[BioC] How to map KEGG gene IDs to gene names?

[Elliot Kleiman]

Hi BioC List from {sunny}San Diego, CA!

[Question]:
* How do you map KEGG gene IDs to textual gene names, gene descriptions
via BioC?

For example, I am interested in knowing which genes are
involved in the calcium signaling pathway in rattus norvegicus,
so I did:

 > library(KEGG)
 > # map pathway id to pathway name
 > KEGGPATHID2NAME$"04020"
[1] "Calcium signaling pathway"

 > library(KEGGSOAP)
 > # get all genes in pathway rno04020
 > csp.genes.rno <- get.genes.by.pathway("path:rno04020")
 > # how many genes are involved?
 > length(csp.genes.rno)
[1] 165
 > # print a few of the results out
 > csp.genes.rno[1:3]
[1] "rno:113995" "rno:114098" "rno:114099"

The problem is, I don't know what "rno:113995" refers to?
[not without visiting the KEGG website]
Instead, I would like to obtain a mapping for each of the retrieved KEGG
gene IDs into textual gene names, gene descriptions, etc.

How do you do that exactly?

Thank you,

Elliot Kleiman

 > # print SessionInfo
 > sessionInfo()
R version 2.6.1 (2007-11-26)
i686-pc-linux-gnu

locale:
LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=C;LC_MONETARY=en_US;LC_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US;LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] KEGG_2.0.1      KEGGSOAP_1.12.0 SSOAP_0.4-6     RCurl_0.8-3
[5] XML_1.93-2

loaded via a namespace (and not attached):
[1] rcompgen_0.1-17 tools_2.6.1

-- 
__________________________
MS graduate student 
Program in Computational Science 
San Diego State University
http://www.csrc.sdsu.edu/