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

Judith Blake jblake at informatics.jax.org
Mon Sep 8 15:09:22 PDT 2008


Gabriel,

The gene association files are non-redundant.  Primary model organisms 
have responsibility for integrating annotations from mulitple sources 
and submitting a non-redundant file to the GOdb.  QC checks on the files 
also remove redundancies.  The details of annotation files are here...

http://www.geneontology.org/GO.format.annotation.shtml

Further details can be obtained from the GO_help desk
http://www.geneontology.org/GO.contacts.shtml

Judy


Gabriel Berriz wrote:
> 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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