[Bioc-devel] GO package

[Nianhua Li]

Dear All,

I have made some changes in the GO package and re-created the related annotation packages by using
    the updated GO.  They are available at bioc 2.0 data annotation repository and the version
number is 1.15.13. This is the first round of test for the change.

The major changes in GO:

1. CHILDREN environment:
GO-GO-relation has been included in the value part.

In 1.15.12 (the old GO):
> get("GO:0000002", GOBPCHILDREN)
[1] "GO:0032042"

In 1.15.13 (the new GO):
> get("GO:0000002", GOBPCHILDREN)
     part_of
"GO:0032042"

Also, all GO IDs have been included in the key part even if they don't
have a child:

In 1.15.12:
> length(GOBPCHILDREN)
[1] 7183

In 1.15.13:
> length(GOBPCHILDREN)
[1] 13155

2. Synonyms:
A new environment called GOSYNONYM has been included. The keys are
synonyms of no-obsolete GO terms that are in the format of "GO:xxxx".
The values are similar to the value part of GOTERM. Synonyms of
obsolete GO terms are still included as keys in GOOBSOLETE.

Synonyms are not included in CHILDREN, PARENTS, OFFSPRING, ANCESTOR,
ENTREZID, ALLENTREZID environments.

3. GOENTREZID environment:
All GO terms are included as keys.

In 1.15.12 (the old GO):
> length(GOENTREZID)
[1] 9407
> length(GOALLENTREZID)
[1] 23305

In 1.15.13 (the new GO):
> length(GOENTREZID)
[1] 22547
> length(GOALLENTREZID)
[1] 22547


The major changes in related annotation packages:

The GO term "all" is not included in the GO2ALLPROBES environment any more.

Hope the changes won't affect your code.


nianhua

Nianhua Li
Computational Biology, Public Health, FHCRC