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

Fiona McCarthy FMcCarthy at
Mon Sep 8 15:28:01 PDT 2008

Hi Gabriel,

I am not sure about rat but I did notice earlier in the year that Ensembl
was reporting GO in a very strange way - it was directly attributing GO
annotations from human orthologs to the chicken & cow genes. This was
causing a lot of apparent redundancies when I scanned the GO annotations
but when I checked them more carefully, many of the Ensembl GO annotations
made no sense.

This happened in version 49 and was supposed to be fixed in version 50.
Does this sound like what you are seeing?


Gabriel Berriz <gberriz at> on Monday, September 08, 2008 at
4:49 PM +0000 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

The AgBase Databases
Department of Basic Sciences
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Tel:   (+ 1) 662 325 5859
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