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

[J.delasHeras at ed.ac.uk]

Hi Rhoda,

thank you for the explanation.

I notice the description of the attributes contain a "(bp)" in them:

GO Term Accession (bp)
GO Term Name (bp)
GO Term Definition (bp)
GO Term Evidence Code (bp)

Initially I thought it mean they referred to Biological Process and  
that CC and MF were missing... until I tried it and realised they are  
generic. It'll probably be good to remove that if it's a leftover, or  
clarify its meaning otherwise.

Is there a mailing list, for instance, I can subscribe to so that I  
find out about this kind of changes in advance, rather than when I'm  
trying to do some work and my scripts cease to function? :)

Thank you for your help!

regards,

Jose


Quoting rhoda at ebi.ac.uk on Fri, 13 May 2011 16:40:00 +0100 (BST):

> 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.
>>
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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
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.