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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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