Dear list,

Context : I'd like to calculate GO enrichments for a list of UniProt identifiers (note that they are "ID" or "Entry name" and NOT "AC" or "Accession").
So I tried to use BioMart to extract the GO-IDs for my list of UniProt identifiers, see code below.
Basically after calling getBM() R doesn't return the command-line any more for more than 5 minutes. I tested this on Linux and Windows -> both same problem, so I suppose either I might be doing wrong or something isn't working right.

Any hints  ?

Thank's in advance,
Wolfgang Raffelsberger


## the code ..
 require(annotate)
 require(biomaRt)

 IDs <- c("MTMR1_HUMAN","MTMR2_HUMAN","MTMR3_HUMAN","MTMR4_HUMAN")  ##  existing UniProt IDs

 uniProt <- useMart("unimart")
 listAttributes(useDataset("uniprot",mart=uniProt))   ## contains "name" and "go_id"
 GO_IDs <- getBM(attributes =c("name","go_id"),values=IDs, mart=useDataset("uniprot",mart=uniProt))
## after >5 minutes the command-line is still not returned ...


## for completeness :
 sessionInfo()

R version 2.12.2 (2011-02-25)
Platform: i386-pc-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=French_France.1252  LC_CTYPE=French_France.1252
[3] LC_MONETARY=French_France.1252 LC_NUMERIC=C
[5] LC_TIME=French_France.1252

attached base packages:
[1] grDevices datasets  splines   graphics  stats     tcltk     utils
[8] methods   base

other attached packages:
[1] biomaRt_2.6.0        annotate_1.28.0      AnnotationDbi_1.12.0
[4] Biobase_2.10.0       svSocket_0.9-51      TinnR_1.0.3
[7] R2HTML_2.2           Hmisc_3.8-3          survival_2.36-5

loaded via a namespace (and not attached):
 [1] cluster_1.13.3  DBI_0.2-5       grid_2.12.2     lattice_0.19-17
 [5] RCurl_1.4-2.1   RSQLite_0.9-4   svMisc_0.9-61   tools_2.12.2
 [9] XML_3.1-0.1     xtable_1.5-6



. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Wolfgang Raffelsberger, PhD
IGBMC,
1 rue Laurent Fries,  67404 Illkirch  Strasbourg,  France
Tel (+33) 388 65 3300         Fax (+33) 388 65 3276
wolfgang.raffelsberger (at) igbmc.fr

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