humann_regroup_table function in Humann v3.6.1
Hi bioBakery team,
I would like to know that which version of Eggnog was used in humann_regroup_table function because I am doing some ID mapping work. And how often would the databses in regroup function be updated? Would they only be updated when a bigger version of Humann is released (like Humann2 to Humann3)?
I am actually not sure of the eggNOG version itself since we didn’t do the annotations ourselves. Most annotations are taken from the UniProt database by looking up the proteins being used as UniRef90/50 representatives. bioBakery 3 was based on UniProt 2019_01, so you might be able to tell from their documentation what eggNOG version was being used at that time.
To date we’ve only been updating these annotation files with our major releases (2.0, 3.0, 4.0 upcoming). That said, you can always look up a more recent set of annotations for your proteins of interest in the current UniProt. While UniRef90_XYZ might not be a representative anymore, unless it’s been retired, XYZ would still be a protein in UniProt. The annotations are taken from the
DR (database reference) lines of the big
.dat file that is bundled with each UniProt release.