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Gene identifier synonym table standard and/or repository?

Valerie Wood val at sanger.ac.uk
Thu Feb 13 09:33:30 PST 2003



i utilize this column for S. pombe too. btw I use "|" to separate multiple
synonyms, is this correct?



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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>

----------------------------------------------------------------------------------
Valerie Wood		       Tel: 01223 494954
S. Pombe Genome Project	       Fax: 01223 494919
The Sanger Institute           email: val at sanger.ac.uk
Wellcome Trust Genome Campus   http://www.sanger.ac.uk/Projects/S_pombe
Cambridge
CB10 1SA



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