[BioC] Arabidopsis annotation package

[Ting-Yuan Liu]

Hi Fangxin,

On Tue, 14 Mar 2006 fhong at salk.edu wrote:

> 
> 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?
> 

The package ath1121501 (version 1.10.0) is built by the public data we 
collected on September 29, 2005.  Any updated information on the data 
website after September 29, 2005 would not be included in the package 
ath1121501 (version 1.10.0).  

> (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?
> 

The package ath1121501 (version 1.11.0) is also built by the 2005-09-25 
data.  The primary reason we re-built these packages (version 1.11.0) is 
to reflect the modification of "environment" data structure in R 
developmental version.  The information are the same between version 
1.10.0 and 1.11.0 of the package ath1121501.  The coming BioConductor 1.8 
release will update the meta data packages (version 1.12.0).  

> 
> 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
> 
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> 

HTH,
Ting-Yuan
______________________________________
Ting-Yuan Liu
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
Seattle, WA, USA