associate GO ID with GO description

Question

[lessismore]

Dear all,

i have an enrichment output file displaying only GO IDs. Two questions: (1) Can somebody suggest a way to associate GO category description to the GO ID? Where do i retrieve such a file? Sorry for the maybe trivial question. (2) Would be also very much appreciated a tip on a tool to perform gene set enrichment analysis (also with custom GO annotation files) and manipulate/visualize the output with R.

Thanks in advance

Answer 1

[Jean-Karim Heriche]

1- You can retrieve the whole ontology from the download page of Gene Ontology web site or use the Bioconductor package GO.db, e.g.

library(GO.db)
GO <- as.list(GOTERM)
my.term <- GO$`GO:0000001`@Term

2- Has already been asked here somewhere. I just don't have time now to locate it for you.

[e.r.zakiev]

there are certain cases (see example below) when a GO:id term isn't recognized but most certainly exists, I assume it's a matter of the GO.db package not coverting secondary terms, how would you deal with these situations?

library(GO.db)
GO <- as.list(GOTERM)
my.term <- GO$`GO:0004872`@Term

Error in GO$`GO:0004872`@Term : 
  no applicable method for `@` applied to an object of class "NULL"

[Jean-Karim Heriche]

Secondary IDs (which come from the merging of terms) should be preserved. An ID not found usually indicates a version mismatch, i.e. the GO.db package uses a different GO database version than the one used for annotations.