020.07" \
| csvtk rename -f 5 -n 2020.07 \
| csvtk mutate2 -n 2020.08 -e '"no rank"' \
| csvtk freq -f "<2020.07,2020.07,2020.08" -nr \
| csvtk pretty
<2020.07 2020.07 2020.08 frequency
no rank isolate no rank 109585
no rank strain no rank 57724
species isolate no rank 660
no rank 198
no rank no rank 186
species no rank 59
no rank serotype no rank 52
isolate no rank 18
no rank no rank no rank 9
species species no rank 3
no rank no rank 2
species strain no rank 2
Lineage taxids remained but lineage changed
Because scientifics name of itself (730) changed, or these of part taxids with higher ranks (8492).
$ pigz -cd taxid-changelog.csv.gz \
| csvtk grep -f taxid -p 730,8492 \
| csvtk pretty
taxid version change change-value name rank lineage lineage-taxids
730 2014-08-01 NEW Haemophilus ducreyi species cellular organisms;Bacteria;Proteobacteria;Gammaproteobacteria;Pasteurellales;Pasteurellaceae;Haemophilus;Haemophilus ducreyi 131567;2;1224;1236;135625;712;724;730
730 2015-06-01 CHANGE_NAME [Haemophilus] ducreyi species cellular organisms;Bacteria;Proteobacteria;Gammaproteobacteria;Pasteurellales;Pasteurellaceae;Haemophilus;[Haemophilus] ducreyi 131567;2;1224;1236;135625;712;724;730
730 2015-06-01 CHANGE_LIN_LIN [Haemophilus] ducreyi species cellular organisms;Bacteria;Proteobacteria;Gammaproteobacteria;Pasteurellales;Pasteurellaceae;Haemophilus;[Haemophilus] ducreyi 131567;2;1224;1236;135625;712;724;730
8492 2014-08-01 NEW Archosauria no rank cellular organisms;Eukaryota;Opisthokonta;Metazoa;Eumetazoa;Bilateria;Deuterostomia;Chordata;Craniata;Vertebrata;Gnathostomata;Teleostomi;Euteleostomi;Sarcopterygii;Dipnotetrapodomorpha;Tetrapoda;Amniota;Sauropsida;Sauria;Testudines + Archosauria group;Archosauria 131567;2759;33154;33208;6072;33213;33511;7711;89593;7742;7776;117570;117571;8287;1338369;32523;32524;8457;32561;1329799;8492
8492 2015-01-01 CHANGE_LIN_LIN Archosauria no rank cellular organisms;Eukaryota;Opisthokonta;Metazoa;Eumetazoa;Bilateria;Deuterostomia;Chordata;Craniata;Vertebrata;Gnathostomata;Teleostomi;Euteleostomi;Sarcopterygii;Dipnotetrapodomorpha;Tetrapoda;Amniota;Sauropsida;Sauria;Archelosauria;Archosauria 131567;2759;33154;33208;6072;33213;33511;7711;89593;7742;7776;117570;117571;8287;1338369;32523;32524;8457;32561;1329799;8492
8492 2020-07-01 CHANGE_RANK Archosauria clade cellular organisms;Eukaryota;Opisthokonta;Metazoa;Eumetazoa;Bilateria;Deuterostomia;Chordata;Craniata;Vertebrata;Gnathostomata;Teleostomi;Euteleostomi;Sarcopterygii;Dipnotetrapodomorpha;Tetrapoda;Amniota;Sauropsida;Sauria;Archelosauria;Archosauria 131567;2759;33154;33208;6072;33213;33511;7711;89593;7742;7776;117570;117571;8287;1338369;32523;32524;8457;32561;1329799;8492
Rank changed from subspecies and species
Steps:
# get taxids which change rank to species
$ pigz -cd taxid-changelog.csv.gz \
| csvtk grep -f change -p CHANGE_RANK \
| csvtk grep -f rank -p species \
| csvtk cut -f taxid \
> t.txt
# filter taxids which change rank from subspecies from species
$ pigz -cd taxid-changelog.csv.gz \
| csvtk grep -f taxid -P t.txt \
| csvtk collapse -f taxid -v rank -s ";" \
| csvtk grep -f rank -r -p "subspecies.*species" \
| csvtk cut -f taxid \
> t.f.txt
# count
$ csvtk nrow t.f.txt
651
When did these happend?
