[BioC] GO.db query error?

[Marc Carlson]

Just to clarify, I did not mean to imply that we are not accurate.  A
better choice of words might be to say that we are slightly less current
(updating twice a year instead of continuously).  But that this is a
deliberate decision which allows us to have annotations that are
versioned, synchronized relative to each other, and time-stamped.  In
turn, this trade-off should aid in making research more reproducible.

  Marc




Marc Carlson wrote:
> 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.
>
>
>   Marc
>
>
>
>
>
> 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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>>
>>     
>
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