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Gene identifier synonym table standard and/or repository?

Karen Christie kchris at genome.Stanford.EDU
Thu Feb 13 10:35:25 PST 2003


SGD is using column 11 already as well. 

When the ORF has a name, e.g. ABD1 or ABF1, this will be in column 3 and
column 11 will contain the feature name, e.g. YBR236C or YKL112W, as well
as any aliases for the gene name, e.g. SBF1. Again, there is no constraint
on these aliases to be unique and they may be identical to a gene name for
a different ORF (feature).

col 3	col 11
-----	------
ABD1    YBR236C
ABF1    YKL112W|SBF1|REB2|OBF1|BAF1


When the ORF has not been given a gene name, column 3 contains the feature
name. In these cases, when column 11 also contains a feature name, the two
features have generally been merged into one with one of the original two
feature names made into an alias for the other.

col 3		col 11
-----		------
YAL037W	
YAL042C-A	YAL043C-A

Depending on what you want to do and how you want to store nomenclature
information, it may be easier to parse this type of info out of the SGD
file I described earlier. 

-Karen


On Thu, 13 Feb 2003, Tanya Berardini wrote:

> 
> 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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