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[Gofriends] Redundancy in go_XXXXXX-assocdb-tables/dbxref.txt

Gabriel Berriz gberriz at hms.harvard.edu
Mon Sep 8 14:49:03 PDT 2008


Dear GO friends,

For some species, the info given in the dbxref table includes IDs from  
multiple databases, which raises the possibility of "cryptic  
redundancies", i.e. associations distinct because they are assigned  
IDs from different databases that in fact refer to the same underlying  
gene product.  For example, if I compare the sets of rat dbxref's that  
have database names RGD and ENSEMBL respectiely, I find that the  
overlap (redundancy) of these two sets of IDs consists of about 1000  
IDs, which is over 5% all the possible rat gene products.  (To compute  
this overlap, I first mapped the RGD IDs to ENSEMBL IDs using the  
mappings provided by Ensembl version 49.)

Would it help to avoid these "cryptic redundancies" if a single  
database (Ensembl, RGD, whatever) was used for each species?

Thanks for your comments,

Gabriel Berriz



=============================================================
Gabriel F. Berriz, PhD
Bioinformatics Developer
Roth Lab
Biological Chemistry and Molecular Pharmacology -- Harvard Medical  
School
Seeley G. Mudd Building 322B
Boston, MA 02115-5701
Telephone: 617.432.3555
Fax: 617.432.3557



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