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

[J.delasHeras at ed.ac.uk]

Hi Steffen,

thank you for your fast reply. Indeed, after I posted my message I  
looked into the attributes and found that there are "generic" GO  
attributes (although their description included a "(bp)" which at  
first I took to mean they referred to "biological process" and I was  
looking for the (mf) and (cc) counterparts...

but then noticed the "namespace_1003" attribute, and this one returns  
BP, MF or CC... so yes indeed, they've all been merged and you have to  
use the namespace attribute if you want to extract cc, bp, mf info.

I didn't know how to connect to archived versions, so that's very  
useful, thank you! It means I can quickly adapt the old scripts to  
continue working straightway and I'll fix them properly when I have  
time.

Thank you!

regards,

Jose


Quoting Steffen Durinck <durinck.steffen at gene.com> on Fri, 13 May 2011  
08:29:07 -0700:

> 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
>> 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.