[BioC] Is GO.db out of date?

Marc Carlson mcarlson at fhcrc.org
Thu Mar 14 21:02:36 CET 2013

Hi Konika,

In order to answer your question, I need to know which version of GO.db 
you are using.  Can you please provide the results from your sessionInfo() ?

GO.db is updated with every release.  So the current release was updated 
last fall.  The version in the development branch (which will become the 
release in a couple weeks), was updated last week.


On 03/14/2013 05:58 AM, konika chawla wrote:
> Hi
> I am using GO.db package for finding GO terms for a given Id.
> I failed to find few of these for example : GO:0001200, GO:0001227, GO:0001228
>   I used the code :
> goterms<-unlist(eapply(GOTERM,function(x) x at Term))
> goterms<-as.matrix(goterms)
> which(rownames(goterms)=="GO:0001200")
>> integer(0)
> In The gene Ontology database "GO:0001200" is for "metal ion regulated sequence-specific DNA binding RNA polymerase II transcription factor activity".
> I also found that GOA has 39117 GO terms while GO.db has 32255 GO terms. I checked the reference manual for GO.db which says it is updated biannually but the last update is of April2012.
> I am wondering if it will be updated soon else please suggest any other package which has similar functionality.
> Or is there any error in the code ??
> Thanks
> Konika Chawla
> PhD Student
> Department of Biology
> 	[[alternative HTML version deleted]]
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