[BioC] GO.db query error?

Marc Carlson mcarlson at fhcrc.org
Tue Jul 21 23:48:06 CEST 2009

Hi Tim,

I suspect that you are not doing anything wrong.  GO changes
frequently.  And this term is simply not present in the GO package that
is online right now.  The GO.db package is a snapshot of GO that matches
the GO to gene mappings from the other .db packages that were also made
at the same time.  So to update it, I actually have to update all of the
packages so that everything will be in sync.  And we actually do this at
least twice a year (with each release of Bioconductor).  Amigo is a web
based platform and so that should usually be more current.  Whether or
not that is an improvement  over what we do depends on whether you want
to place more emphasis on reproducibility or accuracy.


Tim Smith wrote:
> Hi,
> I was trying a simple lookup - essentially looking up the Terms for specific GO IDs (GO:0048663 & GO:0060579). I reporduce the code and error I get:
>> library("GO.db")
>> Term(GOTERM[["GO:0048663"]])
> [1] "neuron fate commitment"
>> Term(GOTERM[["GO:0060579"]])
> Error in function (classes, fdef, mtable)  : 
>   unable to find an inherited method for function "Term", for signature "NULL"
> I checked in AmiGO and both the terms are listed. Am  I doing something wrong?
> thanks!
> PS: My sessionInfo is:
> ---------------------------------------
>> sessionInfo()
> R version 2.9.1 (2009-06-26) 
> i386-pc-mingw32 
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base     
> other attached packages:
>  [1] biomaRt_2.0.0       GO.db_2.2.11        GOstats_2.10.0     
>  [4] graph_1.22.2        Category_2.10.1     org.Hs.eg.db_2.2.11
>  [7] RSQLite_0.7-1       DBI_0.2-4           AnnotationDbi_1.6.1
> [10] Biobase_2.4.1      
> loaded via a namespace (and not attached):
>  [1] annotate_1.22.0   genefilter_1.24.2 GSEABase_1.6.1    RBGL_1.20.0      
>  [5] RCurl_0.98-1      splines_2.9.1     survival_2.35-4   tools_2.9.1      
>  [9] XML_2.5-3         xtable_1..5-5     
> 	[[alternative HTML version deleted]]
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