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Gene identifier synonym table standard and/or repository?

Tanya Berardini tberardi at acoma.stanford.edu
Thu Feb 13 09:14:36 PST 2003


In the TAIR gene_association file, column 11 is populated with
synonyms/aliases for the annotated object.  These may include BAC-based
names from the genome sequencing phase, full names for the lettered
abbreviations (e.g. EMF1 is embryonic flower 1), other aliases for that
gene (e.g. ATROP4 = ROP4 = ATGP3 = ARAC5), Arabidopsis Genome Initiative
(AGI) locus names (of the format ATxgXXXXX), and gene product names.

Tanya


On Thu, 13 Feb 2003, Suzanna Lewis wrote:

> In the gene associations table the 11th column is listed
> as DB_object_synonym. I believe that this column was
> added especially to address this issue. It allows for
> white space and has a cardinality of 0, 1, or >1. I think
> this is a more a problem of the organism databases not
> having made the switch to providing this information
> when the gene associations are submitted. Column 12
> is the db object type (is it a gene, or a protein, or a .....)
> and column 13 is the taxon. I think if these were being
> populated it would perhaps help you.
>
> Any chance of this being put into practice annotators??
>
> -S
>
> On Thursday, February 13, 2003, at 07:54 AM, Fritz Roth wrote:
>
> > Greetings GOphiles,
> >
> > We are working on some new software that uses GO annotation, and we
> > would really like it to support all GO-annotated organisms.  Our chief
> > barrier to doing this is the lack of gene identifier synonym tables
> > for each organism (so that users can enter gene names rather than
> > being restricted to MOD IDS, e.g., SGD or MGI IDs).
> >
> > Is there an agreed GO Consortium standard for gene identifier synonym
> > tables (could be as simple as tab-delimited text with a
> > synonym-uniqueID pair on each line).  If so, is there a repository for
> > such files?  Or is this a GMOD question?
> >
> > Thanks!
> > Fritz Roth
> >
> > -------------------------------------------------
> > Frederick P. Roth, Asst. Professor
> > Harvard Medical School
> > Dept. of Biological Chemistry and Molecular Pharmacology
> > 250 Longwood Avenue, SGMB-322, Boston, MA 02115
> > (617) 432-3551 phone            (617) 432-3557 FAX
> > froth at hms.harvard.edu           http://llama.med.harvard.edu
> > -------------------------------------------------
> >
> >
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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/
260 Panama St.
Stanford, CA 94305
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