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

[Steffen Durinck]

Hi Jose,

It looks like the Ensembl BioMart recently got updated to version 62
and this included some changes in the attributes.

> mart=useMart('ensembl',dataset='hsapiens_gene_ensembl')
> att = listAttributes(mart)
> att[grep('go',att[,1]),]
                                                    name
24                                                 go_id
27                                       go_linkage_type

Possibly the three go ontologies are now combined in only one attribute go_id?
If you check the release notes of Ensembl 62
(http://www.ensembl.org/info/website/news/index.html)
 you'll see:

'Gene Ontology Filter and Attribute section has been modified and all
three domains have now been merged into one'


If needed you can always connect to the previous Ensembl version using:

> ensembl61=useMart('ENSEMBL_MART_ENSEMBL',dataset='hsapiens_gene_ensembl', host='feb2011.archive.ensembl.org')
> att = listAttributes(ensembl61)
> att[grep('go',att[,1]),]
                                                    name
24                              go_biological_process_id
27                    go_biological_process_linkage_type
28                              go_cellular_component_id
29                   go_cellular_component__dm_name_1006
30             go_cellular_component__dm_definition_1006
31                    go_cellular_component_linkage_type
32                              go_molecular_function_id
33                   go_molecular_function__dm_name_1006
34             go_molecular_function__dm_definition_1006
35                    go_molecular_function_linkage_type


Cheers,
Steffen

On Fri, May 13, 2011 at 8:04 AM,  <J.delasHeras at ed.ac.uk> wrote:
>
> 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
>
>
> --
> 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
> Institute for Cell & Molecular Biology        Fax:   +44 (0)131 6507360
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>
>
> --
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