[BioC] GO terms not found in goTools and GO

[Lina Hultin-Rosenberg]

Dear list,

I have retrieved GO terms for lists of human genes using biomaRt, and I 
am now using the packages goTools and GO to get further information 
about the terms. I discovered that one of the terms extracted with 
biomaRt, GO:0060070, does not exist in goTools and GO. Does anyone know 
what might be the problem? I would guess this has to do with the version 
of the Gene Ontology db used, but it would of course be most convenient 
if the different packages used the same GO version.

This are the calls I do and the answer I get:

 >GOTERM$"GO:0060070"
NULL

 >getGoCategory("GO:0060070")
Error in get(x, envir, mode, inherits) : variable "GO:0060070" was not found
Error in Ontology(get(id, env = GOTERM)) :
         error in evaluating the argument 'object' in selecting a method 
for function 'Ontology'


And this is the output from sessionInfo():

 >sessionInfo()
R version 2.5.0 (2007-04-23)
i386-pc-mingw32

locale:
LC_COLLATE=Swedish_Sweden.1252;LC_CTYPE=Swedish_Sweden.1252;LC_MONETARY=
Swedish_Sweden.1252;LC_NUMERIC=C;LC_TIME=Swedish_Sweden.1252

attached base packages:
[1] "tools"     "stats"     "graphics"  "grDevices" "utils" 
"datasets"  "methods"   "base"

other attached packages:
  goTools       GO annotate  Biobase  biomaRt    RCurl      XML
  "1.8.0" "1.16.0" "1.14.1" "1.14.0" "1.10.0"  "0.8-0"  "1.7-1"

Any help or comments would be greatly appreciated!

Best regards,

Lina Rosenberg
Karolinska Biomics Center