[BioC] Arabidopsis annotation package

[fhong@salk.edu]

Hi  there,
I met some questions about arabidopsis annotation package(ath1121501,
version 1.10), I will
be truly grateful if any of you can help  me with some questions.

(1) I tried to get PUBMED ID for probesets (Affy) that have known function
and known pubmed ID from website. However, the "ath1121501PMID" returns NA
for them. For example, probeset "264328_at" has no pubmed ID in the
package, but it has 5 Pubmed ID form NCBI website.

##################
For example:
>  mget("264328_at",ath1121501PMID)
$"264328_at"
[1] NA

##I used 5 pubmed ID from NCBI website
x=pubmed(c("7658471","11130712","14593172","12036262","14742873"))
a <- xmlRoot(x)
buildPubMedAbst(a[[1]])
##########################

So does this mean that package "ath1121501" contains only incomplete
Pubmed ID, thus it can't be used to annotate gene?

(2) I noticed that there were a newer version of "ath1121501" (version
1.11) at
Bioconductor 1.8, does this one contain the complete list of all available
pubmed ID? However, it is built on R 2.3 which is not publicly available
now. Is there any way that I can  obtain it?


Thank you very much!

Bests,
Fangxin

--------------------
Fangxin Hong  Ph.D.
Plant Biology Laboratory
The Salk Institute
10010 N. Torrey Pines Rd.
La Jolla, CA 92037
E-mail: fhong at salk.edu
(Phone): 858-453-4100 ext 1105