[BioC] Any changes in Biomart regarding GO terms? Script crashing today

[J.delasHeras at ed.ac.uk]

I am unable to run a script I have been using quite happily in the  
past, so I suspect a change in the "outside world", but I can't find  
any news about it.

It appears that the usual attributes for GO terms and IDs (CC, BP and  
MF) are not available. (?)

If you try this quick example:

library(biomaRt)
ensembl=useMart("ensembl")
dataset="hsapiens_gene_ensembl"
ensembl=useDataset(dataset, mart=ensembl)

attributes=c("entrezgene",
              "go_cellular_component_id",
              "go_cellular_component__dm_name_1006")

getBM(attributes=attributes,
       filters="entrezgene",
       values=1, mart=ensembl)

It fails with the error:

Error in getBM(attributes = attributes, filters = "entrezgene", values = 1,  :
   Invalid attribute(s): go_cellular_component_id,  
go_cellular_component__dm_name_1006
Please use the function 'listAttributes' to get valid attribute names

and if you list the attributes...

listAttributes(ensembl)

you can see they're indeed not listed...

am I right thinking this has nothing to do with the biomaRt R side of things?

Jose


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Dr. Jose I. de las Heras                      Email: J.delasHeras at ed.ac.uk
The Wellcome Trust Centre for Cell Biology    Phone: +44 (0)131 6507090
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