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Gene identifier synonym table standard and/or repository?

Tanya Berardini tberardi at acoma.stanford.edu
Thu Feb 13 09:39:29 PST 2003


Yes, that's correct. We use "|" to separate multiples as well.  I didn't
make that clear in my previous message, sorry.


On Thu, 13 Feb 2003, Valerie Wood wrote:

>
>
> 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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> > This message is from the GOFriends moderated mailing list.  A list of public
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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
>
>
>
> --
> This message is from the GOFriends moderated mailing list.  A list of public
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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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