Too fuzzy name searching with name2taxid

[tao-bioinfo]

#88

$ echo 'Pholoe glabra' | taxonkit name2taxid -f
Pholoe glabra   2975041

$ echo 2975041 | taxonkit lineage
2975041 cellular organisms;Eukaryota;Viridiplantae;Streptophyta;Streptophytina;Embryophyta;Tracheophyta;Euphyllophyta;Spermatophyta;Magnoliopsida;Mesangiospermae;Liliopsida;Petrosaviidae;Asparagales;Asphodelaceae;Asphodeloideae;Gasteria;Gasteria carinata;Gasteria carinata var. glabra (Salm-Dyck)

The genus has been changed (Pholoe -> Gasteria), seems unreasonable. The "fuzzy" search is too fuzzy.

Pholoe glabra is from https://v4.boldsystems.org/index.php/Public_RecordView?processid=BIOMB241-23.

[shenwei356]

NCBI Taxonomy official website can't return useful matches either. For these taxonomic names changed a lot, you can query the history at https://taxonomy.onecodex.com/ or https://github.com/shenwei356/taxid-changelog . But the two sources did not return any hit ...

From google:

Pholoe glabra is a species of marine worm in the genus Pholoe

Other sources

• https://invertebase.org/stri/taxa/index.php?tid=84918&taxauthid=1&clid=0
• https://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=65076#null

Looks like it exists, but NCBI Taxonomy did not record it.

Try Pholoe glabra

# nothing found in taxid-changelog
$ zcat taxid-changelog.csv.gz | csvtk grep -I -f name -i -p 'Pholoe glabra'
taxid,version,change,change-value,name,rank,lineage,lineage-taxids

# directly on old taxdump files
fd names.dmp.gz | rush 'zgrep -i "Pholoe glabra" || true'

Try only Pholoe, looks like it's what you're looking for

$ echo Pholoe | taxonkit  name2taxid 
Pholoe  222012

$ echo 222012 | taxonkit lineage -nr
222012  cellular organisms;Eukaryota;Opisthokonta;Metazoa;Eumetazoa;Bilateria;Protostomia;Spiralia;Lophotrochozoa;Annelida;Polychaeta;Errantia;Phyllodocida;Pholoidae;Pholoe       Pholoe  genus

Species

222012 [genus] Pholoe
  222013 [species] Pholoe minuta
  318818 [species] Pholoe baltica
  328599 [species] Pholoe pallida
  1888207 [species] Pholoe longa
  2594901 [species] Pholoe assimilis
  2594902 [species] Pholoe inornata
  2644711 [no rank] unclassified Pholoe
    862950 [species] Pholoe sp. CMC01
    868068 [species] Pholoe sp. CMC02
    ...

[tao-bioinfo]

In my opinion, for such case, it is better to return a blank result even under -f