[Bioc-devel] RE: changes to the GO package

John Zhang jzhang at jimmy.harvard.edu
Thu Jun 3 17:17:21 CEST 2004


The GO package (1.6.0 for devel) has experienced dramatic changes, which have 
been announced in bioC NEWS and I am restating those changes to bioC developers 
in case bioC NEWS was not received.

1. GOTERM has been replaced by GOTERMS. Values of this environment are 
   lists of GOTerms objects. Each GOTerms object has 6 slots (GOId - GO       
   identifier, Ontology - the specific GO ontology term for the GO id, 
   Synonym - other synonymous terms, Secondary - secondary GO ids that were
   merged to the primary GO id, Definition - further definition of
   the GO ontology term, Category - the GO ontology category. Can be
   MF - molecular function, CC - cellular component, or BP -
   biological process)
2. New environments ANCESTOR and OFFSPRING have been added to each of the 
   three categories (BP, CC, and MF) to map GO ids to all the ancestor and 
   offspring along the GO tree. 
If your code/example deals with GO terms, GO 1.6.0 may cause trouble. Please 
write to me if you have any objection to the changes. Otherwise, I will assume 
that you will take care of the incompatibility.

Sorry for the trouble but the changes are for the better(I think).


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