The number of digits in NCBI Taxonomy ID have any meaningful concet?
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6.8 years ago
m.koohi.m ▴ 120

I am wondering if the number of digits in NCBI Taxonomy ID have any meaningful concept? As I checked the 3 and 4 digits refer to group and species and more than 4 digit Ids refer to the strains? Is that true?

For example:

Tax ID: 536 Chromobacterium violaceum

Tax ID: 243365 Chromobacterium violaceum ATCC 12472

NCBI Taxonomy species • 1.5k views
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Entering edit mode
6.8 years ago
5heikki 10k

I don't think so. Prokaryote taxa for which pure cultures have existed for a long time can be expected to have relatively few digits in their IDs..

Are taxids stable?

Taxids are assigned sequentially as taxa are added to the taxonomy database, and are never reused for a different taxon once they have been assigned. When two taxa are determined to be synonymous they are merged, and the taxid that disappears becomes a ‘secondary’ taxid for the one that remains. Taxa are occasionally removed from the taxonomy database (particularly internal nodes, during a taxonomic revision) – these taxids are deleted, and are not reused. Lists of merged and deleted taxids are included in the taxonomy dump files on the ftp site.

The public web pages at the NCBI only show taxa that are linked to public sequence entries. If a taxid is linked to a public sequence entry that is later removed, or assigned to a different taxon, the corresponding taxid may disappear from the NCBI web pages without appearing in either the merged or deleted taxid list.

http://www.ncbi.nlm.nih.gov/books/NBK54428/