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Redundant GO IDs... can we try to use only (the first) one of them?

Chris Mungall cjm at fruitfly.bdgp.berkeley.edu
Tue Sep 25 14:45:03 PDT 2001


On Mon, 24 Sep 2001, Michael Ashburner wrote:

> Fritz
> 
> I never seem to have replied to this.
> 
> 1. Yes, the 1st GOid in a comma-separated string of GOids is the primary id,
> the others are secondary and result from merges of GO terms.  This from
> the documentation:
> 
> "When two terms are merged, e.g. term a and term b are merged as terma then the GO_id of termb is made a secondary GO_id.
> Secondary GO_id's are presented as a comma separated list, e.g.: 
> 
> 
> terma ; GO:idterma, GO:idtermb, GO:idtermc, ...
> 
> 
> When a term is split, each new term gets a new GO_id and the original GO_id is a secondary GO_id to each."
> 
> 2. >GO:0003710 is used many times in each gene association table, while ...
> 
> This is a problem of the databases not keeping up with changes in GO !
> FlyBase has a script that checks that all GO_terms<>GOids are current
> & correct, but I do not know how SGD and MGD do it. 
> 
> One possibility is that we have a generic script run on the gene_association
> tables. 
> 
> *** Berkeley/Standford ... could this be done ? .. reporting errors
> back to the contributor of the file ?

When we load the associations into the database we generate (somewhat
wordy) error reports which i've made visible here:

http://www.fruitfly.org/~bio-adm/go-load-logs/

so for instance you can download
http://www.fruitfly.org/~bio-adm/go-load-logs/assocs.gene_association.fb.ERR

and grep it for "secondary ID"

if people will use it, we can make a script that does the check on the
fly, but you may want to look at the above directory for now.
 
> >there are just a few more in Flybase:
> GO:0017104
> GO:0008032
> GO:0003710
> GO:0016940
> GO:0008357
> 
> ... these have been fixed in the last version
> 
> 
> Best
> 
> Michael
> 
> 
> --
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