[Arabidopsis] Gene/loci to phenotype list, database access

John O. Woods via arab-gen%40net.bio.net (by john.woods from mail.utexas.edu)
Fri Aug 22 20:36:23 EST 2008


Hi folks,

I'm trying to obtain a list of Arabidopsis genes/loci along with a set
of phenotypes resulting from knock-downs, knock-outs, and hypomorphic
alleles at those loci.

I would *prefer* that the phenotypes be somewhat curated. For example,
FlyBase has unique identifiers for almost every phenotype, which is
nice because it's easy to automatically associate two genes with the
same phenotype (as opposed to by hand).

I only just started looking at A. thaliana today, so I'm a bit
ignorant. I've noticed TAIR has phenotypes, but I also found a
disclaimer on the FTP related to just such a tab-separated database
there.
"Note that this only represents the data that is in the TAIR database
and that there are bound to be many more loci with germplasms with
phenotypes."

First of all, what's a germplasm and how is it related to phenotype?
Secondly, most organisms' databases don't have every last phenotype
curated; is it worse with TAIR than with those other DBs, or is this
disclaimer just being overly cautious?


Is there a better place to get this data?

I'd love to find an Arabidopsis Chado database I can either access
remotely or download, or really anything I can access easily with
BioPerl. Any pointers?

Thanks so much for the help.

Cheers,
John Woods

ICMB, UT Austin



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