IUBio Biosequences .. Software .. Molbio soft .. Network News .. FTP

A unique new resource for Arabidopsis

Chris Somerville crs at Andrew2.Stanford.EDU
Wed May 10 17:50:50 EST 2000

  TAIR has recently released a new dataset that represents a qualitative leap
forward in our ability to do genetics in Arabidopsis.   In short, Cereon
generously offered the community a comprehensive list of all the polymorphisms
between the Columbia and Landsberg genomes.  At present this represents more
than 35,000 polymorphisms but the dataset will grow as the Columbia genome
sequence progresses toward completion.  This is an incredible resource – no
other organism has such a rich collection of polymorphisms. 
Obviously, this will
greatly facilitate the isolation of genes by map based cloning, among 
other things.

At present the data is available at arabidopsis.org as a set of five 
tab delimited
files (one per chromosome) that can be downloaded into Excel.  In order to
access the data you have to register and agree to a very benign lisencelicense
agreement.   TAIR has implemented a secure, login-protected system in which
any potential user must first agree to the terms of a license by 
clicking through
a couple of buttons on the TAIR web site in much the same way that users
accept license agreements on software.  By agreeing to the terms of 
the license,
academic users will get a username and password to access and use the 
data at no
cost and without any obligations to Cereon.  The only aspect of the agreement
that affects the academic users is that they cannot sell or redistribute the
Cereon data that they obtain from the TAIR site and they cannot publish all of
the data.  Users can publish up to 20 polymorphisms at a time without any
obligations to Cereon.  We believe that this limit of 20 polymorphisms will not
be a problem for academic users since fewer than 20 are typically used in the
map-based cloning of a gene.   Commercial users are not granted any 
right to use
the data and are instructed to contact Cereon for a commercial 
license.  There is
some language in the agreement to the effect that Cereon would be delighted to
learn of any useful discoveries made with the aid of their data. 
Hopefully a few
users will communicate with the company about their discoveries.   I 
think this is
a great model for how a company can share data with the academic community.
We owe a debt of gratitude to Steve Rounsley and colleagues at Cereon who
made the effort to persuade the company lawyers and management that this was
a useful thing to do.  Hopefully, their example will inspire a few 
other companies
to provide access to the reportedly vast amounts of genome-related data that is
at present not generally available.

Chris Somerville
Chris Somerville
Carnegie Institution
260 Panama Street
Stanford CA 94305

More information about the Arab-gen mailing list

Send comments to us at biosci-help [At] net.bio.net