[BioC] GOTERM in GO.db returns NULL

[Marc Carlson]

Hi Shi,

I can confirm that this is just because GO is continuously changing, and 
because our last snapshot of it was in the Spring.  GO will be updated 
very soon (for the fall release).  As always, thanks for letting me know 
about any possible issues that crop up.

  Marc


Shi, Tao wrote:
> Hi list,
>
> I was using GOTERM in GO.db to get the annotations for the GO terms and a few of them return NULL.  But I checked the GO website and using AmiGO, all of them except the last one still exist and have annotations.  The last one, according to this (http://fafner.stanford.edu/pipermail/go/2008-January/015594.html), seems to be obsolete.  There could be other GO terms like these exist.  I'm aware of this could be due to the different version of GO used in the package, but I still want to point out just in case there are other problems.
>
> ...Tao  
>
>
>   
>> GOTERM[["GO:0022904"]]      ## respiratory electron transport chain
>>     
> NULL
>   
>> GOTERM[["GO:0022900"]]      ## electron transport chain
>>     
> NULL
>   
>> GOTERM[["GO:GO:0055114"]]      ## oxidation reduction
>>     
> NULL
>   
>> GOTERM[["GO:0045192"]]      ## low-density lipoprotein catabolic process; obsolete?
>>     
> NULL
>   
>> sessionInfo()
>>     
> R version 2.7.0 (2008-04-22) 
> 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] tools     stats     graphics  grDevices utils     datasets  methods   base     
>
> other attached packages:
> [1] GO.db_2.2.0         AnnotationDbi_1.2.2 RSQLite_0.6-9       DBI_0.2-4           Biobase_2.0.1
>
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