[BioC] IPI to entrez id

[Manca Marco (PATH)]

Hi Viritha,

I have found this old answer to a similar question and I think it should still apply:

<<

Not sure that it is this easy. The IPI are protein identifiers. GO
categories classify genes. Neither the mapping from protein to gene or
gene to GO category is 1:1. GO categories form a hierarchy. So there are
significant decisions to be made in representing IPI identifiers in a
pie chart of GO terms.

Bioconductor maintains 'org' and 'GO' database packages that provide the
necessary link between IPI protein ids and GO gene ontology categories,
via ENTREZ gene ids. Code might look like

  ## once only, to install packages
  source('http://bioconductor.org/biocLite.R')
  biocLite('org.Hs.eg.db', 'GO.db')

  ## from IPI to ENTREZ id, not 1:1
  library(org.Hs.eg.db)
  ipi2eg = revmap(eapply(org.Hs.eg.db, names)) ## NOT 1:1 map

  ## Assume ipiIds is, e.g., c('IPI00008860', 'IPI00019922')
  egIds = revmap(ipi2eg[ipiIds])

  ## get GO terms, also not 1:1
  goIds = eapply(org.Hs.egGO[names(egIds)], names)

You're still left with the problem of resolving multiple mappings and
the hierarchical relationship between GO terms.

Martin

>>


All the best, Marco

--
Marco Manca, MD
University of Maastricht
Faculty of Health, Medicine and Life Sciences (FHML)
Cardiovascular Research Institute (CARIM)

Mailing address: PO Box 616, 6200 MD Maastricht (The Netherlands)
Visiting address: Experimental Vascular Pathology group, Dept of Pathology - Room5.08,  Maastricht University Medical Center, P. Debyelaan 25, 6229  HX Maastricht

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Personal mobile: +31(0)626441205
Twitter: @markomanka


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Da: bioconductor-bounces at r-project.org [bioconductor-bounces at r-project.org] per conto di viritha kaza [viritha.k at gmail.com]
Inviato: mercoledì 16 febbraio 2011 18.15
A: Bioconductor
Oggetto: [BioC] IPI to entrez id

Hi group,
I would like to convert a list of 3000 IPI's to genesymbol and entrez id.
eg : * *  *IPI00658210     *to 57599, WDR48.
I wanted a 1:1 mapping.
Could anyone suggest the function and the package which could help me in the
process.
Thank u in advance,
Viritha

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