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[1], but I discovered they don't support the Ensembl Bacteria database anymore.

Then I tried to do it by hand using AmiGO (actually GOlr[2]), but then I noticed that GO Central focused on human health-related annotations[3], 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?

**References**

 - [1] Following this question https://www.biostars.org/p/1226/
 - [2] http://wiki.geneontology.org/index.php/GOlr
 - [3] http://geneontology.org/faq/what-are-differences-between-data-available-amigo-and-those-quickgo
Check out https://www.biostars.org/p/108669/

**Please use recent version of GeneSCF for successful results.**

You can extract all GO terms from gene ontology for your desired organism (Example below, Escherichia coli [ecocyc]) using simple command from GeneSCF,

(Complete GO for E.coli)

    ./prepare_database -db=GO_all -org=ecocyc
 OR (Biological Process)

    ./prepare_database -db=GO_BP -org=ecocyc

OR (Molecular Functions)

    ./prepare_database -db=GO_MF -org=ecocyc

OR (Cellular Components)

    ./prepare_database -db=GO_CC -org=ecocyc

 

**Advantages**

- Real-time analysis, do not have to depend on enrichment tools to get updated.

- Easy for computational biologists to integrate this simple tool with their NGS pipeline.

- GeneSCF supports more organisms.

- Enrichment analysis for Multiple gene list in single run.

- Enrichment analysis for Multiple gene list using Multiple source database (GO,KEGG, REACTOME and NCG) in single run.

- **Download complete GO terms/Pathways/Functions with associated genes as simple table format in a plain text file (Check "Two step process" below in "GeneSCF USAGE" section)**.