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Gene identifier synonym table standard and/or repository?

Simon Twigger simont at mcw.edu
Thu Feb 13 08:42:08 PST 2003


We have the same thing at RGD in our FTP file  
(http://rgd.mcw.edu/pub/data_release/GENES). Amongst other things we  
have symbol, name, IDs for this gene in RGD, LocusLink, Ratmap and the  
synonyms - both symbol and names.

Simon.

On Thursday, Feb 13, 2003, at 10:07 America/Chicago, Judith Blake wrote:

> for MGI, there is a tab-delimited file on the MGI ftp server  that  
> supplies IDs, symbol, name, synonyms. But the synonyms are for gene  
> symbols not names.
>
> I don't know of a general repository for such information
>
> Judy
>
>
> At 10:54 AM 2/13/2003, you 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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>
>
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>
------------------------------------------------------------------------ 
--------------------------
Simon Twigger, Ph.D.
Assistant Professor, Bioinformatics Research Center

Medical College of Wisconsin
8701 Watertown Plank Road,
Milwaukee, WI, 53226
tel. 414-456-8802, fax 414-456-6595


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