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

[rhoda at ebi.ac.uk]

Hi Jose
The three GO sections have been merged into one. See here for news about
ensembl BioMart changes:

http://www.ensembl.org/info/website/news/index.html#team-Mart

These are the names of the attributes you now need to look for:

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE Query>
<Query  virtualSchemaName = "default" formatter = "TSV" header = "0"
uniqueRows = "0" count = "" datasetConfigVersion = "0.6" >

	<Dataset name = "hsapiens_gene_ensembl" interface = "default" >
		<Attribute name = "go_id" />
		<Attribute name = "name_1006" />
		<Attribute name = "definition_1006" />
		<Attribute name = "go_linkage_type" />
		<Attribute name = "namespace_1003" />
	</Dataset>
</Query>

These attribute names correspond to:

GO Term Accession
GO Term Name
GO Term Definition
GO Term Evidence Code
GO domain

I will give the internal names (i.e. name_1006) a more descriptive and
meaningful name for the next release. Apologies for any confusion caused.
Regards
Rhoda


>
> 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
> Swann Building, Mayfield Road
> University of Edinburgh
> Edinburgh EH9 3JR
> UK
>
>
> --
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>