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Gene identifier synonym table standard and/or repository?

Nicolas Thierry-Mieg Nicolas.Thierry-Mieg at imag.fr
Thu Feb 13 10:20:29 PST 2003


hi Fritz,

If you really want to store information on many organisms (and perhaps 
other types of information than "just" GO associations), I think you 
will have to build a local database relying on some general protein or 
gene database, e.g. SwissProt/TrEMBL, PIR, or perhaps Ensembl.
This goes beyond GO, it's the very thorny problem of building a 
federative biological database...

I maintain such a database for internal use, as a basis for studying 
protein-protein interactions.
Using a single protein database "backbone" such as SwissProt/TrEMBL is 
the easy solution, but it means some information from your sources is 
lost (hopefully not too much). For example 5000 of the 23500 wormbase GO 
associations are discarded in my database, because either the name of 
the gene was not clearly found in my protein database (3500 here), or 
several different proteins matched that name (1500).
But at least the annotations that do get added to my database are clean.

I'm not sure if this type of approach is what you need: if you only want 
go annotations for a few organisms, you can probably do better by just 
looking for synonym tables for your chosen organisms; but if it is don't 
hesitate to contact me if you want further info:-)

regards,
Nicolas Thierry-Mieg


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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Nicolas Thierry-Mieg, PhD
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