[BioC] help with protein IPI annotation mappings

Steffen Durinck durincks at mail.nih.gov
Fri Jan 5 14:57:00 CET 2007


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
>
> 791 Union Drive
>
> Indianapolis, IN 46202
>
>  
>
> Preferred Mailing Address:
>
>  
>
> 15032 Hunter Court
>
> Westfield, IN  46074
>
>  
>
> (317) 490-5129 Work, & Mobile
>
>  
>
> (317) 663-0513 Home (no voice mail please)
>
> 1-(317)-536-2730 FAX
>
>
> 	[[alternative HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>   


-- 
Steffen Durinck, Ph.D.

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

Phone: 301-402-8103
Address:
Advanced Technology Center,
8717 Grovemont Circle
Gaithersburg, MD 20877



More information about the Bioconductor mailing list