[BioC] help with protein IPI annotation mappings

[Kimpel, Mark William]

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 

 

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-----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 
>
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-- 
Steffen Durinck, Ph.D.

Oncogenomics Section
Pediatric Oncology Branch
National Cancer Institute, National Institutes of Health
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