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Gene identifier synonym table standard and/or repository?

Suzanna Lewis suzi at fruitfly.org
Thu Feb 13 08:51:35 PST 2003


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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