What I want is retrieve GO terms associated to the genes from one organism directly from Ensemble Bacteria database.
I know this was possible at certain point after EnsembleGenomes abandoned the BioMart suite (acording to this post), but I couldn't fin anything in the documentation. Particularly, I searched this in
but I couldn't fin anything about GO terms.
I know this was possible back then with BioMart:
- Obtaining a list of genes of a certain organism (e.g. E. Coli Tax ID 562)
- Selecting the mart ensemblbacteria
- Using the dataset of the organism you needed
- Filter the dataset by your gene IDs and retrieve 'go_id' attribute from filtered rows.
but now that's no longer an option. I really don't know how to do this and even if it's possible at all.
I know there are tools (like GeneSFC) and services (like QuickGO) which can do similar things, but that's exactly why I'm trying to do this, because I want to benchmark and compare which results I obtain from the Emsemble and compare (and complement) it with other results.