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Gene identifier synonym table standard and/or repository?

Ewan Birney birney at ebi.ac.uk
Thu Feb 13 08:46:34 PST 2003


On Thu, 13 Feb 2003, 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
> 

;) You can use the Ensembl system for metozoans - it has nearly all 
metozoans in, and has extensive Xref tables, including synonyms in many 
cases. This is fully downloadable either from the mysql tables and/or via
mart view (which also allows specific query restrictions): go for:

http://www.ensembl.org/EnsMart/

hit "start", select a genome, select "ensembl genes", select "entire 
genome", don't put any filters and then use all the Xrefs in output.


More generally though, attempting to track every synonym mentioned at some 
point and organise it into anything that looks sensible across all genomes 
is ... well... interesting to say the least.







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