[BioC] downloading GO from biomart through bioconductor

Marc Carlson mcarlson at fhcrc.org
Sat Nov 5 00:52:34 CET 2011

Hi Brian,

There is also the GO.db package.  As for which resource will work best 
for you, that will really depend on what you need more: very current 
annotations or the stability of a version-ed release?  You have a whole 
range of options here.  GO will always be the most current, but really, 
biomaRt is usually very current as well.  If you have found 
discrepancies please provide a reproducible example that people can test.


On 11/02/2011 03:53 PM, Brian Tsai wrote:
> hi all,
> i'm debating on whether to download GO annotations through biomart or just
> get them from GO directly.  The advantage to me of getting it through
> biomart is that i can get the ID format i need right away.  However, when i
> compare the annotations from Biomart, versus GO directly, there seems to be
> a huge discrepancy, mainly in two areas:
> 1) # of annotations - direct download from GO seems to obtain hundreds of
> thousands more annotations.
> 2) evidence types - biomart seems to not use a lot of the evidence codes
> that i find from the direct-GO approach, mostly from the 'computational
> analysis' evidence codes.
> both #1 and #2 leads me to think Biomart doesn't update its annotations
> often, but i'm not sure if i'm just not grabbing it correctly -- does
> anyone know how often they update?
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