All Possible NCBI Taxonomy Ranks

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It was bothering me that nowhere on the NCBI website are all possible taxonomic ‘ranks’ actually described.

I eventually decided to go back to basics and literally download the raw data the NCBI taxonomy website is based on - the infamous taxonomy.dmp, find the column that gives a rank for every single tax. ID, and collapse to all unique values.

To do this I downloaded and extracted the taxonomy dump as follows:

wget ftp://ftp.ncbi.nih.gov/pub/taxonomy/new_taxdump/new_taxdump.zip
unzip new_taxdump.zip


Then after hunting through all the files, the one I wanted was nodes.dmp

The rank is recorded in the third column,

\$ head nodes.dmp
1 | 1 | no rank |   | 8 | 0 | 1 | 0 | 0 | 0 | 0 | 0 |   |   ||  0 | 0 | 0 |
2 | 131567  | superkingdom  |   | 0 | 0 | 11  | 0 | 0 | 0 | 0 | 0 |   | ||  0 | 0 | 1 |
6 | 335928  | genus |   | 0 | 1 | 11  | 1 | 0 | 1 | 0 | 0 |   |   ||  0 | 0 | 1 |
7 | 6 | species | AC  | 0 | 1 | 11  | 1 | 0 | 1 | 1 | 0 |   |   ||  1 | 0 | 1 |
9 | 32199 | species | BA  | 0 | 1 | 11  | 1 | 0 | 1 | 1 | 0 |   |   ||  1 | 0 | 1 |
10  | 1706371 | genus |   | 0 | 1 | 11  | 1 | 0 | 1 | 0 | 0 |   |   ||  0 | 0 | 1 |
11  | 1707  | species | CG  | 0 | 1 | 11  | 1 | 0 | 1 | 1 | 0 | effective current name; |   |   | 1 | 0 | 1 |
13  | 203488  | genus |   | 0 | 1 | 11  | 1 | 0 | 1 | 0 | 0 |   |   ||  0 | 0 | 1 |
14  | 13  | species | DT  | 0 | 1 | 11  | 1 | 0 | 1 | 1 | 0 |   |   ||  1 | 0 | 1 |
16  | 32011 | genus |   | 0 | 1 | 11  | 1 | 0 | 1 | 0 | 0 |   |   ||  0 | 0 | 1 |



So to extract the column using and collapse to single values, run the following bash-fu

cat nodes.dmp | cut -d '|' -f 3  | sort | uniq


You get the following result

biotype
class
cohort
family
forma
forma specialis
genotype
genus
infraclass
infraorder
isolate
kingdom
morph
no rank
order
parvorder
pathogroup
phylum
section
series
serogroup
serotype
species
species group
species subgroup
strain
subclass
subcohort
subfamily
subgenus
subkingdom
suborder
subphylum
subsection
subspecies
subtribe
subvariety
superclass
superfamily
superkingdom
superorder
superphylum
tribe
varietas


Note that this doesn’t actually give you the hierarchy of all the wierd and wonderful ‘custom’ groups taxonomists have come up with. However I found by googling ‘NCBI taxonomy ' I could find enough examples that told me approximately where they fell compared to the standard ranks (even if they are technically analogous e.g. strain vs varietas)

The ones I did find:

• parvorder - comes after order
• section - comes after genus
• ‘strain’, ‘morph’, ‘forma specialis’ - comes after species

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