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[Gofriends] Automatic translation of alt IDs

Scott Cain scott at scottcain.net
Fri Apr 9 13:28:03 PDT 2010


Hello all,

Recently, there was a bug report for the Chado GFF loader to make it
respect altIDs.  The Chado database only stores the primary ID for a
term in the cvterm table, which is where the loader looks for terms,
and what the loader would need to make links from a feature to its GO
term.  While the alternate IDs are stored in the dbxref table as
accessions, the loader doesn't currently look there.

The question I have is this: is it acceptable for the loader to
automatically modify the GO term that a feature has been annotated
with to a new term without getting the "OK" from the user?  I am
worried that there is some loss of information or that the change
implies something that was not originally intended.  If, on the other
hand, the altID == primaryID from an annotation perspective, then I
can add code to the loader just transfer the annotation to the new ID.
 Does that make sense?

Thanks,
Scott


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research



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