Form and variety
donovan-h-parks opened this issue · 2 comments
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.
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 |
Great - thanks!