[Bioc-devel] RE: changes to the GO package
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 GOTERM has been replaced by GOTERMS.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 -
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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