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

Michael Ashburner (Genetics) ma11 at gen.cam.ac.uk
Mon Sep 24 01:52:39 PDT 2001


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 ?

>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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