[BioC] Arabidopsis annotation package

[Ting-Yuan Liu]

Hi Fangxin,

On Wed, 15 Mar 2006 fhong at salk.edu wrote:

> Hi Ting-Yuan,
> 
> Thank you for your reply.
> 
> >
> > 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).
> What public data you collected? Cause I search for gene At1g04100
> (264328_at)at NCBI website, the pubmed IDs associated with this gene were
> all published before 2004 and two of them were published before 2000. I
> think NCBI have these information before September 29, 2005. So I am
> little confused why package ath1121501 doesn't contain them?
> 

The data we used to build ath1121501 (1.10.0) is from TAIR 
(http://www.arabidopsis.org/), not NCBI.  We are unable to find 
downloadable data from NCBI ftp site to build Arabidopsis thaliana 
packages.  

> 
> 
> 
> > 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).
> Will version 1.11 contain chromosome lenght which will enable us to use
> geneplot package.
> 

We will try to find the information of chromosome lenght. 

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


> 
>  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
> 
>