I want to get all the GO terms under the biological process GO domain for any organism -right now, I need all the biological process associated to all gene products of E. coli (non-IEA ideally).
I'm new in the field of bioinformatics (I'm a software engineer by education) and right now I'm struggling with the great number of interconnected databases I'm finding.
At first, I tried with the R library biomaRt, but I discovered they don't support the Ensembl Bacteria database anymore.
Then I tried to do it by hand using AmiGO (actually GOlr), but then I noticed that GO Central focused on human health-related annotations, so I supposed I would loose a lot of useful annotations for non-human species. After that I wanted to try QuickGO, but then I thought that with so many databases, repositories and tools around, it's a bit hard to know how exhaustive my request will be.
Should I stick with Ensemble databases and ditch biomaRt as a library? Or using a combination of GOlr(AmiGO) and GAnnotation(QuickGO) enough?