Form and variety

[donovan-h-parks]

Hi. Quick question. What do the form and variety attributes for -abundance-per mean? I've always taken variety to be a synonym of subspecies and am not clear what form means in terms of taxonomy. Thanks.

[muellan]

Hi. Yeah, as always with this bio stuff it's kind of a mess. The taxonomic ranks "form" and "varietas"/"variety" are both defined in the NCBI taxonomy, yet how they are applied to sequences is sometimes not very consistent. The relationship is form -> variety -> subspecies -> species -> subgenus -> genus -> ... . In our experiments with bacterial samples and eucariotic genomes in foodstuff we didn't look at levels below species, and according to my experience "subspecies" is the lowest level that makes any sense right now.

Below is a list of all taxonomic rank names that are recognized by MetaCache (lowest rank first) and to what rank they are mapped internally:

NCBI name(s)	MetaCache rank
sequence	sequence
genome	sequence
form	form
forma	form
variety	variety
varietas	variety
subspecies	subspecies
species	species
species group	subgenus
species subgroup	subgenus
subgenus	subgenus
genus	genus
subtribe	subtribe
tribe	tribe
subfamily	subfamily
family	family
superfamily	suborder
parvorder	suborder
infraorder	suborder
suborder	suborder
order	order
superorder	subclass
infraclass	subclass
subclass	subclass
class	class
superclass	subphylum
subphylum	subphylum
phylum	phylum
division	phylum
superphylum	subkingdom
subkingdom	subkingdom
kingdom	kingdom
subdomain	kingdom
superkingdom	domain
domain	domain
root	root

[donovan-h-parks]

Great - thanks!