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Change in Monthly GODATABASE Content

Mike Cherry cherry at genome.Stanford.EDU
Tue Nov 8 10:45:46 PST 2005


This is for those using the monthly versions of the GO mysql database  
available from:

   http://www.godatabase.org/dev/database/

The GO "full" database, recreated monthly, contains all gene  
associations no matter what evidence code the annotation contains.   
Beginning with the November 1, 2005 release of GO "full" database is  
using the filtered association files.  The major result of this  
filtering is that annotations are limited by species to a particular  
model organism project.  This filtering process is described in more  
detail in the web page at:

   http://www.geneontology.org/GO.annotation.shtml#script

The Nov 1 release of the GO "full" database thus has many no, or few,  
redundant annotations and thus the association table is smaller in size.

The GO "full" database is not used by AmiGO.  The AmiGO interface  
works from the GO "lite" database.  GO "lite" database is updated  
three times a week, while only one release to the FTP site is  
provided per week.  The GO "lite" database, and thus AmiGO, has been  
using the new filtering results since the October 9th release.  GO  
"lite" database is identical to the monthly release except all  
annotations with IEA evidence are excluded.

The GO Consortium provides one more database, called "term".  The GO  
"term" database is build nightly and only contains the ontologies and  
no associations.

-Mike


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