[BioC] help with protein IPI annotation mappings

[Steffen Durinck]

Hi Mark,

I quickly scanned the attributes and filters and it looks like you 
currently can not use genbank accession numbers with Ensembl.
To be sure you could ask the Ensembl helpdesk:  helpdesk at ensembl.org if 
genbank accession numbers are in their database and what the name of the 
corresponding filter is.  If they don't have genbank ids you could ask  
them if there is a possibility to include genbank ids in future releases.
Whatever information Ensembl makes available is retrievable through the 
biomaRt package and questions or suggestions related to the data 
present  in Ensembl can be best addressed to their helpdesk.  Make sure 
you let them know you are using the BioMart version of Ensembl.

Cheers,
Steffen


Kimpel, Mark William wrote:
> Steffen,
>
> Your code to convert IPI to entrezgene ID's worked like charm. Now I
> have run into another problem. I have discovered that some of the ID's I
> need to map are GenBank ID's of the form (GI:XXXX). I have used
> listAttributes(ensembl) and cannot figure out which, if any correspond
> to the NCBI GI. A previous post in this list indicated that this should
> be possible, but I must be missing something.
>
> Thanks,
> Mark
>
> Mark W. Kimpel MD 
>
>  
>
> (317) 490-5129 Work, & Mobile
>
>  
>
> (317) 663-0513 Home (no voice mail please)
>
> 1-(317)-536-2730 FAX
>
> -----Original Message-----
> From: Steffen Durinck [mailto:durincks at mail.nih.gov] 
> Sent: Friday, January 05, 2007 8:57 AM
> To: Kimpel, Mark William
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] help with protein IPI annotation mappings
>
> Hi Mark,
>
> I don't have an IPI id to test this but biomaRt should be able to do 
> what you want.
> Here's how:
>
> library(biomaRt)
> ipiID = c("your","list","of","IPI","IDs")
> ensembl=useMart("ensembl", dataset="rnorvegicus_gene_ensembl")
> getBM(attributes=c("ipi","entezgene"), filters="ipi", values=ipiID, 
> mart=ensembl)
>
> you could probably make the result of the query a little cleaner by:
>
> getBM(attributes=c("ipi","entezgene"), filters=c("ipi","with_ipi"), 
> values=list(ids=ipiID,""), mart=ensembl)
>
> best,
> Steffen
>
>
>
> Kimpel, Mark William wrote:
>   
>> I need to map a list of rat International Protein Index accession ids
>>     
> to
>   
>> EntrezGene. The proteins have been identified using mass spectroscopy
>> and thus do not necessarily correspond to any particular affy chipset.
>> How would I do this in BioC? Can biomaRt handle this?
>>
>>  
>>
>> Thanks,
>>
>> Mark
>>
>>  
>>
>> Mark W. Kimpel MD 
>>
>>  
>>
>>  
>>
>> Official Business Address:
>>
>>  
>>
>> Department of Psychiatry
>>
>> Indiana University School of Medicine
>>
>> PR M116
>>
>> Institute of Psychiatric Research
>>
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>>
>> Indianapolis, IN 46202
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>>
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>>
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>>
>>
>> 	[[alternative HTML version deleted]]
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-- 
Steffen Durinck, Ph.D.

Oncogenomics Section
Pediatric Oncology Branch
National Cancer Institute, National Institutes of Health
URL: http://home.ccr.cancer.gov/oncology/oncogenomics/

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