[BioC] GO terms not found in goTools and GO

[Wolfgang Huber]

Dear Lena,

the point to realize is that biomaRt queries an online database (you
didn't tell us which one you use), while the GO package is assembled and
packaged by friendly curators in Seattle every couple of months.

According to this site
http://www.ebi.ac.uk/ego/DisplayGoTerm?id=GO:0060070
your term was last modified 2007-03-16, which could explain why it is
not yet in the latest GO package (version 1.17.0).

If you want an consistent set of GO terms throughout, please use the
humanLLmappings (soon to be humanEGmappings) package for gene-GO
associations, not biomaRt. If you use biomaRt, you need to spend more
effort dealing with the dynamic nature of genome annotation (this is not
our fault, this is the state of the science).

Best wishes
 Wolfgang

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Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber


Lina Hultin-Rosenberg ha scritto:
> 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 Ce
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