[BioC] Go terms attributes not available on Biomart ensembl

[Steve Lianoglou]

Hi,

There was an email to this list a few days ago about a similar (I
think) problem with GO queries failing. It seems appropriate here(?).
Apparently the identifiers for GO stuffs has changed, see the thread
that starts here:

https://stat.ethz.ch/pipermail/bioconductor/2011-May/039435.html

The original poster was querying with something like:

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

And was getting errors.

Apparently:

"""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
""""

Hope that helps,

-steve



On Tue, May 17, 2011 at 2:44 AM, Wolfgang Huber <whuber at embl.de> wrote:
> Konika
>
> thanks. Your 'sample code' is incomplete. How did you define the object
> 'ensembl'?
>
>        Best wishes
>        Wolfgang
>
>
> chawla scripsit 05/15/2011 11:53 PM:
>>
>> Hi
>> I have used BiomaRt to retrieve GO terms for affymetrix probe Ids using
>> mart ensembl.
>> But suddenly all the GO terms attributes have vanished from the list of
>> attributes.
>> I used the sample code to test.
>>
>>  > affyids = c("202763_at", "209310_s_at", "207500_at")
>>  > getBM(attributes = c("affy_hg_u133_plus_2",
>> "go_biological_process_id", "chromosome_name", "start_position",
>> + "end_position", "band"), filters = "affy_hg_u133_plus_2", values =
>> affyids, mart = ensembl)
>> Error in getBM(attributes = c("affy_hg_u133_plus_2",
>> "go_biological_process_id", :
>> Invalid attribute(s): go_biological_process_id
>> Please use the function 'listAttributes' to get valid attribute names
>>
>> I am thus unable to reproduce previous results.
>> Have no idea how this could happen, If anyone can help it will be great.
>> Thanks
>> Konika
>>
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>
>
> --
>
>
> Wolfgang Huber
> EMBL
> http://www.embl.de/research/units/genome_biology/huber
>
> _______________________________________________
> Bioconductor mailing list
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>



-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact