Turning GO Terms to GO IDs

Question

[kevluv93]

I recently ran gene enrichment on a transcriptome set using Plant MetGenMap. The outputs gave me a list of GO terms that are enriched and their p-values, but many of the GO terms are redundant (like binding is enriched and nucleotide binding is enriched). I'm planning on plugging this dataset into revigo to condense the redundant terms, but I need a good way to turn a large list of GO terms to GO IDs that doesn't involve me typing each individual term into the AmiGO search bar one at a time. Any thoughts? Thank you!

[Endre Bakken Stovner]

Do you have examples of go-terms and go-ids? Anyways, you probably want the R package GO.db

[kevluv93]

Wait, is GO.db an R package or a text file with conversions? I've never used R before, I just type in library(GO.db) and R knows where to get that package?

Example GO terms: Nucleotide binding, nucleic acid binding, RNA Binding, DNA Binding

[Endre Bakken Stovner]

GO.db is a package that contains the data you need.

To install:

source("http://bioconductor.org/biocLite.R")
biocLite("GO.db")

If you have not used R before, this might not be the easiest way.

[kevluv93]

If there's a text file available with GO terms to GO IDs, I can just do it in excel. Not ideal, but it'll work. I'm going to have to learn R at some point, but right now I can deal with this.

Answer 1

[Sukhi Singh]

Try this
Converting Gene Ontology Names To Go Ids