[BioC] usage of "all" category in annotation data

[Michael Newton]

I'm seeking advice on the use of the "all" component in various
annotation data packages relative to GO.

Using R version 2.4.1 and (e.g.) hgu133plus version 1.14.0,

library(hgu133plus2)   ## an Affy data package
x <- as.list( hgu133plus2GO2ALLPROBES )  ##probe sets for each GO term

xa <- unique( x[["all"]] )    ## holds probe sets associated to "all"

xbp <- unique( x[["GO:0008150"]] )    # biological process
xmf <- unique( x[["GO:0003674"]] )    # molecular function
xcc <- unique( x[["GO:0005575"]] )    # cellular component

## note that the following is true

all( xa == xbp )

But further checks show that the molecular function probe sets are not
a subset of "all".

I was under the impression that "all" is the union of MF, BP, and CC,
but in the few libraries I've checked, "all" equals BP.  I haven't
found a discussion of the matter in the few vignettes that might be
relevant.

Is "all" really "BP", or is it supposed to be the union?

thanks,

-Michael N.

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