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Gene identifier synonym table standard and/or repository?

Karen Christie kchris at genome.Stanford.EDU
Thu Feb 13 08:45:18 PST 2003


Hi Fritz,

SGD also has a file on our ftp site that provides this sort of
nomenclature information for S. cerevisiae, as well as other details on
each gene.

The file is called:
  chromosomal_feature.tab 

It, and a README with a full description of the columns, is located in
this directory:
  ftp://genome-ftp.stanford.edu/pub/yeast/data_download/chromosomal_feature/

For your purpose, the potentially relevant columns are:

1) Feature (mandatory)
2) Gene (optional)
3) Alias (optional, multiples separated by |)
9) SGDID (mandatory)

Beware of the 'Alias' column though, as these are not necessarily
unique and may also overlap the name space of the 'Gene' column, that
is a gene name may have been used as an alias for a different
gene. Feature names, i.e. YOR153W, are always unique.

Regards,

-Karen


On Thu, 13 Feb 2003, 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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