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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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