4.8 years ago by
So it sounds like you want to get genes mapped to GO terms. We used to get those from blast2GO. But with my most recent attempt to make new annotations, it appears that they may have gone commercial on us. :( So how we (as a project) will get those terms mapped in the future is currently unknown. But right now we still have some reasonably current mappings from back when they still were sharing them.
And you can get organism annotations for a whole range of things by using the development version of AnnotationHub like this (please note that for this to work you have to be using the devel branch as AnnotationHub has changed DRASTICALLY). Anyhow here goes:
ah = AnnotationHub()
ahs = subset(ah, ah$rdataclass=="OrgDb")
## Then look at the available taxonomy IDs:
availSpecies = unique(ahs$species)
## Then choose the one you want (hopefully it's in there) and do this:
finalAh = subset(ahs, ahs$species=="Pseudomonas mendocina_NK-01")
org = finalAh[]
## Then you can get data from this object in the usual way (like so):
k = head(keys(org, keytype='ENTREZID'))
head(select(org, k, 'GO', 'ENTREZID'))
Anyhow this is currently the widest range of pre-made OrgDb objects that we provide access to. But if someone could point me to a more complete resource for GO to gene mappings we could probably do even better.
Hope this helps!