[BioC] Go terms attributes not available on Biomart, ensembl

[chawla]

Hi
I had also tried

ensembl=useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl")
goterms=getBM(attributes = c("affy_hg_u133a_2", "go_biological_process_id","entrezgene"), filters = "affy_hg_u133a_2", values = data[,1], mart = ensembl)

but got the same error
I guess its because of change in Go attribute names.
Thanks
Konika

On 18-05-2011 12:00, bioconductor-request at r-project.org wrote:
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> Today's Topics:
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>     1. Re: Go terms attributes not available on Biomart ensembl
>        (Steve Lianoglou)
>     2. connecting to ensembl (Stefan Kroeger)
>     3. Re: Ggallus BS genome package (Namyoung Jung)
>     4. SSOAP functions (Michael Gormley)
>     5. Re: microRNA hg build? (Marc Carlson)
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>     7. arrayQualityMetrics for Affymetrix miRNA chip
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>     8.  about limma linear models (Gordon K Smyth)
>     9. Re: connecting to ensembl (Herv? Pag?s)
>    10. Re: Ggallus BS genome package (Herv? Pag?s)
>    11. Re: alternative to matchprobes (Herv? Pag?s)
>    12. extract intensity values from AffyBatch (Assa Yeroslaviz)
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>    14. Re: extract intensity values from AffyBatch (Assa Yeroslaviz)
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>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 17 May 2011 08:52:28 -0400
> From: Steve Lianoglou<mailinglist.honeypot at gmail.com>
> To: Wolfgang Huber<whuber at embl.de>
> Cc: bioconductor at r-project.org
> Subject: Re: [BioC] Go terms attributes not available on Biomart
> 	ensembl
> Message-ID:<BANLkTi=3zFd5hAwds=YxPQnGXsh97++6=A at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> 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
>>
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>
>