[BioC] Re: metaData

[John Zhang]

New versions of annotation data packages have been put on the web for 
downloading. Please let me know if there is any problem.

New features include:

1. Values for the GO environment of platform specific package (e. g. hgu95av2GO) 
now is a list that contains sub lists. Names of the list are the GO ids 
corresponding to a probe id and each element of the sub lists has three elements 
named "GOID", "Evidence", and "Ontology" for GO id, evidence code and ontology 
(MF, BP, CC). For example:

> library(hgu95av2)
> lookUp(ls(hgu95av2GO)[25], "hgu95av2", "GO")
$"GO:0005126"
$"GO:0005126"$GOID
[1] "GO:0005126"

$"GO:0005126"$Evidence
[1] "TAS"

$"GO:0005126"$Ontology
[1] "MF"


$"GO:0006952"
$"GO:0006952"$GOID
[1] "GO:0006952"

$"GO:0006952"$Evidence
[1] "IEA"

$"GO:0006952"$Ontology
[1] "BP"


$"GO:0005576"
$"GO:0005576"$GOID
[1] "GO:0005576"

$"GO:0005576"$Evidence
[1] "IEA"

$"GO:0005576"$Ontology
[1] "CC"

2. The GO package has two new environments GOGO2LL and GOLL2GO and the GOTERM 
environment contains GO terms for all the three (MF, BP, CC) categories with the 
terms named by MF, BP, or CC.

3. The KEGG package has KEGGEXTID2PATHID and KEGGPATHID2EXTID environments with 
mappings/reverser mappings between pathway ids and external ids. External ids 
are LocusLink ids for human, mouse, and rat and ORF for yeast.