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Gene identifier synonym table standard and/or repository?

Tanya Berardini tberardi at acoma.stanford.edu
Wed Feb 26 10:08:35 PST 2003


Judy,

The same general scheme is used by us at TAIR.  Any name that has been
used in the literature to describe a particular gene is included in the
synonym column.  We also include the AGI (Arabidopsis Genome Initiative)
locus name for the gene (of a standard format, in this case, AT_gxxxxx,
where _ is the chromosome the gene is located on and the xxxxx represent a
unique numerical identifier for the gene) in this column.

Tanya


On Tue, 25 Feb 2003, Mike Cherry wrote:

> Judy,
>
> For Saccharomyces a gene name synonym is typically a published name
> that for many reasons is not currently the "standard" name (aka the
> approved name).  The typical cause of synonyms is that multiple names
> have been published for the locus.  There are cases when the community
> renames a set of loci from names assigned from phenotypes to names
> describing function.  The synonym column in the GO association file
> also includes the systematic ORF designation once a gene name is
> assigned.  This allows users to find a particular gene via AmiGO using
> all published names and the systematic ORF name.
>
> -Mike
>
>
> On Tuesday, February 25, 2003, at 04:02 PM, Judy Sprague wrote:
>
> > ZFIN is interested in learning how other databases are defining the
> > column 11
> > field 'synonym'.  Are these symbols that were formerly approved
> > nomenclature or
> > any symbol that has been used to refer to a given gene?
> >
> > Judy
>
>
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Tanya Berardini, Ph.D.			tberardi at acoma.stanford.edu
The Arabidopsis Information Resource	FAX: (650) 325-6857
Carnegie Institution of Washington	Tel: (650) 325-1521 ext. 325
Department of Plant Biology		URL: http://arabidopsis.org/
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