$ pigz -cd taxid-changelog.csv.gz \
| csvtk grep -f taxid -P t.f.txt \
| csvtk grep -f change -p CHANGE_RANK \
| csvtk grep -f rank -p species \
| csvtk freq -f version -k \
| csvtk pretty
version frequency
2014-09-01 14
2014-11-01 29
2014-12-01 6
2015-01-01 1
2015-02-01 9
2015-03-01 5
2015-04-01 3
2015-05-01 2
2015-06-01 3
2015-07-01 3
2015-08-01 3
2015-09-01 3
2015-10-01 6
2015-11-01 2
2016-01-01 4
2016-03-01 6
2016-04-01 4
2016-05-01 1
2016-06-01 105
2016-08-01 11
2016-09-01 6
2016-10-01 2
2016-11-01 6
2016-12-01 20
2017-01-01 10
2017-02-01 2
2017-03-01 8
2017-04-01 1
2017-05-01 6
2017-06-01 2
2017-07-01 3
2017-08-01 5
2017-09-01 43
2017-10-01 6
2017-12-01 9
2018-01-01 4
2018-02-01 4
2018-03-01 3
2018-04-01 9
2018-05-01 3
2018-06-01 2
2018-07-01 22
2018-08-01 7
2018-09-01 4
2018-10-01 2
2018-11-01 1
2018-12-01 1
2019-01-01 7
2019-02-01 1
2019-03-01 2
2019-04-01 4
2019-05-01 5
2019-06-01 3
2019-08-01 6
2019-09-01 3
2019-10-01 1
2019-11-01 4
2019-11-01 4
2019-12-01 1
2020-02-01 6
2020-03-01 9
2020-04-01 2
2020-05-01 6
2020-06-01 170
2020-07-01 5
2020-08-01 5
2020-09-01 1
2020-10-01 7
2020-11-01 8
Examples:
$ pigz -cd taxid-changelog.csv.gz \
| csvtk grep -f taxid -p 8757,40746,41264 \
| csvtk cut -f -lineage,-lineage-taxids \
| csvtk pretty
taxid version change change-value name rank
8757 2014-08-01 NEW Sistrurus catenatus tergeminus subspecies
8757 2014-08-01 ABSORB 8761 Sistrurus catenatus tergeminus subspecies
8757 2017-08-01 CHANGE_NAME Sistrurus tergeminus subspecies
8757 2017-08-01 CHANGE_LIN_LEN Sistrurus tergeminus subspecies
8757 2017-12-01 CHANGE_RANK Sistrurus tergeminus species
40746 2014-08-01 NEW Langloisia setosissima subsp. punctata subspecies
40746 2014-12-01 ABSORB 1570882 Langloisia punctata species
40746 2014-12-01 CHANGE_NAME Langloisia punctata species
40746 2014-12-01 CHANGE_RANK Langloisia punctata species
40746 2014-12-01 CHANGE_LIN_LEN Langloisia punctata species
40746 2019-06-01 CHANGE_LIN_LIN Langloisia punctata species
41264 2014-08-01 NEW Gerbilliscus kempi gambiana subspecies
41264 2014-08-01 ABSORB 410304 Gerbilliscus kempi gambiana subspecies
41264 2014-12-01 CHANGE_NAME Gerbilliscus gambianus species
41264 2014-12-01 CHANGE_RANK Gerbilliscus gambianus species
41264 2014-12-01 CHANGE_LIN_LEN Gerbilliscus gambianus species
41264 2017-04-01 CHANGE_LIN_TAX Gerbilliscus gambianus species
A superkingdom disappeared
$ pigz -cd taxid-changelog.csv.gz \
| csvtk grep -f rank -p superkingdom \
| csvtk pretty
taxid version change change-value name rank lineage lineage-taxids
2 2014-08-01 NEW Bacteria superkingdom cellular organisms;Bacteria 131567;2
2157 2014-08-01 NEW Archaea superkingdom cellular organisms;Archaea 131567;2157
2759 2014-08-01 NEW Eukaryota superkingdom cellular organisms;Eukaryota 131567;2759
10239 2014-08-01 NEW Viruses superkingdom Viruses 10239
12884 2014-08-01 NEW Viroids superkingdom Viroids 12884
12884 2019-05-01 DELETE Viroids superkingdom Viroids 12884
to be continue ...
Method
Data source: https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump_archive/
Dependencies:
- rush, https://github.com/shenwei356/rush/
- taxonkit, https://github.com/shenwei356/taxonkit/, version 0.4.3 or later
Hardware requirements:
- DISK: > 15 GiB
- RAM: >= 48 GiB (48.7 GiB for 85 archives, in 12min39s)
Steps:
mkdir -p archive; cd archive;
# --------- download ---------
# option 1
# for fast network connection
wget ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump_archive/taxdmp*.zip
# option 2
# for bad network connection like mine
url=https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump_archive/
wget $url -O - -o /dev/null \
| grep taxdmp | perl -ne '/(taxdmp_.+?.zip)/; print "$1\n";' \
| rush -j 2 -v url=$url 'axel -n 5 {url}/{}' \
--immediate-output -c -C _download.rush
# --------- unzip ---------
ls taxdmp*.zip \
| rush -j 1 'unzip {} names.dmp nodes.dmp merged.dmp delnodes.dmp -d {@_(.+)\.}' \
-c -C _unzip.rush
# --------- create log ---------
cd ..
time taxonkit taxid-changelog -i archive -o taxid-changelog.csv.gz --verbose
Citation
Shen, W., Ren, H., TaxonKit: a practical and efficient NCBI Taxonomy toolkit, Journal of Genetics and Genomics, https://doi.org/10.1016/j.jgg.2021.03.006
Contributing
We welcome pull requests, bug fixes and issue reports.